b2ar_salmeterol-analysis2.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/enf/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:1350: UserWarning:  This call to matplotlib.use() has no effect\n",
      "because the backend has already been chosen;\n",
      "matplotlib.use() must be called *before* pylab, matplotlib.pyplot,\n",
      "or matplotlib.backends is imported for the first time.\n",
      "\n",
      "  warnings.warn(_use_error_msg)\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import matplotlib\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "# changing matplotlib the default style\n",
    "matplotlib.style.use('ggplot')\n",
    "\n",
    "from PDB_Order_Fixer import PDB_Order_Fixer\n",
    "import mdtraj as md\n",
    "import os\n",
    "import numpy as np\n",
    "import h5py\n",
    "\n",
    "import datetime\n",
    "import glob\n",
    "import copy\n",
    "from functools import partial \n",
    "import operator\n",
    "import time\n",
    "\n",
    "import random \n",
    "import subprocess\n",
    "from subprocess import Popen\n",
    "import sys\n",
    "from io_functions import *\n",
    "from custom_clusterer import *\n",
    "from custom_tica import *\n",
    "from custom_featurizer import *\n",
    "from pdb_editing import *\n",
    "from analysis import *\n",
    "from io_functions import *\n",
    "#from topology_fixing import *\n",
    "from subsampling import *\n",
    "from conversions import *\n",
    "from custom_msm import *\n",
    "#from grids import *\n",
    "from docking_analysis import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import io_functions\n",
    "from imp import reload\n",
    "reload(io_functions)\n",
    "from io_functions import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from operator import itemgetter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "In this iPython notebook, we will featurize MOR ligand binding simulation by pairwise distances between the ligand and different receptor residues. We will then perform tICA and prospectively build an MSM. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "we are operating on biox3\n"
     ]
    }
   ],
   "source": [
    "from detect_intermediates import *\n",
    "from interpret_tICs import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 265, 266, 267, 268, 269, 270, 271, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342]\n",
      "There are 274 common residues between input structures\n"
     ]
    }
   ],
   "source": [
    "from get_variable_names import *\n",
    "inactive_dir = \"/home/enf/md_simulations/b2ar/reference_receptors/2RH1_prepped-A.pdb\"\n",
    "active_dir = \"/home/enf/md_simulations/b2ar/reference_receptors/3P0G_pymol_prepped-A.pdb\"\n",
    "simulation_structure = \"/home/enf/md_simulations/b2ar/reference_receptors/ionized.pdb\"\n",
    "common_residues_pkl = \"/home/enf/md_simulations/b2ar/reference_receptors/common_residues.pkl\"\n",
    "contact_residues = find_common_residues([inactive_dir, active_dir, simulation_structure], common_residues_pkl)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "exacycle = False\n",
    "\n",
    "\n",
    "n_clusters = 300\n",
    "lag_time = 5\n",
    "if exacycle:\n",
    "  lag_time *= 2\n",
    "\n",
    "msm_lag_time = 5\n",
    "n_components = 10\n",
    "n_samples = 10\n",
    "n_macrostates = 25\n",
    "n_trees = 100\n",
    "\n",
    "precision = \"SP\"\n",
    "\n",
    "sparse = True\n",
    "wolf = True\n",
    "\n",
    "is_sparse = \"\"\n",
    "if(sparse): is_sparse = \"sparse-\"\n",
    "\n",
    "shrinkage_string = \"\"\n",
    "rho_string = \"\"\n",
    "if wolf and not sparse:\n",
    "  wolf_string = \"_wolf_\"\n",
    "  shrinkage = None\n",
    "  shrinkage_string = \"autoShrinkage\"\n",
    "  rho = None\n",
    "  rho_string = \"\"\n",
    "elif wolf and sparse:\n",
    "  wolf_string = \"_wolf_\"\n",
    "  shrinkage = None\n",
    "  shrinkage_string = \"autoShrinkage\"\n",
    "  rho = 0.005\n",
    "  rho_string = \"_rho0pt005\"\n",
    "else:\n",
    "  wolf_string = \"\"\n",
    "  shrinkage = 0.001\n",
    "  shrinkage_string = \"0pt001\"\n",
    "  rho = None\n",
    "  rho_string = \"\"\n",
    "\n",
    "traj_ext = \".h5\"\n",
    "base = \"/home/enf/md_simulations/b2ar/Salmeterol\"\n",
    "traj_dir = \"/home/enf/md_simulations/b2ar/Salmeterol/h5_trajectories\"\n",
    "structure = None\n",
    "iterative = False\n",
    "featurize_parallel = True\n",
    "\n",
    "sampling_method = \"random\"\n",
    "precision = \"SP\"\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'feature_name' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-14-f54c13e7cc6e>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mori_feature_name\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcopy\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdeepcopy\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfeature_name\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m: name 'feature_name' is not defined"
     ]
    }
   ],
   "source": [
    "feature_name = \"contacts_within_6pt6_angstroms\"\n",
    "ori_feature_name = copy.deepcopy(feature_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "rho = 0.1\n",
    "rho_string = \"0pt1\"\n",
    "lag_time = 5\n",
    "n_components = 10\n",
    "n_clusters = 1500\n",
    "\n",
    "rho = 0.01\n",
    "rho_string = \"0pt01\"\n",
    "lag_time=50\n",
    "ori_feature_name = copy.deepcopy(feature_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far\n",
      "/home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far\n"
     ]
    }
   ],
   "source": [
    "schemes = [\"closest-heavy\", \"CA\"]\n",
    "feature_name = \"%s-CA-py3-far\" %ori_feature_name\n",
    "#feature_name = \"%s_phi_psi_chi2\" %feature_name\n",
    "(active_ref_dir, inactive_ref_dir, simulation_ref_dir, scripts_dir,\n",
    "          ligand_dir, agonist_dir, inverse_agonist_dir, biased_agonist_dir, ref_receptors_dir, whole_trajectory_pnas,\n",
    "          sasa_file) = get_base_files(base)\n",
    "\n",
    "tica_dir = get_tica_dir(base, is_sparse, lag_time, n_components, feature_name, \n",
    "                                 wolf_string, shrinkage_string, rho_string)\n",
    "#tica_dir = \"%s-with-inactive\" %tica_dir\n",
    "tica_dir = \"%s-backup\" %tica_dir\n",
    "ori_tica_dir = copy.deepcopy(tica_dir)\n",
    "#tica_dir = \"%s-normalized\" % ori_tica_dir\n",
    "features_dir = get_features_dir(base, feature_name)\n",
    "\n",
    "landmarks_dir = get_landmarks_dir(tica_dir)\n",
    "analysis_dir = get_analysis_dir(tica_dir, n_clusters, sampling_method)\n",
    "gmm_dir = get_gmm_dir(tica_dir)\n",
    "rf_dir = get_rf_dir(tica_dir)\n",
    "\n",
    "\n",
    "ref_tica_dir, ref_tica_coords = get_ref_tica_dirs(tica_dir)\n",
    "\n",
    "graph_file = get_graph_file(tica_dir, msm_lag_time, n_clusters)\n",
    "\n",
    "pnas_titles =  [\"tm6_tm3_dist\", \"rmsd_npxxy_inactive\", \"rmsd_npxxy_active\", \"rmsd_connector_inactive\", \"rmsd_connector_active\"]\n",
    "pnas_features_dir = analysis_dir\n",
    "\n",
    "\n",
    "(clusterer_dir, msm_model_dir, macrostate_dir, features_known, model_dir, projected_features_dir,\n",
    "         projection_operator_dir, ktica_fit_model_filename, ktica_projected_data_filename, nystroem_data_filename,\n",
    "         mutual_information_csv, pearson_csv) = get_tica_files(base, tica_dir, n_clusters, msm_lag_time, n_macrostates)\n",
    "\n",
    "(standardized_features_dir, feature_residues_csv, feature_residues_pkl,\n",
    "          contact_csv, ref_features_dir) = get_feature_files(features_dir)\n",
    "\n",
    "(kmeans_csv, tica_coords_csv, features_csv, active_rmsd_dir, inactive_rmsd_dir, active_pnas_dir, inactive_pnas_joined, active_pnas_joined,\n",
    "        clusters_map_file, ktica_clusters_map_file, analysis_file, combined_file, docking_summary, docking_joined, docking_z_scores_csv,\n",
    "        aggregate_docking, aggregate_docking_joined, docking_pnas_joined, aggregate_docking_pnas, aggregate_docking_pnas_joined, docking_multiple_ligands,\n",
    "        docking_distances_file, docking_pdf, mmgbsa_docking_distances, pnas_coords, mmgbsa_dir, mmgbsa_csv, mmgbsa_pdf, aggregate_mmgbsa,\n",
    "        aggregate_mmgbsa_joined, aggregate_mmgbsa_pnas_joined, mmgbsa_z_scores_csv, active_clusters_csv, intermediate_clusters_csv,\n",
    "        inactive_clusters_csv, pnas_clusters_averages, tica_clusters_averages, tica_classes_csv, tica_samples_csv, subgraph_save_base,\n",
    "        degree_save_base, degree_map_csv, degree_z_map_csv, aggregate_docking_pnas_degree_z_joined, tic_residue_csv, feature_coefs_csv,\n",
    "        duplicated_feature_coefs_csv) = get_analysis_files(analysis_dir, n_clusters, tica_dir, tica_dir, sampling_method, n_samples, precision,\n",
    "                                                           msm_lag_time)\n",
    "\n",
    "(inactive_pnas_distances_dir, active_pnas_distances_dir, active_pnas_all_distances_dir,\n",
    "          inactive_pnas_distances_new_csv, active_pnas_distances_new_csv, active_pnas_joined, active_pnas_means, pnas_coords_dir,\n",
    "          pnas_coords_csv, pnas_all_coords_csv, pnas_coords_hexbin_dir, pnas_coords_co_crystallized_docking_dir,\n",
    "          pnas_coords_active_colors_dir, user_defined_features_file, reaction_coordinates_trajs_file) = get_pnas_files(whole_trajectory_pnas, pnas_features_dir)\n",
    "\n",
    "features_dir = get_features_dir(base, feature_name)\n",
    "\n",
    "\n",
    "\n",
    "graph_file = get_graph_file(tica_dir, msm_lag_time, n_clusters)\n",
    "(scripts_dir, pymol_fixpdb_dir) = get_script_dir(scripts_dir)\n",
    "(save_dir, reimaged_dir, mae_dir, combined_reimaged_dir, grid_dir, docking_dir) = get_docking_dirs(tica_dir, n_clusters, n_components, n_samples, sampling_method, precision)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "features_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "208\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<AsyncMapResult: chdir>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from ipyparallel import Client\n",
    "rc = Client()\n",
    "print(len(rc.ids))\n",
    "dview = rc[:]\n",
    "dview.map(os.chdir, ['/home/enf/b2ar_analysis/conformation']*len(rc.ids))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import custom_featurizer\n",
    "reload (custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "f338a_trajectories = [t for t in get_trajectory_files(traj_dir, \".h5\") if \"f338a\" in t]\n",
    "fix_chain_names(f338a_trajectories, None)\n",
    "#featurize_contacts_custom(traj_dir, features_dir = features_dir, traj_ext = traj_ext, contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "#                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "#                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_17.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_1.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_17.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_1.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_134.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_134.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_44.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_44.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_114.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_114.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_8.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_8.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_24.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_24.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_204.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_204.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_22.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_22.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_15.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_15.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_185.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_185.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_255.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_255.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_170.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_170.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_186.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_reseeded_rep_186.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_45.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_45.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_10.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_10.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_80.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_80.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_135.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_201.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_rep_102.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/apo_rep_13.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_141.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_16.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_224.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_66.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_196.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R38.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R38.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_142.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_121.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_232.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_71.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_69.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_202.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_27.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_168.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_233.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_249.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_72.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_7.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_13.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_259.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_308.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_281.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_31.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_309.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_172.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_208.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_283.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_73.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R4.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R4.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_311.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_239.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_312.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_48.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_76.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_43.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_391.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_84.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_500.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_5.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_253.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_85.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_426.dataset\n",
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      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R41.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_117.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_p_rep_437.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_52.dataset\n",
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      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/bu72_reseeded_rep_88.dataset\n",
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      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_150.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_186.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_186.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_89.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_89.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_55.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_55.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R48.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R48.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_56.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_56.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_9.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_9.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R19.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R19.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_57.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_57.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_90.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_90.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_58.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_58.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_91.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_91.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_59.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_59.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_92.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_92.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_6.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_6.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R49.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R49.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_93.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_93.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_60.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_60.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_94.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_94.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_95.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_95.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R2.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R2.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_96.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf_reseeded_r_rep_96.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R5.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R5.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R20.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R20.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R50.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R50.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R21.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R21.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R51.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R51.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R52.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R52.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R22.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R22.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R53.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R53.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R23.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R23.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R54.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R54.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R24.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R24.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R55.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R55.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R25.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R25.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R56.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R56.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R26.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R26.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R57.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R57.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R27.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R27.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R58.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R58.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R28.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R28.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R59.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R59.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R29.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R29.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R6.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R6.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R3.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R3.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R60.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R60.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R30.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R30.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R7.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R7.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R31.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R31.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_1.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_1.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_100.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_100.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_101.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_101.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_102.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_102.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_103.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_103.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_104.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_104.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R32.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R32.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_105.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_105.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_106.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_106.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_107.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_107.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_108.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/suf__rep_108.dataset\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R33.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R33.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R34.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R34.h5\n",
      "save_file = /home/enf/md_simulations/MOR/h8_reimaged/trajectories/user_defined_features/f338a_RUN_R35.dataset\n",
      "featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R35.h5\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/user_defined_features.h5\"... (<class 'list'>)\n"
     ]
    }
   ],
   "source": [
    "user_defined_features_dir = \"%s/user_defined_features\" %traj_dir\n",
    "if not os.path.exists(user_defined_features_dir):\n",
    "    os.makedirs(user_defined_features_dir)\n",
    "compute_user_defined_features_wrapper(traj_dir, traj_ext, inactive_dir, active_dir, None,\n",
    "                                        feature_name_residues_dict, user_defined_features_file, worker_pool=None, \n",
    "                                        save_dir=user_defined_features_dir, parallel=True, overwrite=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_user_defined_features_file = \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\"\n",
    "ref_user_defined_features_dir = \"%s/ref_user_defined_features\" %traj_dir\n",
    "if not os.path.exists(ref_user_defined_features_dir):\n",
    "    os.makedirs(ref_user_defined_features_dir)\n",
    "\n",
    "compute_user_defined_features_wrapper(ref_receptors_dir, \".pdb\", inactive_dir, active_dir, None,\n",
    "                                        feature_name_residues_dict, ref_user_defined_features_file, worker_pool=None, \n",
    "                                        save_dir=ref_user_defined_features_dir, parallel=False, overwrite=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "traj_dir = \"/home/enf/md_simulations/MOR/h8_reimaged/trajectories\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "already featurized\n",
      "structure\n",
      "/home/enf/md_simulations/MOR/4dkl_R_for_conformation.pdb\n",
      "structure\n",
      "None\n",
      "mdraj_index_combinations[0:10]\n",
      "[(41, 73), (41, 114), (41, 108), (41, 248), (41, 166), (41, 84), (41, 13), (41, 76), (41, 74), (41, 18)]\n",
      "contact_features[0:10]\n",
      "[[TYR106, ILE138], [TYR106, ARG179], [TYR106, VAL173], [TYR106, HIS319], [TYR106, LEU231], [TYR106, TYR149], [TYR106, VAL78], [TYR106, LYS141], [TYR106, LEU139], [TYR106, LEU83]]\n",
      "About to compute 35255 features\n",
      "(1, 35255)\n",
      "cutoff\n",
      "0.66\n",
      "distances[0:10]\n",
      "[[ 2.53460574  0.61586297  1.52706683 ...,  1.51371932  3.94720888\n",
      "   2.2300899 ]]\n",
      "There are 955 residue-residue contacts below cutoff in structure.\n",
      "structure\n",
      "/home/enf/md_simulations/MOR/5c1m.pdb\n",
      "structure\n",
      "None\n",
      "mdraj_index_combinations[0:10]\n",
      "[(54, 86), (54, 127), (54, 121), (54, 267), (54, 179), (54, 97), (54, 26), (54, 89), (54, 87), (54, 31)]\n",
      "contact_features[0:10]\n",
      "[[TYR106, ILE138], [TYR106, ARG179], [TYR106, VAL173], [TYR106, HIS319], [TYR106, LEU231], [TYR106, TYR149], [TYR106, VAL78], [TYR106, LYS141], [TYR106, LEU139], [TYR106, LEU83]]\n",
      "About to compute 35255 features\n",
      "(1, 35255)\n",
      "cutoff\n",
      "0.66\n",
      "distances[0:10]\n",
      "[[ 2.67791724  0.63610411  1.40252936 ...,  1.48673296  3.71989655\n",
      "   2.46465921]]\n",
      "There are 1010 residue-residue contacts below cutoff in structure.\n",
      "dihedral_residues:\n",
      "[]\n",
      "looking at 1204 pairs for trajectory\n",
      "There are 2408 features to be used in featurization.\n",
      "Saving contact feature residue pairs to disk.\n",
      "About to featurize trajectories based on the chosen featurization scheme.\n",
      "[ALA102 to ALA184, ALA102 to ARG165, ALA102 to ARG179, ALA102 to ARG182, ALA102 to ASN183, ALA102 to ASN188, ALA102 to ASP164, ALA102 to ILE107, ALA102 to LYS185, ALA102 to MET161, ALA102 to PHE178, ALA102 to PRO181, ALA102 to THR180, ALA111 to ASN332, ALA111 to ASN86, ALA111 to GLY82, ALA111 to GLY85, ALA111 to ILE93, ALA111 to LEU116, ALA111 to MET90, ALA111 to PHE87, ALA111 to PRO333, ALA111 to THR118, ALA111 to THR157, ALA111 to TYR106, ALA111 to TYR336, ALA111 to VAL89, ALA113 to ASN150, ALA113 to ASN86, ALA113 to ILE146, ALA113 to ILE155, ALA113 to MET151, ALA113 to MET90, ALA113 to PHE108, ALA113 to PHE152, ALA113 to SER154, ALA113 to SER329, ALA113 to THR118, ALA113 to THR153, ALA113 to THR157, ALA113 to TRP192, ALA113 to TYR149, ALA115 to ASN150, ALA115 to ASN86, ALA115 to GLY82, ALA115 to ILE146, ALA115 to LEU110, ALA115 to LEU83, ALA115 to MET90, ALA115 to PHE87, ALA115 to SER329, ALA115 to THR120, ALA117 to ASN150, ALA117 to ASP147, ALA117 to GLN124, ALA117 to ILE146, ALA117 to LEU112, ALA117 to LEU83, ALA117 to MET151, ALA117 to PRO122, ALA117 to SER154, ALA117 to SER329, ALA117 to TYR326, ALA168 to ALA175, ALA168 to ARG179, ALA168 to LEU275, ALA168 to PHE178, ALA168 to VAL163, ALA168 to VAL173, ALA175 to ASP164, ALA175 to ILE167, ALA175 to THR180, ALA175 to VAL169, ALA184 to ARG179, ALA184 to ASP164, ALA184 to ILE105, ALA184 to PHE178, ALA184 to THR101, ALA184 to THR103, ALA184 to THR160, ALA184 to TYR106, ALA184 to VAL189, ALA197 to TRP192, ALA197 to TYR149, ALA197 to VAL202, ALA206 to ASN137, ALA206 to CYS140, ALA206 to CYS217, ALA206 to ILE142, ALA206 to ILE144, ALA206 to LEU219, ALA206 to LYS141, ALA206 to PRO201, ALA206 to SER145, ALA206 to THR218, ALA206 to THR220, ALA240 to CYS235, ALA240 to HIS297, ALA240 to ILE155, ALA240 to ILE234, ALA240 to MET151, ALA240 to PHE152, ALA240 to PHE156, ALA240 to PHE289, ALA240 to TRP293, ALA240 to VAL245, ALA287 to CYS292, ALA287 to ILE248, ALA287 to TYR252, ALA287 to VAL282, ALA304 to ASN230, ALA304 to GLU229, ALA304 to LYS233, ALA304 to TYR299, ALA323 to ASN328, ALA323 to CYS292, ALA323 to ILE296, ALA323 to ILE71, ALA323 to LEU121, ALA323 to LEU74, ALA323 to TRP318, ALA323 to TYR75, ALA323 to VAL78, ALA337 to ARG345, ALA337 to ASN332, ALA337 to ASN342, ALA337 to ILE107, ALA337 to ILE93, ALA337 to LEU110, ALA337 to LEU331, ALA337 to LYS344, ALA337 to MET161, ALA337 to MET281, ALA337 to PHE343, ALA337 to PHE347, ALA337 to VAL89, ALA68 to ALA73, ALA68 to LEU129, ALA68 to LEU74, ALA68 to SER125, ALA68 to TYR128, ALA68 to VAL316, ALA73 to VAL78, ARG165 to ARG179, ARG165 to ARG276, ARG165 to ARG280, ARG165 to ASN274, ARG165 to ASP340, ARG165 to CYS170, ARG165 to CYS251, ARG165 to ILE278, ARG165 to LEU158, ARG165 to LEU275, ARG165 to LEU283, ARG165 to LEU335, ARG165 to LEU339, ARG165 to MET255, ARG165 to MET281, ARG165 to PHE178, ARG165 to THR103, ARG165 to THR160, ARG165 to THR279, ARG165 to TYR106, ARG165 to TYR252, ARG165 to TYR336, ARG165 to VAL282, ARG165 to VAL285, ARG179 to ASP164, ARG179 to HIS171, ARG179 to ILE167, ARG179 to ILE278, ARG179 to LYS174, ARG179 to MET161, ARG179 to THR101, ARG179 to THR103, ARG179 to TYR106, ARG179 to VAL169, ARG182 to ILE105, ARG182 to VAL187, ARG211 to ASP216, ARG211 to THR132, ARG258 to CYS170, ARG258 to GLY253, ARG258 to HIS171, ARG258 to PRO172, ARG258 to TYR166, ARG258 to VAL169, ARG273 to ARG280, ARG273 to ILE278, ARG276 to LYS185, ARG276 to MET281, ARG276 to VAL169, ARG277 to ASP340, ARG277 to GLU341, ARG277 to LEU339, ARG277 to LYS344, ARG277 to VAL282, ARG280 to GLU341, ARG280 to ILE256, ARG280 to LEU275, ARG280 to LEU339, ARG280 to PHE338, ARG280 to VAL285, ARG345 to ASP340, ARG345 to LYS98, ARG345 to PHE338, ARG95 to LYS100, ARG95 to MET90, ASN104 to ASN109, ASN104 to ASN342, ASN104 to ASP340, ASN104 to ILE93, ASN104 to LYS98, ASN104 to MET281, ASN104 to MET99, ASN104 to PHE343, ASN104 to THR97, ASN104 to VAL89, ASN109 to ASN150, ASN109 to ASN188, ASN109 to ASN191, ASN109 to ASP114, ASN109 to ILE93, ASN109 to MET90, ASN109 to MET99, ASN109 to PHE156, ASN109 to SER154, ASN109 to THR153, ASN109 to THR157, ASN109 to THR160, ASN109 to TRP192, ASN109 to VAL187, ASN109 to VAL189, ASN127 to ASP216, ASN127 to CYS217, ASN127 to HIS319, ASN127 to ILE215, ASN127 to PHE135, ASN127 to PRO122, ASN127 to PRO134, ASN127 to THR132, ASN127 to TRP133, ASN137 to CYS217, ASN137 to ILE142, ASN137 to LYS209, ASN137 to THR207, ASN137 to THR208, ASN150 to ASP114, ASN150 to GLY325, ASN150 to ILE155, ASN150 to LEU110, ASN150 to LEU112, ASN150 to LEU116, ASN150 to PHE289, ASN150 to SER145, ASN150 to SER195, ASN150 to SER329, ASN150 to THR120, ASN150 to TRP192, ASN150 to TRP293, ASN150 to TYR326, ASN183 to ASN188, ASN183 to ASP177, ASN183 to ILE105, ASN183 to LEU176, ASN183 to PHE178, ASN183 to TYR106, ASN188 to ILE105, ASN188 to ILE107, ASN188 to ILE193, ASN188 to LEU110, ASN188 to PHE108, ASN188 to THR153, ASN188 to THR157, ASN188 to THR160, ASN188 to TYR106, ASN191 to ILE155, ASN191 to ILE186, ASN191 to LEU158, ASN191 to PHE152, ASN191 to PHE156, ASN191 to SER154, ASN191 to SER196, ASN191 to THR153, ASN191 to THR157, ASN191 to THR160, ASN191 to TYR106, ASN191 to TYR149, ASN230 to CYS235, ASN230 to LEU305, ASN230 to PHE221, ASN230 to THR225, ASN274 to GLU341, ASN274 to THR279, ASN328 to ASP114, ASN328 to CYS292, ASN328 to ILE155, ASN328 to ILE290, ASN328 to LEU110, ASN328 to LEU158, ASN328 to LEU335, ASN328 to PHE289, ASN328 to PRO333, ASN328 to SER154, ASN328 to TRP293, ASN328 to TYR336, ASN328 to VAL285, ASN328 to VAL288, ASN328 to VAL291, ASN328 to VAL78, ASN332 to ASN86, ASN332 to ASP114, ASN332 to ILE107, ASN332 to ILE155, ASN332 to LEU110, ASN332 to LEU158, ASN332 to PHE289, ASN332 to PHE338, ASN332 to SER154, ASN332 to THR327, ASN332 to TRP293, ASN332 to VAL285, ASN332 to VAL288, ASN332 to VAL89, ASN342 to LYS98, ASN342 to MET99, ASN342 to PHE347, ASN342 to THR101, ASN342 to THR103, ASN342 to THR97, ASN342 to TYR336, ASN342 to VAL92, ASN86 to ASP114, ASN86 to CYS330, ASN86 to ILE107, ASN86 to LEU110, ASN86 to LEU112, ASN86 to LEU116, ASN86 to LEU331, ASN86 to PHE338, ASN86 to PRO333, ASN86 to SER329, ASN86 to THR118, ASN86 to TYR336, ASN86 to TYR91, ASN86 to VAL81, ASP114 to CYS330, ASP114 to GLY82, ASP114 to ILE155, ASP114 to LEU158, ASP114 to LEU331, ASP114 to LEU83, ASP114 to PRO333, ASP114 to SER119, ASP114 to SER154, ASP114 to SER329, ASP114 to THR153, ASP114 to TYR326, ASP114 to TYR336, ASP147 to GLN124, ASP147 to ILE142, ASP147 to LEU116, ASP147 to LEU121, ASP147 to PHE152, ASP147 to THR118, ASP147 to THR120, ASP147 to TRP293, ASP147 to TYR326, ASP164 to CYS159, ASP164 to CYS251, ASP164 to PHE178, ASP164 to THR103, ASP164 to THR180, ASP164 to TYR106, ASP164 to VAL169, ASP177 to PRO172, ASP216 to CYS140, ASP216 to GLY131, ASP216 to LYS209, ASP216 to THR132, ASP216 to THR207, ASP216 to THR208, ASP216 to TRP133, ASP216 to TYR210, ASP340 to ILE107, ASP340 to ILE278, ASP340 to LEU335, ASP340 to MET161, ASP340 to MET281, ASP340 to MET99, ASP340 to PRO333, ASP340 to THR103, ASP340 to VAL334, CYS140 to CYS217, CYS140 to ILE146, CYS140 to LEU219, CYS140 to PHE135, CYS140 to SER145, CYS140 to THR207, CYS140 to THR208, CYS140 to THR218, CYS140 to TRP133, CYS140 to VAL202, CYS159 to CYS251, CYS159 to ILE247, CYS159 to ILE248, CYS159 to MET243, CYS159 to PHE239, CYS159 to PHE289, CYS159 to PRO244, CYS159 to SER154, CYS159 to TYR252, CYS159 to TYR336, CYS159 to VAL245, CYS159 to VAL286, CYS170 to CYS251, CYS170 to ILE256, CYS170 to LEU254, CYS170 to LEU257, CYS170 to LEU259, CYS170 to LEU275, CYS170 to MET255, CYS190 to LYS185, CYS190 to PHE156, CYS190 to SER195, CYS190 to SER196, CYS217 to GLY136, CYS217 to ILE144, CYS217 to LEU139, CYS217 to LYS141, CYS217 to LYS209, CYS217 to THR132, CYS217 to THR207, CYS217 to THR208, CYS217 to TRP133, CYS217 to VAL143, CYS235 to ILE198, CYS235 to PHE152, CYS235 to PHE241, CYS251 to ILE256, CYS251 to LEU246, CYS251 to SER162, CYS251 to TYR166, CYS251 to VAL163, CYS292 to CYS321, CYS292 to GLY325, CYS292 to HIS297, CYS292 to ILE322, CYS292 to LEU324, CYS292 to LEU331, CYS292 to SER329, CYS292 to THR327, CYS292 to TYR326, CYS321 to HIS297, CYS321 to ILE296, CYS321 to LEU74, CYS321 to PRO295, CYS321 to TRP293, CYS321 to TYR299, CYS321 to TYR326, CYS321 to VAL316, CYS330 to CYS79, CYS330 to GLY325, CYS330 to GLY82, CYS330 to GLY85, CYS330 to ILE77, CYS330 to LEU121, CYS330 to LEU335, CYS330 to LEU83, CYS330 to THR118, CYS330 to VAL78, CYS330 to VAL80, CYS330 to VAL81, CYS346 to GLU341, CYS346 to LEU88, CYS346 to LYS98, CYS346 to MET99, CYS346 to PHE338, CYS346 to THR97, CYS346 to TYR96, CYS346 to VAL92, CYS79 to LEU121, CYS79 to LEU74, CYS79 to PHE84, CYS79 to PRO122, CYS79 to SER119, CYS79 to THR118, CYS79 to THR120, CYS79 to TYR326, GLN124 to HIS319, GLN124 to ILE322, GLN124 to LEU129, GLN124 to PHE135, GLN124 to TRP133, GLN124 to TYR326, GLN124 to TYR75, GLN124 to VAL143, GLN314 to HIS319, GLN314 to ILE308, GLN314 to LYS303, GLN314 to PRO309, GLN314 to THR307, GLN314 to TYR299, GLU229 to ILE234, GLU229 to LEU219, GLU229 to PHE221, GLU229 to PRO224, GLU229 to SER222, GLU229 to THR218, GLU310 to THR315, GLU341 to TYR336, GLY131 to GLY213, GLY131 to ILE215, GLY131 to SER125, GLY131 to SER214, GLY131 to VAL126, GLY136 to LYS141, GLY136 to THR207, GLY136 to THR208, GLY199 to ILE144, GLY199 to ILE146, GLY199 to LEU194, GLY199 to LYS141, GLY199 to PHE152, GLY199 to PHE204, GLY199 to SER145, GLY199 to TYR148, GLY199 to TYR149, GLY213 to THR132, GLY253 to ILE247, GLY253 to ILE248, GLY253 to VAL282, GLY325 to ILE296, GLY325 to PHE320, GLY325 to TRP293, GLY325 to VAL291, GLY325 to VAL78, GLY82 to ILE77, GLY82 to LEU331, GLY82 to LEU88, GLY82 to PHE87, GLY82 to PRO333, GLY82 to SER329, GLY82 to SER76, GLY82 to THR118, GLY82 to TYR326, GLY85 to MET90, GLY85 to PHE338, GLY85 to PRO333, GLY85 to SER329, GLY85 to TYR336, GLY85 to VAL334, GLY85 to VAL80, HIS171 to LEU176, HIS171 to PHE178, HIS171 to TYR166, HIS223 to TRP228, HIS297 to ILE155, HIS297 to ILE238, HIS297 to ILE302, HIS297 to LYS233, HIS297 to MET151, HIS297 to PHE237, HIS297 to PHE241, HIS297 to PHE289, HIS297 to VAL236, HIS319 to ILE71, HIS319 to LEU324, HIS319 to LEU74, HIS319 to THR67, HIS319 to TYR128, HIS319 to TYR299, HIS319 to TYR75, ILE105 to ILE186, ILE105 to ILE93, ILE105 to LEU110, ILE105 to LYS100, ILE105 to LYS185, ILE105 to MET99, ILE105 to PRO181, ILE105 to THR157, ILE105 to THR180, ILE107 to ILE93, ILE107 to LEU112, ILE107 to MET161, ILE107 to MET281, ILE107 to MET90, ILE107 to PHE338, ILE107 to PHE343, ILE107 to THR157, ILE107 to TYR336, ILE107 to VAL282, ILE107 to VAL89, ILE138 to MET203, ILE138 to THR208, ILE138 to TRP133, ILE138 to VAL143, ILE142 to MET203, ILE142 to THR120, ILE142 to TYR149, ILE144 to LEU139, ILE144 to LEU219, ILE144 to MET203, ILE144 to THR120, ILE144 to THR207, ILE144 to THR218, ILE144 to TRP133, ILE144 to TYR149, ILE144 to VAL202, ILE146 to LEU116, ILE146 to LYS141, ILE146 to MET151, ILE146 to MET203, ILE146 to SER119, ILE146 to THR118, ILE146 to THR120, ILE146 to THR153, ILE146 to VAL202, ILE155 to ILE242, ILE155 to ILE248, ILE155 to ILE290, ILE155 to LEU110, ILE155 to MET243, ILE155 to PHE239, ILE155 to PHE241, ILE155 to PHE289, ILE155 to PRO244, ILE155 to THR160, ILE155 to TRP293, ILE155 to VAL245, ILE167 to LEU176, ILE167 to LYS174, ILE167 to MET255, ILE167 to PHE178, ILE167 to PRO172, ILE167 to SER162, ILE167 to VAL173, ILE186 to PRO181, ILE193 to ILE198, ILE193 to THR153, ILE193 to TYR149, ILE198 to LEU232, ILE198 to MET151, ILE198 to MET203, ILE198 to MET205, ILE198 to PHE152, ILE198 to PHE239, ILE198 to SER145, ILE198 to TYR148, ILE198 to TYR149, ILE198 to VAL236, ILE215 to LYS209, ILE215 to PRO134, ILE215 to THR132, ILE215 to THR208, ILE215 to TRP133, ILE215 to TYR210, ILE234 to ILE242, ILE234 to ILE301, ILE234 to PHE239, ILE238 to LEU231, ILE238 to LYS233, ILE238 to MET243, ILE238 to PHE152, ILE238 to PRO244, ILE242 to ILE247, ILE242 to PHE237, ILE242 to PHE289, ILE242 to VAL236, ILE247 to LEU158, ILE247 to SER162, ILE247 to THR160, ILE247 to TYR252, ILE247 to VAL163, ILE248 to ILE290, ILE248 to LEU158, ILE248 to MET243, ILE248 to MET255, ILE248 to PHE289, ILE248 to SER162, ILE248 to THR160, ILE248 to TYR336, ILE248 to VAL163, ILE248 to VAL282, ILE248 to VAL285, ILE248 to VAL286, ILE256 to ILE278, ILE256 to LEU275, ILE256 to LEU283, ILE256 to THR279, ILE256 to VAL169, ILE256 to VAL282, ILE278 to LEU259, ILE278 to LEU283, ILE278 to LEU339, ILE278 to MET255, ILE278 to THR101, ILE278 to THR103, ILE290 to LEU158, ILE290 to PHE241, ILE290 to PRO295, ILE290 to THR249, ILE290 to VAL245, ILE290 to VAL285, ILE296 to ILE301, ILE296 to ILE322, ILE296 to LEU324, ILE296 to MET151, ILE296 to TRP318, ILE296 to VAL291, ILE298 to LYS303, ILE298 to PHE237, ILE298 to PHE241, ILE298 to TRP293, ILE301 to ILE306, ILE301 to LYS233, ILE301 to PHE237, ILE301 to VAL236, ILE302 to ILE308, ILE302 to THR307, ILE308 to LYS303, ILE308 to TRP318, ILE308 to TYR299, ILE322 to LEU121, ILE322 to PRO295, ILE322 to SER317, ILE322 to THR327, ILE322 to TRP293, ILE322 to TYR128, ILE322 to TYR75, ILE322 to VAL300, ILE322 to VAL78, ILE69 to LEU129, ILE69 to LEU74, ILE69 to TYR128, ILE71 to LEU129, ILE71 to PHE320, ILE71 to SER125, ILE71 to SER317, ILE71 to SER76, ILE71 to THR312, ILE71 to THR315, ILE71 to TYR128, ILE71 to VAL316, ILE71 to VAL66, ILE77 to LEU121, ILE77 to LEU83, ILE77 to MET72, ILE93 to LEU88, ILE93 to LYS100, ILE93 to LYS98, ILE93 to MET99, ILE93 to PHE108, ILE93 to PHE343, ILE93 to THR101, ILE93 to THR103, ILE93 to TYR106, LEU110 to LEU158, LEU110 to MET161, LEU110 to PHE289, LEU110 to PRO333, LEU110 to SER154, LEU110 to SER329, LEU110 to THR153, LEU110 to THR157, LEU110 to TYR336, LEU110 to VAL285, LEU112 to MET90, LEU112 to SER119, LEU112 to THR153, LEU112 to TRP192, LEU116 to LEU121, LEU116 to LEU83, LEU116 to MET90, LEU116 to PHE87, LEU116 to TRP192, LEU116 to TYR149, LEU116 to TYR326, LEU121 to LEU74, LEU121 to SER76, LEU121 to TYR128, LEU121 to TYR326, LEU121 to TYR75, LEU121 to VAL126, LEU121 to VAL143, LEU121 to VAL78, LEU121 to VAL80, LEU129 to MET65, LEU129 to MET72, LEU139 to PHE123, LEU139 to TRP133, LEU158 to PHE289, LEU158 to PRO244, LEU158 to THR153, LEU158 to TRP293, LEU158 to TYR252, LEU158 to TYR336, LEU158 to VAL163, LEU158 to VAL282, LEU158 to VAL285, LEU158 to VAL286, LEU194 to MET243, LEU194 to PHE152, LEU194 to PHE156, LEU194 to PHE239, LEU194 to TYR149, LEU194 to VAL189, LEU200 to MET205, LEU200 to SER145, LEU200 to SER195, LEU200 to TRP192, LEU200 to TYR149, LEU219 to LEU232, LEU219 to LYS209, LEU219 to MET203, LEU219 to MET205, LEU219 to PHE204, LEU219 to PRO201, LEU219 to THR207, LEU219 to THR225, LEU219 to TYR148, LEU219 to VAL202, LEU231 to THR225, LEU231 to TRP226, LEU231 to VAL236, LEU232 to MET205, LEU232 to PHE221, LEU232 to PHE237, LEU232 to TYR148, LEU232 to TYR227, LEU232 to VAL202, LEU246 to PHE241, LEU254 to LEU259, LEU254 to THR249, LEU254 to TYR166, LEU254 to VAL169, LEU257 to LEU275, LEU257 to TYR252, LEU259 to LEU275, LEU259 to VAL169, LEU275 to MET255, LEU275 to PRO172, LEU275 to VAL169, LEU283 to LEU339, LEU283 to MET161, LEU283 to MET255, LEU283 to SER162, LEU283 to TYR252, LEU283 to VAL288, LEU305 to VAL300, LEU324 to LEU331, LEU324 to LEU74, LEU324 to PRO295, LEU324 to SER329, LEU324 to THR294, LEU324 to TRP293, LEU324 to TYR75, LEU324 to VAL288, LEU324 to VAL291, LEU324 to VAL78, LEU331 to TYR326, LEU331 to TYR336, LEU331 to VAL288, LEU331 to VAL78, LEU331 to VAL81, LEU335 to MET161, LEU335 to MET281, LEU335 to PHE289, LEU335 to VAL284, LEU335 to VAL285, LEU335 to VAL286, LEU335 to VAL288, LEU339 to LYS344, LEU339 to MET281, LEU339 to PRO333, LEU339 to VAL282, LEU339 to VAL284, LEU339 to VAL285, LEU339 to VAL334, LEU74 to PHE320, LEU74 to THR327, LEU74 to VAL316, LEU83 to LEU88, LEU83 to MET90, LEU83 to PRO122, LEU83 to SER119, LEU83 to SER329, LEU83 to THR118, LEU83 to THR120, LEU83 to VAL78, LEU88 to PHE338, LEU88 to PHE343, LEU88 to PHE347, LYS100 to PRO181, LYS100 to THR180, LYS100 to VAL92, LYS100 to VAL94, LYS141 to MET203, LYS141 to MET205, LYS141 to PHE204, LYS141 to PRO201, LYS141 to THR207, LYS141 to THR208, LYS141 to TRP133, LYS141 to VAL202, LYS185 to MET99, LYS185 to THR180, LYS185 to TYR106, LYS209 to SER214, LYS209 to THR218, LYS209 to THR220, LYS233 to LYS303, LYS233 to PHE221, LYS233 to TRP228, LYS233 to TRP318, LYS233 to TYR148, LYS233 to VAL300, LYS303 to TRP318, LYS344 to PHE338, LYS344 to TYR336, LYS98 to VAL92, MET130 to PHE135, MET130 to SER125, MET130 to SER214, MET151 to PHE156, MET151 to PHE241, MET151 to PHE289, MET151 to SER195, MET151 to TRP293, MET151 to VAL236, MET161 to MET281, MET161 to PHE156, MET161 to THR103, MET161 to TYR106, MET161 to TYR166, MET161 to TYR252, MET161 to TYR336, MET161 to VAL282, MET161 to VAL285, MET161 to VAL286, MET203 to SER145, MET203 to TYR149, MET203 to VAL143, MET205 to PHE221, MET205 to SER222, MET205 to THR218, MET205 to THR220, MET243 to PHE156, MET243 to PHE237, MET255 to SER162, MET255 to THR249, MET255 to THR279, MET255 to TYR166, MET255 to VAL163, MET255 to VAL169, MET255 to VAL250, MET255 to VAL282, MET281 to PHE343, MET281 to THR103, MET281 to TYR252, MET281 to TYR336, MET281 to VAL286, MET281 to VAL334, MET65 to THR70, MET72 to SER125, MET72 to THR67, MET72 to TYR128, MET72 to VAL126, MET72 to VAL66, MET90 to PHE108, MET90 to PHE343, MET99 to PHE108, MET99 to PHE343, MET99 to PRO181, MET99 to TYR106, MET99 to VAL89, MET99 to VAL92, MET99 to VAL94, PHE108 to THR103, PHE108 to THR157, PHE108 to TYR336, PHE108 to TYR91, PHE108 to VAL89, PHE108 to VAL94, PHE123 to PHE135, PHE123 to PRO134, PHE123 to THR132, PHE123 to TRP133, PHE123 to TYR128, PHE123 to VAL143, PHE135 to PRO122, PHE135 to THR208, PHE135 to VAL126, PHE135 to VAL143, PHE152 to PHE237, PHE152 to PHE239, PHE152 to PHE241, PHE152 to SER195, PHE152 to SER196, PHE152 to THR157, PHE152 to TRP293, PHE152 to VAL236, PHE156 to PHE239, PHE156 to PHE241, PHE156 to PRO244, PHE156 to SER195, PHE156 to SER196, PHE156 to TRP192, PHE156 to VAL187, PHE178 to THR160, PHE178 to TYR106, PHE178 to VAL163, PHE178 to VAL173, PHE178 to VAL187, PHE204 to THR220, PHE221 to TRP226, PHE221 to TRP228, PHE237 to PRO244, PHE237 to THR294, PHE239 to PRO244, PHE241 to PHE289, PHE241 to PRO295, PHE241 to THR294, PHE241 to TRP293, PHE241 to VAL236, PHE289 to PRO244, PHE289 to PRO295, PHE289 to SER154, PHE289 to THR294, PHE289 to TYR336, PHE289 to VAL245, PHE289 to VAL284, PHE313 to TRP318, PHE313 to TYR299, PHE320 to PRO295, PHE320 to THR315, PHE320 to THR327, PHE320 to TYR75, PHE338 to PHE343, PHE338 to PHE84, PHE338 to PRO333, PHE338 to VAL89, PHE338 to VAL92, PHE343 to PRO333, PHE343 to THR97, PHE343 to TYR336, PHE343 to VAL89, PHE343 to VAL92, PHE347 to PHE84, PHE347 to TYR96, PHE347 to VAL92, PHE84 to PRO333, PHE84 to THR118, PHE84 to VAL89, PHE87 to PRO333, PHE87 to SER119, PHE87 to THR118, PHE87 to VAL92, PRO122 to TYR75, PRO134 to VAL126, PRO172 to TYR166, PRO181 to THR101, PRO181 to THR103, PRO201 to SER195, PRO201 to SER196, PRO201 to TYR149, PRO244 to THR249, PRO295 to VAL300, PRO309 to THR315, PRO333 to THR327, PRO333 to VAL81, PRO333 to VAL89, SER119 to TYR326, SER119 to VAL143, SER125 to SER76, SER125 to THR120, SER125 to TYR75, SER145 to VAL202, SER154 to SER195, SER154 to SER329, SER154 to TRP293, SER154 to TYR149, SER162 to THR157, SER162 to THR249, SER162 to TYR106, SER162 to TYR252, SER162 to TYR336, SER162 to VAL250, SER162 to VAL282, SER162 to VAL286, SER195 to THR153, SER195 to TYR148, SER195 to TYR149, SER196 to THR153, SER196 to TYR149, SER196 to VAL189, SER196 to VAL202, SER214 to THR132, SER214 to TRP133, SER222 to TRP228, SER222 to TYR227, SER317 to THR312, SER317 to TYR299, SER329 to THR118, SER329 to TRP293, SER329 to VAL78, SER329 to VAL81, SER76 to THR70, SER76 to VAL81, THR101 to THR180, THR101 to TYR106, THR103 to THR180, THR103 to TYR336, THR103 to VAL282, THR118 to THR327, THR118 to TYR326, THR118 to TYR75, THR118 to VAL78, THR118 to VAL80, THR118 to VAL81, THR120 to TRP133, THR120 to TYR326, THR120 to VAL143, THR132 to VAL126, THR153 to TRP192, THR153 to TYR148, THR157 to TRP192, THR157 to TYR106, THR160 to TYR106, THR160 to VAL187, THR180 to TYR106, THR207 to THR218, THR207 to THR220, THR207 to VAL202, THR208 to THR218, THR208 to THR220, THR208 to TRP133, THR218 to VAL202, THR220 to THR225, THR249 to VAL282, THR249 to VAL286, THR279 to TYR252, THR279 to VAL169, THR279 to VAL284, THR294 to TYR299, THR294 to VAL245, THR311 to VAL316, THR312 to THR67, THR312 to TRP318, THR315 to THR67, THR315 to TYR128, THR315 to TYR299, THR327 to TYR75, THR327 to VAL288, THR327 to VAL78, THR67 to TYR128, THR67 to VAL316, THR70 to TYR75, THR70 to VAL316, THR97 to TYR91, THR97 to VAL89, THR97 to VAL92, TRP133 to VAL126, TRP133 to VAL143, TRP192 to TYR149, TRP192 to VAL187, TRP293 to TYR326, TRP293 to VAL288, TRP318 to TYR128, TRP318 to TYR299, TRP318 to TYR75, TRP318 to VAL300, TYR106 to TYR336, TYR106 to VAL187, TYR128 to TYR326, TYR128 to TYR75, TYR148 to VAL143, TYR148 to VAL202, TYR148 to VAL236, TYR149 to VAL202, TYR166 to TYR252, TYR166 to VAL250, TYR252 to TYR336, TYR252 to VAL163, TYR252 to VAL282, TYR252 to VAL284, TYR252 to VAL285, TYR252 to VAL286, TYR299 to VAL316, TYR326 to TYR75, TYR326 to VAL143, TYR326 to VAL78, TYR336 to VAL285, TYR336 to VAL286, TYR336 to VAL89, TYR75 to VAL80, TYR91 to TYR96, VAL236 to VAL300, VAL245 to VAL250, VAL245 to VAL286, VAL286 to VAL291, VAL334 to VAL81, VAL334 to VAL89, VAL89 to VAL94, ALA102_CA to ALA184_CA, ALA102_CA to ARG165_CA, ALA102_CA to ARG179_CA, ALA102_CA to ARG182_CA, ALA102_CA to ASN183_CA, ALA102_CA to ASN188_CA, ALA102_CA to ASP164_CA, ALA102_CA to ILE107_CA, ALA102_CA to LYS185_CA, ALA102_CA to MET161_CA, ALA102_CA to PHE178_CA, ALA102_CA to PRO181_CA, ALA102_CA to THR180_CA, ALA111_CA to ASN332_CA, ALA111_CA to ASN86_CA, ALA111_CA to GLY82_CA, ALA111_CA to GLY85_CA, ALA111_CA to ILE93_CA, ALA111_CA to LEU116_CA, ALA111_CA to MET90_CA, ALA111_CA to PHE87_CA, ALA111_CA to PRO333_CA, ALA111_CA to THR118_CA, ALA111_CA to THR157_CA, ALA111_CA to TYR106_CA, ALA111_CA to TYR336_CA, ALA111_CA to VAL89_CA, ALA113_CA to ASN150_CA, ALA113_CA to ASN86_CA, ALA113_CA to ILE146_CA, ALA113_CA to ILE155_CA, ALA113_CA to MET151_CA, ALA113_CA to MET90_CA, ALA113_CA to PHE108_CA, ALA113_CA to PHE152_CA, ALA113_CA to SER154_CA, ALA113_CA to SER329_CA, ALA113_CA to THR118_CA, ALA113_CA to THR153_CA, ALA113_CA to THR157_CA, ALA113_CA to TRP192_CA, ALA113_CA to TYR149_CA, ALA115_CA to ASN150_CA, ALA115_CA to ASN86_CA, ALA115_CA to GLY82_CA, ALA115_CA to ILE146_CA, ALA115_CA to LEU110_CA, ALA115_CA to LEU83_CA, ALA115_CA to MET90_CA, ALA115_CA to PHE87_CA, ALA115_CA to SER329_CA, ALA115_CA to THR120_CA, ALA117_CA to ASN150_CA, ALA117_CA to ASP147_CA, ALA117_CA to GLN124_CA, ALA117_CA to ILE146_CA, ALA117_CA to LEU112_CA, ALA117_CA to LEU83_CA, ALA117_CA to MET151_CA, ALA117_CA to PRO122_CA, ALA117_CA to SER154_CA, ALA117_CA to SER329_CA, ALA117_CA to TYR326_CA, ALA168_CA to ALA175_CA, ALA168_CA to ARG179_CA, ALA168_CA to LEU275_CA, ALA168_CA to PHE178_CA, ALA168_CA to VAL163_CA, ALA168_CA to VAL173_CA, ALA175_CA to ASP164_CA, ALA175_CA to ILE167_CA, ALA175_CA to THR180_CA, ALA175_CA to VAL169_CA, ALA184_CA to ARG179_CA, ALA184_CA to ASP164_CA, ALA184_CA to ILE105_CA, ALA184_CA to PHE178_CA, ALA184_CA to THR101_CA, ALA184_CA to THR103_CA, ALA184_CA to THR160_CA, ALA184_CA to TYR106_CA, ALA184_CA to VAL189_CA, ALA197_CA to TRP192_CA, ALA197_CA to TYR149_CA, ALA197_CA to VAL202_CA, ALA206_CA to ASN137_CA, ALA206_CA to CYS140_CA, ALA206_CA to CYS217_CA, ALA206_CA to ILE142_CA, ALA206_CA to ILE144_CA, ALA206_CA to LEU219_CA, ALA206_CA to LYS141_CA, ALA206_CA to PRO201_CA, ALA206_CA to SER145_CA, ALA206_CA to THR218_CA, ALA206_CA to THR220_CA, ALA240_CA to CYS235_CA, ALA240_CA to HIS297_CA, ALA240_CA to ILE155_CA, ALA240_CA to ILE234_CA, ALA240_CA to MET151_CA, ALA240_CA to PHE152_CA, ALA240_CA to PHE156_CA, ALA240_CA to PHE289_CA, ALA240_CA to TRP293_CA, ALA240_CA to VAL245_CA, ALA287_CA to CYS292_CA, ALA287_CA to ILE248_CA, ALA287_CA to TYR252_CA, ALA287_CA to VAL282_CA, ALA304_CA to ASN230_CA, ALA304_CA to GLU229_CA, ALA304_CA to LYS233_CA, ALA304_CA to TYR299_CA, ALA323_CA to ASN328_CA, ALA323_CA to CYS292_CA, ALA323_CA to ILE296_CA, ALA323_CA to ILE71_CA, ALA323_CA to LEU121_CA, ALA323_CA to LEU74_CA, ALA323_CA to TRP318_CA, ALA323_CA to TYR75_CA, ALA323_CA to VAL78_CA, ALA337_CA to ARG345_CA, ALA337_CA to ASN332_CA, ALA337_CA to ASN342_CA, ALA337_CA to ILE107_CA, ALA337_CA to ILE93_CA, ALA337_CA to LEU110_CA, ALA337_CA to LEU331_CA, ALA337_CA to LYS344_CA, ALA337_CA to MET161_CA, ALA337_CA to MET281_CA, ALA337_CA to PHE343_CA, ALA337_CA to PHE347_CA, ALA337_CA to VAL89_CA, ALA68_CA to ALA73_CA, ALA68_CA to LEU129_CA, ALA68_CA to LEU74_CA, ALA68_CA to SER125_CA, ALA68_CA to TYR128_CA, ALA68_CA to VAL316_CA, ALA73_CA to VAL78_CA, ARG165_CA to ARG179_CA, ARG165_CA to ARG276_CA, ARG165_CA to ARG280_CA, ARG165_CA to ASN274_CA, ARG165_CA to ASP340_CA, ARG165_CA to CYS170_CA, ARG165_CA to CYS251_CA, ARG165_CA to ILE278_CA, ARG165_CA to LEU158_CA, ARG165_CA to LEU275_CA, ARG165_CA to LEU283_CA, ARG165_CA to LEU335_CA, ARG165_CA to LEU339_CA, ARG165_CA to MET255_CA, ARG165_CA to MET281_CA, ARG165_CA to PHE178_CA, ARG165_CA to THR103_CA, ARG165_CA to THR160_CA, ARG165_CA to THR279_CA, ARG165_CA to TYR106_CA, ARG165_CA to TYR252_CA, ARG165_CA to TYR336_CA, ARG165_CA to VAL282_CA, ARG165_CA to VAL285_CA, ARG179_CA to ASP164_CA, ARG179_CA to HIS171_CA, ARG179_CA to ILE167_CA, ARG179_CA to ILE278_CA, ARG179_CA to LYS174_CA, ARG179_CA to MET161_CA, ARG179_CA to THR101_CA, ARG179_CA to THR103_CA, ARG179_CA to TYR106_CA, ARG179_CA to VAL169_CA, ARG182_CA to ILE105_CA, ARG182_CA to VAL187_CA, ARG211_CA to ASP216_CA, ARG211_CA to THR132_CA, ARG258_CA to CYS170_CA, ARG258_CA to GLY253_CA, ARG258_CA to HIS171_CA, ARG258_CA to PRO172_CA, ARG258_CA to TYR166_CA, ARG258_CA to VAL169_CA, ARG273_CA to ARG280_CA, ARG273_CA to ILE278_CA, ARG276_CA to LYS185_CA, ARG276_CA to MET281_CA, ARG276_CA to VAL169_CA, ARG277_CA to ASP340_CA, ARG277_CA to GLU341_CA, ARG277_CA to LEU339_CA, ARG277_CA to LYS344_CA, ARG277_CA to VAL282_CA, ARG280_CA to GLU341_CA, ARG280_CA to ILE256_CA, ARG280_CA to LEU275_CA, ARG280_CA to LEU339_CA, ARG280_CA to PHE338_CA, ARG280_CA to VAL285_CA, ARG345_CA to ASP340_CA, ARG345_CA to LYS98_CA, ARG345_CA to PHE338_CA, ARG95_CA to LYS100_CA, ARG95_CA to MET90_CA, ASN104_CA to ASN109_CA, ASN104_CA to ASN342_CA, ASN104_CA to ASP340_CA, ASN104_CA to ILE93_CA, ASN104_CA to LYS98_CA, ASN104_CA to MET281_CA, ASN104_CA to MET99_CA, ASN104_CA to PHE343_CA, ASN104_CA to THR97_CA, ASN104_CA to VAL89_CA, ASN109_CA to ASN150_CA, ASN109_CA to ASN188_CA, ASN109_CA to ASN191_CA, ASN109_CA to ASP114_CA, ASN109_CA to ILE93_CA, ASN109_CA to MET90_CA, ASN109_CA to MET99_CA, ASN109_CA to PHE156_CA, ASN109_CA to SER154_CA, ASN109_CA to THR153_CA, ASN109_CA to THR157_CA, ASN109_CA to THR160_CA, ASN109_CA to TRP192_CA, ASN109_CA to VAL187_CA, ASN109_CA to VAL189_CA, ASN127_CA to ASP216_CA, ASN127_CA to CYS217_CA, ASN127_CA to HIS319_CA, ASN127_CA to ILE215_CA, ASN127_CA to PHE135_CA, ASN127_CA to PRO122_CA, ASN127_CA to PRO134_CA, ASN127_CA to THR132_CA, ASN127_CA to TRP133_CA, ASN137_CA to CYS217_CA, ASN137_CA to ILE142_CA, ASN137_CA to LYS209_CA, ASN137_CA to THR207_CA, ASN137_CA to THR208_CA, ASN150_CA to ASP114_CA, ASN150_CA to GLY325_CA, ASN150_CA to ILE155_CA, ASN150_CA to LEU110_CA, ASN150_CA to LEU112_CA, ASN150_CA to LEU116_CA, ASN150_CA to PHE289_CA, ASN150_CA to SER145_CA, ASN150_CA to SER195_CA, ASN150_CA to SER329_CA, ASN150_CA to THR120_CA, ASN150_CA to TRP192_CA, ASN150_CA to TRP293_CA, ASN150_CA to TYR326_CA, ASN183_CA to ASN188_CA, ASN183_CA to ASP177_CA, ASN183_CA to ILE105_CA, ASN183_CA to LEU176_CA, ASN183_CA to PHE178_CA, ASN183_CA to TYR106_CA, ASN188_CA to ILE105_CA, ASN188_CA to ILE107_CA, ASN188_CA to ILE193_CA, ASN188_CA to LEU110_CA, ASN188_CA to PHE108_CA, ASN188_CA to THR153_CA, ASN188_CA to THR157_CA, ASN188_CA to THR160_CA, ASN188_CA to TYR106_CA, ASN191_CA to ILE155_CA, ASN191_CA to ILE186_CA, ASN191_CA to LEU158_CA, ASN191_CA to PHE152_CA, ASN191_CA to PHE156_CA, ASN191_CA to SER154_CA, ASN191_CA to SER196_CA, ASN191_CA to THR153_CA, ASN191_CA to THR157_CA, ASN191_CA to THR160_CA, ASN191_CA to TYR106_CA, ASN191_CA to TYR149_CA, ASN230_CA to CYS235_CA, ASN230_CA to LEU305_CA, ASN230_CA to PHE221_CA, ASN230_CA to THR225_CA, ASN274_CA to GLU341_CA, ASN274_CA to THR279_CA, ASN328_CA to ASP114_CA, ASN328_CA to CYS292_CA, ASN328_CA to ILE155_CA, ASN328_CA to ILE290_CA, ASN328_CA to LEU110_CA, ASN328_CA to LEU158_CA, ASN328_CA to LEU335_CA, ASN328_CA to PHE289_CA, ASN328_CA to PRO333_CA, ASN328_CA to SER154_CA, ASN328_CA to TRP293_CA, ASN328_CA to TYR336_CA, ASN328_CA to VAL285_CA, ASN328_CA to VAL288_CA, ASN328_CA to VAL291_CA, ASN328_CA to VAL78_CA, ASN332_CA to ASN86_CA, ASN332_CA to ASP114_CA, ASN332_CA to ILE107_CA, ASN332_CA to ILE155_CA, ASN332_CA to LEU110_CA, ASN332_CA to LEU158_CA, ASN332_CA to PHE289_CA, ASN332_CA to PHE338_CA, ASN332_CA to SER154_CA, ASN332_CA to THR327_CA, ASN332_CA to TRP293_CA, ASN332_CA to VAL285_CA, ASN332_CA to VAL288_CA, ASN332_CA to VAL89_CA, ASN342_CA to LYS98_CA, ASN342_CA to MET99_CA, ASN342_CA to PHE347_CA, ASN342_CA to THR101_CA, ASN342_CA to THR103_CA, ASN342_CA to THR97_CA, ASN342_CA to TYR336_CA, ASN342_CA to VAL92_CA, ASN86_CA to ASP114_CA, ASN86_CA to CYS330_CA, ASN86_CA to ILE107_CA, ASN86_CA to LEU110_CA, ASN86_CA to LEU112_CA, ASN86_CA to LEU116_CA, ASN86_CA to LEU331_CA, ASN86_CA to PHE338_CA, ASN86_CA to PRO333_CA, ASN86_CA to SER329_CA, ASN86_CA to THR118_CA, ASN86_CA to TYR336_CA, ASN86_CA to TYR91_CA, ASN86_CA to VAL81_CA, ASP114_CA to CYS330_CA, ASP114_CA to GLY82_CA, ASP114_CA to ILE155_CA, ASP114_CA to LEU158_CA, ASP114_CA to LEU331_CA, ASP114_CA to LEU83_CA, ASP114_CA to PRO333_CA, ASP114_CA to SER119_CA, ASP114_CA to SER154_CA, ASP114_CA to SER329_CA, ASP114_CA to THR153_CA, ASP114_CA to TYR326_CA, ASP114_CA to TYR336_CA, ASP147_CA to GLN124_CA, ASP147_CA to ILE142_CA, ASP147_CA to LEU116_CA, ASP147_CA to LEU121_CA, ASP147_CA to PHE152_CA, ASP147_CA to THR118_CA, ASP147_CA to THR120_CA, ASP147_CA to TRP293_CA, ASP147_CA to TYR326_CA, ASP164_CA to CYS159_CA, ASP164_CA to CYS251_CA, ASP164_CA to PHE178_CA, ASP164_CA to THR103_CA, ASP164_CA to THR180_CA, ASP164_CA to TYR106_CA, ASP164_CA to VAL169_CA, ASP177_CA to PRO172_CA, ASP216_CA to CYS140_CA, ASP216_CA to GLY131_CA, ASP216_CA to LYS209_CA, ASP216_CA to THR132_CA, ASP216_CA to THR207_CA, ASP216_CA to THR208_CA, ASP216_CA to TRP133_CA, ASP216_CA to TYR210_CA, ASP340_CA to ILE107_CA, ASP340_CA to ILE278_CA, ASP340_CA to LEU335_CA, ASP340_CA to MET161_CA, ASP340_CA to MET281_CA, ASP340_CA to MET99_CA, ASP340_CA to PRO333_CA, ASP340_CA to THR103_CA, ASP340_CA to VAL334_CA, CYS140_CA to CYS217_CA, CYS140_CA to ILE146_CA, CYS140_CA to LEU219_CA, CYS140_CA to PHE135_CA, CYS140_CA to SER145_CA, CYS140_CA to THR207_CA, CYS140_CA to THR208_CA, CYS140_CA to THR218_CA, CYS140_CA to TRP133_CA, CYS140_CA to VAL202_CA, CYS159_CA to CYS251_CA, CYS159_CA to ILE247_CA, CYS159_CA to ILE248_CA, CYS159_CA to MET243_CA, CYS159_CA to PHE239_CA, CYS159_CA to PHE289_CA, CYS159_CA to PRO244_CA, CYS159_CA to SER154_CA, CYS159_CA to TYR252_CA, CYS159_CA to TYR336_CA, CYS159_CA to VAL245_CA, CYS159_CA to VAL286_CA, CYS170_CA to CYS251_CA, CYS170_CA to ILE256_CA, CYS170_CA to LEU254_CA, CYS170_CA to LEU257_CA, CYS170_CA to LEU259_CA, CYS170_CA to LEU275_CA, CYS170_CA to MET255_CA, CYS190_CA to LYS185_CA, CYS190_CA to PHE156_CA, CYS190_CA to SER195_CA, CYS190_CA to SER196_CA, CYS217_CA to GLY136_CA, CYS217_CA to ILE144_CA, CYS217_CA to LEU139_CA, CYS217_CA to LYS141_CA, CYS217_CA to LYS209_CA, CYS217_CA to THR132_CA, CYS217_CA to THR207_CA, CYS217_CA to THR208_CA, CYS217_CA to TRP133_CA, CYS217_CA to VAL143_CA, CYS235_CA to ILE198_CA, CYS235_CA to PHE152_CA, CYS235_CA to PHE241_CA, CYS251_CA to ILE256_CA, CYS251_CA to LEU246_CA, CYS251_CA to SER162_CA, CYS251_CA to TYR166_CA, CYS251_CA to VAL163_CA, CYS292_CA to CYS321_CA, CYS292_CA to GLY325_CA, CYS292_CA to HIS297_CA, CYS292_CA to ILE322_CA, CYS292_CA to LEU324_CA, CYS292_CA to LEU331_CA, CYS292_CA to SER329_CA, CYS292_CA to THR327_CA, CYS292_CA to TYR326_CA, CYS321_CA to HIS297_CA, CYS321_CA to ILE296_CA, CYS321_CA to LEU74_CA, CYS321_CA to PRO295_CA, CYS321_CA to TRP293_CA, CYS321_CA to TYR299_CA, CYS321_CA to TYR326_CA, CYS321_CA to VAL316_CA, CYS330_CA to CYS79_CA, CYS330_CA to GLY325_CA, CYS330_CA to GLY82_CA, CYS330_CA to GLY85_CA, CYS330_CA to ILE77_CA, CYS330_CA to LEU121_CA, CYS330_CA to LEU335_CA, CYS330_CA to LEU83_CA, CYS330_CA to THR118_CA, CYS330_CA to VAL78_CA, CYS330_CA to VAL80_CA, CYS330_CA to VAL81_CA, CYS346_CA to GLU341_CA, CYS346_CA to LEU88_CA, CYS346_CA to LYS98_CA, CYS346_CA to MET99_CA, CYS346_CA to PHE338_CA, CYS346_CA to THR97_CA, CYS346_CA to TYR96_CA, CYS346_CA to VAL92_CA, CYS79_CA to LEU121_CA, CYS79_CA to LEU74_CA, CYS79_CA to PHE84_CA, CYS79_CA to PRO122_CA, CYS79_CA to SER119_CA, CYS79_CA to THR118_CA, CYS79_CA to THR120_CA, CYS79_CA to TYR326_CA, GLN124_CA to HIS319_CA, GLN124_CA to ILE322_CA, GLN124_CA to LEU129_CA, GLN124_CA to PHE135_CA, GLN124_CA to TRP133_CA, GLN124_CA to TYR326_CA, GLN124_CA to TYR75_CA, GLN124_CA to VAL143_CA, GLN314_CA to HIS319_CA, GLN314_CA to ILE308_CA, GLN314_CA to LYS303_CA, GLN314_CA to PRO309_CA, GLN314_CA to THR307_CA, GLN314_CA to TYR299_CA, GLU229_CA to ILE234_CA, GLU229_CA to LEU219_CA, GLU229_CA to PHE221_CA, GLU229_CA to PRO224_CA, GLU229_CA to SER222_CA, GLU229_CA to THR218_CA, GLU310_CA to THR315_CA, GLU341_CA to TYR336_CA, GLY131_CA to GLY213_CA, GLY131_CA to ILE215_CA, GLY131_CA to SER125_CA, GLY131_CA to SER214_CA, GLY131_CA to VAL126_CA, GLY136_CA to LYS141_CA, GLY136_CA to THR207_CA, GLY136_CA to THR208_CA, GLY199_CA to ILE144_CA, GLY199_CA to ILE146_CA, GLY199_CA to LEU194_CA, GLY199_CA to LYS141_CA, GLY199_CA to PHE152_CA, GLY199_CA to PHE204_CA, GLY199_CA to SER145_CA, GLY199_CA to TYR148_CA, GLY199_CA to TYR149_CA, GLY213_CA to THR132_CA, GLY253_CA to ILE247_CA, GLY253_CA to ILE248_CA, GLY253_CA to VAL282_CA, GLY325_CA to ILE296_CA, GLY325_CA to PHE320_CA, GLY325_CA to TRP293_CA, GLY325_CA to VAL291_CA, GLY325_CA to VAL78_CA, GLY82_CA to ILE77_CA, GLY82_CA to LEU331_CA, GLY82_CA to LEU88_CA, GLY82_CA to PHE87_CA, GLY82_CA to PRO333_CA, GLY82_CA to SER329_CA, GLY82_CA to SER76_CA, GLY82_CA to THR118_CA, GLY82_CA to TYR326_CA, GLY85_CA to MET90_CA, GLY85_CA to PHE338_CA, GLY85_CA to PRO333_CA, GLY85_CA to SER329_CA, GLY85_CA to TYR336_CA, GLY85_CA to VAL334_CA, GLY85_CA to VAL80_CA, HIS171_CA to LEU176_CA, HIS171_CA to PHE178_CA, HIS171_CA to TYR166_CA, HIS223_CA to TRP228_CA, HIS297_CA to ILE155_CA, HIS297_CA to ILE238_CA, HIS297_CA to ILE302_CA, HIS297_CA to LYS233_CA, HIS297_CA to MET151_CA, HIS297_CA to PHE237_CA, HIS297_CA to PHE241_CA, HIS297_CA to PHE289_CA, HIS297_CA to VAL236_CA, HIS319_CA to ILE71_CA, HIS319_CA to LEU324_CA, HIS319_CA to LEU74_CA, HIS319_CA to THR67_CA, HIS319_CA to TYR128_CA, HIS319_CA to TYR299_CA, HIS319_CA to TYR75_CA, ILE105_CA to ILE186_CA, ILE105_CA to ILE93_CA, ILE105_CA to LEU110_CA, ILE105_CA to LYS100_CA, ILE105_CA to LYS185_CA, ILE105_CA to MET99_CA, ILE105_CA to PRO181_CA, ILE105_CA to THR157_CA, ILE105_CA to THR180_CA, ILE107_CA to ILE93_CA, ILE107_CA to LEU112_CA, ILE107_CA to MET161_CA, ILE107_CA to MET281_CA, ILE107_CA to MET90_CA, ILE107_CA to PHE338_CA, ILE107_CA to PHE343_CA, ILE107_CA to THR157_CA, ILE107_CA to TYR336_CA, ILE107_CA to VAL282_CA, ILE107_CA to VAL89_CA, ILE138_CA to MET203_CA, ILE138_CA to THR208_CA, ILE138_CA to TRP133_CA, ILE138_CA to VAL143_CA, ILE142_CA to MET203_CA, ILE142_CA to THR120_CA, ILE142_CA to TYR149_CA, ILE144_CA to LEU139_CA, ILE144_CA to LEU219_CA, ILE144_CA to MET203_CA, ILE144_CA to THR120_CA, ILE144_CA to THR207_CA, ILE144_CA to THR218_CA, ILE144_CA to TRP133_CA, ILE144_CA to TYR149_CA, ILE144_CA to VAL202_CA, ILE146_CA to LEU116_CA, ILE146_CA to LYS141_CA, ILE146_CA to MET151_CA, ILE146_CA to MET203_CA, ILE146_CA to SER119_CA, ILE146_CA to THR118_CA, ILE146_CA to THR120_CA, ILE146_CA to THR153_CA, ILE146_CA to VAL202_CA, ILE155_CA to ILE242_CA, ILE155_CA to ILE248_CA, ILE155_CA to ILE290_CA, ILE155_CA to LEU110_CA, ILE155_CA to MET243_CA, ILE155_CA to PHE239_CA, ILE155_CA to PHE241_CA, ILE155_CA to PHE289_CA, ILE155_CA to PRO244_CA, ILE155_CA to THR160_CA, ILE155_CA to TRP293_CA, ILE155_CA to VAL245_CA, ILE167_CA to LEU176_CA, ILE167_CA to LYS174_CA, ILE167_CA to MET255_CA, ILE167_CA to PHE178_CA, ILE167_CA to PRO172_CA, ILE167_CA to SER162_CA, ILE167_CA to VAL173_CA, ILE186_CA to PRO181_CA, ILE193_CA to ILE198_CA, ILE193_CA to THR153_CA, ILE193_CA to TYR149_CA, ILE198_CA to LEU232_CA, ILE198_CA to MET151_CA, ILE198_CA to MET203_CA, ILE198_CA to MET205_CA, ILE198_CA to PHE152_CA, ILE198_CA to PHE239_CA, ILE198_CA to SER145_CA, ILE198_CA to TYR148_CA, ILE198_CA to TYR149_CA, ILE198_CA to VAL236_CA, ILE215_CA to LYS209_CA, ILE215_CA to PRO134_CA, ILE215_CA to THR132_CA, ILE215_CA to THR208_CA, ILE215_CA to TRP133_CA, ILE215_CA to TYR210_CA, ILE234_CA to ILE242_CA, ILE234_CA to ILE301_CA, ILE234_CA to PHE239_CA, ILE238_CA to LEU231_CA, ILE238_CA to LYS233_CA, ILE238_CA to MET243_CA, ILE238_CA to PHE152_CA, ILE238_CA to PRO244_CA, ILE242_CA to ILE247_CA, ILE242_CA to PHE237_CA, ILE242_CA to PHE289_CA, ILE242_CA to VAL236_CA, ILE247_CA to LEU158_CA, ILE247_CA to SER162_CA, ILE247_CA to THR160_CA, ILE247_CA to TYR252_CA, ILE247_CA to VAL163_CA, ILE248_CA to ILE290_CA, ILE248_CA to LEU158_CA, ILE248_CA to MET243_CA, ILE248_CA to MET255_CA, ILE248_CA to PHE289_CA, ILE248_CA to SER162_CA, ILE248_CA to THR160_CA, ILE248_CA to TYR336_CA, ILE248_CA to VAL163_CA, ILE248_CA to VAL282_CA, ILE248_CA to VAL285_CA, ILE248_CA to VAL286_CA, ILE256_CA to ILE278_CA, ILE256_CA to LEU275_CA, ILE256_CA to LEU283_CA, ILE256_CA to THR279_CA, ILE256_CA to VAL169_CA, ILE256_CA to VAL282_CA, ILE278_CA to LEU259_CA, ILE278_CA to LEU283_CA, ILE278_CA to LEU339_CA, ILE278_CA to MET255_CA, ILE278_CA to THR101_CA, ILE278_CA to THR103_CA, ILE290_CA to LEU158_CA, ILE290_CA to PHE241_CA, ILE290_CA to PRO295_CA, ILE290_CA to THR249_CA, ILE290_CA to VAL245_CA, ILE290_CA to VAL285_CA, ILE296_CA to ILE301_CA, ILE296_CA to ILE322_CA, ILE296_CA to LEU324_CA, ILE296_CA to MET151_CA, ILE296_CA to TRP318_CA, ILE296_CA to VAL291_CA, ILE298_CA to LYS303_CA, ILE298_CA to PHE237_CA, ILE298_CA to PHE241_CA, ILE298_CA to TRP293_CA, ILE301_CA to ILE306_CA, ILE301_CA to LYS233_CA, ILE301_CA to PHE237_CA, ILE301_CA to VAL236_CA, ILE302_CA to ILE308_CA, ILE302_CA to THR307_CA, ILE308_CA to LYS303_CA, ILE308_CA to TRP318_CA, ILE308_CA to TYR299_CA, ILE322_CA to LEU121_CA, ILE322_CA to PRO295_CA, ILE322_CA to SER317_CA, ILE322_CA to THR327_CA, ILE322_CA to TRP293_CA, ILE322_CA to TYR128_CA, ILE322_CA to TYR75_CA, ILE322_CA to VAL300_CA, ILE322_CA to VAL78_CA, ILE69_CA to LEU129_CA, ILE69_CA to LEU74_CA, ILE69_CA to TYR128_CA, ILE71_CA to LEU129_CA, ILE71_CA to PHE320_CA, ILE71_CA to SER125_CA, ILE71_CA to SER317_CA, ILE71_CA to SER76_CA, ILE71_CA to THR312_CA, ILE71_CA to THR315_CA, ILE71_CA to TYR128_CA, ILE71_CA to VAL316_CA, ILE71_CA to VAL66_CA, ILE77_CA to LEU121_CA, ILE77_CA to LEU83_CA, ILE77_CA to MET72_CA, ILE93_CA to LEU88_CA, ILE93_CA to LYS100_CA, ILE93_CA to LYS98_CA, ILE93_CA to MET99_CA, ILE93_CA to PHE108_CA, ILE93_CA to PHE343_CA, ILE93_CA to THR101_CA, ILE93_CA to THR103_CA, ILE93_CA to TYR106_CA, LEU110_CA to LEU158_CA, LEU110_CA to MET161_CA, LEU110_CA to PHE289_CA, LEU110_CA to PRO333_CA, LEU110_CA to SER154_CA, LEU110_CA to SER329_CA, LEU110_CA to THR153_CA, LEU110_CA to THR157_CA, LEU110_CA to TYR336_CA, LEU110_CA to VAL285_CA, LEU112_CA to MET90_CA, LEU112_CA to SER119_CA, LEU112_CA to THR153_CA, LEU112_CA to TRP192_CA, LEU116_CA to LEU121_CA, LEU116_CA to LEU83_CA, LEU116_CA to MET90_CA, LEU116_CA to PHE87_CA, LEU116_CA to TRP192_CA, LEU116_CA to TYR149_CA, LEU116_CA to TYR326_CA, LEU121_CA to LEU74_CA, LEU121_CA to SER76_CA, LEU121_CA to TYR128_CA, LEU121_CA to TYR326_CA, LEU121_CA to TYR75_CA, LEU121_CA to VAL126_CA, LEU121_CA to VAL143_CA, LEU121_CA to VAL78_CA, LEU121_CA to VAL80_CA, LEU129_CA to MET65_CA, LEU129_CA to MET72_CA, LEU139_CA to PHE123_CA, LEU139_CA to TRP133_CA, LEU158_CA to PHE289_CA, LEU158_CA to PRO244_CA, LEU158_CA to THR153_CA, LEU158_CA to TRP293_CA, LEU158_CA to TYR252_CA, LEU158_CA to TYR336_CA, LEU158_CA to VAL163_CA, LEU158_CA to VAL282_CA, LEU158_CA to VAL285_CA, LEU158_CA to VAL286_CA, LEU194_CA to MET243_CA, LEU194_CA to PHE152_CA, LEU194_CA to PHE156_CA, LEU194_CA to PHE239_CA, LEU194_CA to TYR149_CA, LEU194_CA to VAL189_CA, LEU200_CA to MET205_CA, LEU200_CA to SER145_CA, LEU200_CA to SER195_CA, LEU200_CA to TRP192_CA, LEU200_CA to TYR149_CA, LEU219_CA to LEU232_CA, LEU219_CA to LYS209_CA, LEU219_CA to MET203_CA, LEU219_CA to MET205_CA, LEU219_CA to PHE204_CA, LEU219_CA to PRO201_CA, LEU219_CA to THR207_CA, LEU219_CA to THR225_CA, LEU219_CA to TYR148_CA, LEU219_CA to VAL202_CA, LEU231_CA to THR225_CA, LEU231_CA to TRP226_CA, LEU231_CA to VAL236_CA, LEU232_CA to MET205_CA, LEU232_CA to PHE221_CA, LEU232_CA to PHE237_CA, LEU232_CA to TYR148_CA, LEU232_CA to TYR227_CA, LEU232_CA to VAL202_CA, LEU246_CA to PHE241_CA, LEU254_CA to LEU259_CA, LEU254_CA to THR249_CA, LEU254_CA to TYR166_CA, LEU254_CA to VAL169_CA, LEU257_CA to LEU275_CA, LEU257_CA to TYR252_CA, LEU259_CA to LEU275_CA, LEU259_CA to VAL169_CA, LEU275_CA to MET255_CA, LEU275_CA to PRO172_CA, LEU275_CA to VAL169_CA, LEU283_CA to LEU339_CA, LEU283_CA to MET161_CA, LEU283_CA to MET255_CA, LEU283_CA to SER162_CA, LEU283_CA to TYR252_CA, LEU283_CA to VAL288_CA, LEU305_CA to VAL300_CA, LEU324_CA to LEU331_CA, LEU324_CA to LEU74_CA, LEU324_CA to PRO295_CA, LEU324_CA to SER329_CA, LEU324_CA to THR294_CA, LEU324_CA to TRP293_CA, LEU324_CA to TYR75_CA, LEU324_CA to VAL288_CA, LEU324_CA to VAL291_CA, LEU324_CA to VAL78_CA, LEU331_CA to TYR326_CA, LEU331_CA to TYR336_CA, LEU331_CA to VAL288_CA, LEU331_CA to VAL78_CA, LEU331_CA to VAL81_CA, LEU335_CA to MET161_CA, LEU335_CA to MET281_CA, LEU335_CA to PHE289_CA, LEU335_CA to VAL284_CA, LEU335_CA to VAL285_CA, LEU335_CA to VAL286_CA, LEU335_CA to VAL288_CA, LEU339_CA to LYS344_CA, LEU339_CA to MET281_CA, LEU339_CA to PRO333_CA, LEU339_CA to VAL282_CA, LEU339_CA to VAL284_CA, LEU339_CA to VAL285_CA, LEU339_CA to VAL334_CA, LEU74_CA to PHE320_CA, LEU74_CA to THR327_CA, LEU74_CA to VAL316_CA, LEU83_CA to LEU88_CA, LEU83_CA to MET90_CA, LEU83_CA to PRO122_CA, LEU83_CA to SER119_CA, LEU83_CA to SER329_CA, LEU83_CA to THR118_CA, LEU83_CA to THR120_CA, LEU83_CA to VAL78_CA, LEU88_CA to PHE338_CA, LEU88_CA to PHE343_CA, LEU88_CA to PHE347_CA, LYS100_CA to PRO181_CA, LYS100_CA to THR180_CA, LYS100_CA to VAL92_CA, LYS100_CA to VAL94_CA, LYS141_CA to MET203_CA, LYS141_CA to MET205_CA, LYS141_CA to PHE204_CA, LYS141_CA to PRO201_CA, LYS141_CA to THR207_CA, LYS141_CA to THR208_CA, LYS141_CA to TRP133_CA, LYS141_CA to VAL202_CA, LYS185_CA to MET99_CA, LYS185_CA to THR180_CA, LYS185_CA to TYR106_CA, LYS209_CA to SER214_CA, LYS209_CA to THR218_CA, LYS209_CA to THR220_CA, LYS233_CA to LYS303_CA, LYS233_CA to PHE221_CA, LYS233_CA to TRP228_CA, LYS233_CA to TRP318_CA, LYS233_CA to TYR148_CA, LYS233_CA to VAL300_CA, LYS303_CA to TRP318_CA, LYS344_CA to PHE338_CA, LYS344_CA to TYR336_CA, LYS98_CA to VAL92_CA, MET130_CA to PHE135_CA, MET130_CA to SER125_CA, MET130_CA to SER214_CA, MET151_CA to PHE156_CA, MET151_CA to PHE241_CA, MET151_CA to PHE289_CA, MET151_CA to SER195_CA, MET151_CA to TRP293_CA, MET151_CA to VAL236_CA, MET161_CA to MET281_CA, MET161_CA to PHE156_CA, MET161_CA to THR103_CA, MET161_CA to TYR106_CA, MET161_CA to TYR166_CA, MET161_CA to TYR252_CA, MET161_CA to TYR336_CA, MET161_CA to VAL282_CA, MET161_CA to VAL285_CA, MET161_CA to VAL286_CA, MET203_CA to SER145_CA, MET203_CA to TYR149_CA, MET203_CA to VAL143_CA, MET205_CA to PHE221_CA, MET205_CA to SER222_CA, MET205_CA to THR218_CA, MET205_CA to THR220_CA, MET243_CA to PHE156_CA, MET243_CA to PHE237_CA, MET255_CA to SER162_CA, MET255_CA to THR249_CA, MET255_CA to THR279_CA, MET255_CA to TYR166_CA, MET255_CA to VAL163_CA, MET255_CA to VAL169_CA, MET255_CA to VAL250_CA, MET255_CA to VAL282_CA, MET281_CA to PHE343_CA, MET281_CA to THR103_CA, MET281_CA to TYR252_CA, MET281_CA to TYR336_CA, MET281_CA to VAL286_CA, MET281_CA to VAL334_CA, MET65_CA to THR70_CA, MET72_CA to SER125_CA, MET72_CA to THR67_CA, MET72_CA to TYR128_CA, MET72_CA to VAL126_CA, MET72_CA to VAL66_CA, MET90_CA to PHE108_CA, MET90_CA to PHE343_CA, MET99_CA to PHE108_CA, MET99_CA to PHE343_CA, MET99_CA to PRO181_CA, MET99_CA to TYR106_CA, MET99_CA to VAL89_CA, MET99_CA to VAL92_CA, MET99_CA to VAL94_CA, PHE108_CA to THR103_CA, PHE108_CA to THR157_CA, PHE108_CA to TYR336_CA, PHE108_CA to TYR91_CA, PHE108_CA to VAL89_CA, PHE108_CA to VAL94_CA, PHE123_CA to PHE135_CA, PHE123_CA to PRO134_CA, PHE123_CA to THR132_CA, PHE123_CA to TRP133_CA, PHE123_CA to TYR128_CA, PHE123_CA to VAL143_CA, PHE135_CA to PRO122_CA, PHE135_CA to THR208_CA, PHE135_CA to VAL126_CA, PHE135_CA to VAL143_CA, PHE152_CA to PHE237_CA, PHE152_CA to PHE239_CA, PHE152_CA to PHE241_CA, PHE152_CA to SER195_CA, PHE152_CA to SER196_CA, PHE152_CA to THR157_CA, PHE152_CA to TRP293_CA, PHE152_CA to VAL236_CA, PHE156_CA to PHE239_CA, PHE156_CA to PHE241_CA, PHE156_CA to PRO244_CA, PHE156_CA to SER195_CA, PHE156_CA to SER196_CA, PHE156_CA to TRP192_CA, PHE156_CA to VAL187_CA, PHE178_CA to THR160_CA, PHE178_CA to TYR106_CA, PHE178_CA to VAL163_CA, PHE178_CA to VAL173_CA, PHE178_CA to VAL187_CA, PHE204_CA to THR220_CA, PHE221_CA to TRP226_CA, PHE221_CA to TRP228_CA, PHE237_CA to PRO244_CA, PHE237_CA to THR294_CA, PHE239_CA to PRO244_CA, PHE241_CA to PHE289_CA, PHE241_CA to PRO295_CA, PHE241_CA to THR294_CA, PHE241_CA to TRP293_CA, PHE241_CA to VAL236_CA, PHE289_CA to PRO244_CA, PHE289_CA to PRO295_CA, PHE289_CA to SER154_CA, PHE289_CA to THR294_CA, PHE289_CA to TYR336_CA, PHE289_CA to VAL245_CA, PHE289_CA to VAL284_CA, PHE313_CA to TRP318_CA, PHE313_CA to TYR299_CA, PHE320_CA to PRO295_CA, PHE320_CA to THR315_CA, PHE320_CA to THR327_CA, PHE320_CA to TYR75_CA, PHE338_CA to PHE343_CA, PHE338_CA to PHE84_CA, PHE338_CA to PRO333_CA, PHE338_CA to VAL89_CA, PHE338_CA to VAL92_CA, PHE343_CA to PRO333_CA, PHE343_CA to THR97_CA, PHE343_CA to TYR336_CA, PHE343_CA to VAL89_CA, PHE343_CA to VAL92_CA, PHE347_CA to PHE84_CA, PHE347_CA to TYR96_CA, PHE347_CA to VAL92_CA, PHE84_CA to PRO333_CA, PHE84_CA to THR118_CA, PHE84_CA to VAL89_CA, PHE87_CA to PRO333_CA, PHE87_CA to SER119_CA, PHE87_CA to THR118_CA, PHE87_CA to VAL92_CA, PRO122_CA to TYR75_CA, PRO134_CA to VAL126_CA, PRO172_CA to TYR166_CA, PRO181_CA to THR101_CA, PRO181_CA to THR103_CA, PRO201_CA to SER195_CA, PRO201_CA to SER196_CA, PRO201_CA to TYR149_CA, PRO244_CA to THR249_CA, PRO295_CA to VAL300_CA, PRO309_CA to THR315_CA, PRO333_CA to THR327_CA, PRO333_CA to VAL81_CA, PRO333_CA to VAL89_CA, SER119_CA to TYR326_CA, SER119_CA to VAL143_CA, SER125_CA to SER76_CA, SER125_CA to THR120_CA, SER125_CA to TYR75_CA, SER145_CA to VAL202_CA, SER154_CA to SER195_CA, SER154_CA to SER329_CA, SER154_CA to TRP293_CA, SER154_CA to TYR149_CA, SER162_CA to THR157_CA, SER162_CA to THR249_CA, SER162_CA to TYR106_CA, SER162_CA to TYR252_CA, SER162_CA to TYR336_CA, SER162_CA to VAL250_CA, SER162_CA to VAL282_CA, SER162_CA to VAL286_CA, SER195_CA to THR153_CA, SER195_CA to TYR148_CA, SER195_CA to TYR149_CA, SER196_CA to THR153_CA, SER196_CA to TYR149_CA, SER196_CA to VAL189_CA, SER196_CA to VAL202_CA, SER214_CA to THR132_CA, SER214_CA to TRP133_CA, SER222_CA to TRP228_CA, SER222_CA to TYR227_CA, SER317_CA to THR312_CA, SER317_CA to TYR299_CA, SER329_CA to THR118_CA, SER329_CA to TRP293_CA, SER329_CA to VAL78_CA, SER329_CA to VAL81_CA, SER76_CA to THR70_CA, SER76_CA to VAL81_CA, THR101_CA to THR180_CA, THR101_CA to TYR106_CA, THR103_CA to THR180_CA, THR103_CA to TYR336_CA, THR103_CA to VAL282_CA, THR118_CA to THR327_CA, THR118_CA to TYR326_CA, THR118_CA to TYR75_CA, THR118_CA to VAL78_CA, THR118_CA to VAL80_CA, THR118_CA to VAL81_CA, THR120_CA to TRP133_CA, THR120_CA to TYR326_CA, THR120_CA to VAL143_CA, THR132_CA to VAL126_CA, THR153_CA to TRP192_CA, THR153_CA to TYR148_CA, THR157_CA to TRP192_CA, THR157_CA to TYR106_CA, THR160_CA to TYR106_CA, THR160_CA to VAL187_CA, THR180_CA to TYR106_CA, THR207_CA to THR218_CA, THR207_CA to THR220_CA, THR207_CA to VAL202_CA, THR208_CA to THR218_CA, THR208_CA to THR220_CA, THR208_CA to TRP133_CA, THR218_CA to VAL202_CA, THR220_CA to THR225_CA, THR249_CA to VAL282_CA, THR249_CA to VAL286_CA, THR279_CA to TYR252_CA, THR279_CA to VAL169_CA, THR279_CA to VAL284_CA, THR294_CA to TYR299_CA, THR294_CA to VAL245_CA, THR311_CA to VAL316_CA, THR312_CA to THR67_CA, THR312_CA to TRP318_CA, THR315_CA to THR67_CA, THR315_CA to TYR128_CA, THR315_CA to TYR299_CA, THR327_CA to TYR75_CA, THR327_CA to VAL288_CA, THR327_CA to VAL78_CA, THR67_CA to TYR128_CA, THR67_CA to VAL316_CA, THR70_CA to TYR75_CA, THR70_CA to VAL316_CA, THR97_CA to TYR91_CA, THR97_CA to VAL89_CA, THR97_CA to VAL92_CA, TRP133_CA to VAL126_CA, TRP133_CA to VAL143_CA, TRP192_CA to TYR149_CA, TRP192_CA to VAL187_CA, TRP293_CA to TYR326_CA, TRP293_CA to VAL288_CA, TRP318_CA to TYR128_CA, TRP318_CA to TYR299_CA, TRP318_CA to TYR75_CA, TRP318_CA to VAL300_CA, TYR106_CA to TYR336_CA, TYR106_CA to VAL187_CA, TYR128_CA to TYR326_CA, TYR128_CA to TYR75_CA, TYR148_CA to VAL143_CA, TYR148_CA to VAL202_CA, TYR148_CA to VAL236_CA, TYR149_CA to VAL202_CA, TYR166_CA to TYR252_CA, TYR166_CA to VAL250_CA, TYR252_CA to TYR336_CA, TYR252_CA to VAL163_CA, TYR252_CA to VAL282_CA, TYR252_CA to VAL284_CA, TYR252_CA to VAL285_CA, TYR252_CA to VAL286_CA, TYR299_CA to VAL316_CA, TYR326_CA to TYR75_CA, TYR326_CA to VAL143_CA, TYR326_CA to VAL78_CA, TYR336_CA to VAL285_CA, TYR336_CA to VAL286_CA, TYR336_CA to VAL89_CA, TYR75_CA to VAL80_CA, TYR91_CA to TYR96_CA, VAL236_CA to VAL300_CA, VAL245_CA to VAL250_CA, VAL245_CA to VAL286_CA, VAL286_CA to VAL291_CA, VAL334_CA to VAL81_CA, VAL334_CA to VAL89_CA, VAL89_CA to VAL94_CA]\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R1.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R1.h5 has shape: \n",
      "(135, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R10.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R10.h5 has shape: \n",
      "(471, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R11.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R11.h5 has shape: \n",
      "(496, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R12.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R12.h5 has shape: \n",
      "(486, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R13.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R13.h5 has shape: \n",
      "(510, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R14.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R14.h5 has shape: \n",
      "(464, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R15.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R15.h5 has shape: \n",
      "(479, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R16.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R16.h5 has shape: \n",
      "(500, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R17.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R17.h5 has shape: \n",
      "(497, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R18.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R18.h5 has shape: \n",
      "(504, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R19.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R19.h5 has shape: \n",
      "(454, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R2.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R2.h5 has shape: \n",
      "(134, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R20.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R20.h5 has shape: \n",
      "(525, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R21.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R21.h5 has shape: \n",
      "(554, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R22.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R22.h5 has shape: \n",
      "(493, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R23.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R23.h5 has shape: \n",
      "(539, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R24.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R24.h5 has shape: \n",
      "(452, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R25.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R25.h5 has shape: \n",
      "(239, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R26.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R26.h5 has shape: \n",
      "(240, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R27.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R27.h5 has shape: \n",
      "(226, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R28.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R28.h5 has shape: \n",
      "(232, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R29.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R29.h5 has shape: \n",
      "(194, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R3.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R3.h5 has shape: \n",
      "(121, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R30.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R30.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R31.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R31.h5 has shape: \n",
      "(220, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R32.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R32.h5 has shape: \n",
      "(203, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R33.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R33.h5 has shape: \n",
      "(229, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R34.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R34.h5 has shape: \n",
      "(183, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R35.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R35.h5 has shape: \n",
      "(234, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R36.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R36.h5 has shape: \n",
      "(227, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R37.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R37.h5 has shape: \n",
      "(226, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R38.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R38.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R39.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R39.h5 has shape: \n",
      "(232, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R4.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R4.h5 has shape: \n",
      "(96, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R40.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R40.h5 has shape: \n",
      "(224, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R41.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R41.h5 has shape: \n",
      "(232, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R42.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R42.h5 has shape: \n",
      "(238, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R43.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R43.h5 has shape: \n",
      "(241, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R44.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R44.h5 has shape: \n",
      "(233, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R45.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R45.h5 has shape: \n",
      "(234, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R46.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R46.h5 has shape: \n",
      "(230, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R47.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R47.h5 has shape: \n",
      "(225, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R48.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R48.h5 has shape: \n",
      "(236, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R49.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R49.h5 has shape: \n",
      "(230, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R5.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R5.h5 has shape: \n",
      "(73, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R50.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R50.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R51.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R51.h5 has shape: \n",
      "(215, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R52.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R52.h5 has shape: \n",
      "(243, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R53.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R53.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R54.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R54.h5 has shape: \n",
      "(237, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R55.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R55.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R56.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R56.h5 has shape: \n",
      "(230, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R57.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R57.h5 has shape: \n",
      "(235, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R58.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R58.h5 has shape: \n",
      "(238, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R59.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R59.h5 has shape: \n",
      "(245, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R6.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R6.h5 has shape: \n",
      "(78, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R60.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R60.h5 has shape: \n",
      "(243, 2408)\n",
      "Featurizing /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R7.h5\n",
      "looking at 1204 pairs for trajectory\n",
      "looking at 1204 pairs for trajectory\n",
      "new features /home/enf/md_simulations/MOR/h8_reimaged/trajectories/f338a_RUN_R7.h5 has shape: \n",
      "(68, 2408)\n",
      "Completed featurizing\n"
     ]
    }
   ],
   "source": [
    "import custom_featurizer\n",
    "reload(custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "featurize_contacts_custom(traj_dir, features_dir = features_dir, traj_ext = traj_ext, contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes, binarize=None, redo=False, within_turn=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "fit_normalizer(features_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pickle\n",
    "with open(feature_residues_pkl, \"rb\") as f:\n",
    "    feature_residues = pickle.load(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(ALA240 to TRP293, 104),\n",
       " (ASN150 to TRP293, 259),\n",
       " (ASN328 to TRP293, 304),\n",
       " (ASN332 to TRP293, 320),\n",
       " (ASP147 to TRP293, 366),\n",
       " (CYS321 to TRP293, 457),\n",
       " (GLY325 to TRP293, 534),\n",
       " (ILE155 to TRP293, 628),\n",
       " (ILE298 to TRP293, 713),\n",
       " (ILE322 to TRP293, 727),\n",
       " (LEU158 to TRP293, 794),\n",
       " (LEU324 to TRP293, 855),\n",
       " (MET151 to TRP293, 928),\n",
       " (PHE152 to TRP293, 1000),\n",
       " (PHE241 to TRP293, 1023),\n",
       " (SER154 to TRP293, 1080),\n",
       " (SER329 to TRP293, 1104),\n",
       " (TRP293 to TYR326, 1166),\n",
       " (TRP293 to VAL288, 1167),\n",
       " (ALA240_CA to TRP293_CA, 1308),\n",
       " (ASN150_CA to TRP293_CA, 1463),\n",
       " (ASN328_CA to TRP293_CA, 1508),\n",
       " (ASN332_CA to TRP293_CA, 1524),\n",
       " (ASP147_CA to TRP293_CA, 1570),\n",
       " (CYS321_CA to TRP293_CA, 1661),\n",
       " (GLY325_CA to TRP293_CA, 1738),\n",
       " (ILE155_CA to TRP293_CA, 1832),\n",
       " (ILE298_CA to TRP293_CA, 1917),\n",
       " (ILE322_CA to TRP293_CA, 1931),\n",
       " (LEU158_CA to TRP293_CA, 1998),\n",
       " (LEU324_CA to TRP293_CA, 2059),\n",
       " (MET151_CA to TRP293_CA, 2132),\n",
       " (PHE152_CA to TRP293_CA, 2204),\n",
       " (PHE241_CA to TRP293_CA, 2227),\n",
       " (SER154_CA to TRP293_CA, 2284),\n",
       " (SER329_CA to TRP293_CA, 2308),\n",
       " (TRP293_CA to TYR326_CA, 2370),\n",
       " (TRP293_CA to VAL288_CA, 2371)]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[(feature_residues[i], i) for i in range(0,len(feature_residues)) if \"TRP293\" in str(feature_residues[i])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import custom_tica\n",
    "reload(custom_tica)\n",
    "from custom_tica import *\n",
    "fit_and_transform(features_directory = features_dir, model_dir = tica_dir, stride=5, lag_time = lag_time, n_components = n_components, sparse = sparse, wolf = wolf, rho = rho, shrinkage = shrinkage, parallel=True, traj_ext = traj_ext, normalize=True, partial_fit=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 123,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "already featurized\n",
      "already featurized\n",
      "structure\n",
      "/home/enf/md_simulations/MOR/4dkl_R_for_conformation.pdb\n",
      "structure\n",
      "None\n",
      "mdraj_index_combinations[0:10]\n",
      "[(41, 73), (41, 114), (41, 108), (41, 248), (41, 166), (41, 84), (41, 13), (41, 76), (41, 74), (41, 18)]\n",
      "contact_features[0:10]\n",
      "[[TYR106, ILE138], [TYR106, ARG179], [TYR106, VAL173], [TYR106, HIS319], [TYR106, LEU231], [TYR106, TYR149], [TYR106, VAL78], [TYR106, LYS141], [TYR106, LEU139], [TYR106, LEU83]]\n",
      "About to compute 35255 features\n",
      "(1, 35255)\n",
      "cutoff\n",
      "0.66\n",
      "distances[0:10]\n",
      "[[ 2.53460574  0.61586297  1.52706683 ...,  1.51371932  3.94720888\n",
      "   2.2300899 ]]\n",
      "There are 955 residue-residue contacts below cutoff in structure.\n",
      "structure\n",
      "/home/enf/md_simulations/MOR/5c1m.pdb\n",
      "structure\n",
      "None\n",
      "mdraj_index_combinations[0:10]\n",
      "[(54, 86), (54, 127), (54, 121), (54, 267), (54, 179), (54, 97), (54, 26), (54, 89), (54, 87), (54, 31)]\n",
      "contact_features[0:10]\n",
      "[[TYR106, ILE138], [TYR106, ARG179], [TYR106, VAL173], [TYR106, HIS319], [TYR106, LEU231], [TYR106, TYR149], [TYR106, VAL78], [TYR106, LYS141], [TYR106, LEU139], [TYR106, LEU83]]\n",
      "About to compute 35255 features\n",
      "(1, 35255)\n",
      "cutoff\n",
      "0.66\n",
      "distances[0:10]\n",
      "[[ 2.67791724  0.63610411  1.40252936 ...,  1.48673296  3.71989655\n",
      "   2.46465921]]\n",
      "There are 1010 residue-residue contacts below cutoff in structure.\n",
      "dihedral_residues:\n",
      "[]\n",
      "looking at 1204 pairs for trajectory\n",
      "There are 2408 features to be used in featurization.\n",
      "Saving contact feature residue pairs to disk.\n",
      "About to featurize trajectories based on the chosen featurization scheme.\n",
      "[ALA102 to ALA184, ALA102 to ARG165, ALA102 to ARG179, ALA102 to ARG182, ALA102 to ASN183, ALA102 to ASN188, ALA102 to ASP164, ALA102 to ILE107, ALA102 to LYS185, ALA102 to MET161, ALA102 to PHE178, ALA102 to PRO181, ALA102 to THR180, ALA111 to ASN332, ALA111 to ASN86, ALA111 to GLY82, ALA111 to GLY85, ALA111 to ILE93, ALA111 to LEU116, ALA111 to MET90, ALA111 to PHE87, ALA111 to PRO333, ALA111 to THR118, ALA111 to THR157, ALA111 to TYR106, ALA111 to TYR336, ALA111 to VAL89, ALA113 to ASN150, ALA113 to ASN86, ALA113 to ILE146, ALA113 to ILE155, ALA113 to MET151, ALA113 to MET90, ALA113 to PHE108, ALA113 to PHE152, ALA113 to SER154, ALA113 to SER329, ALA113 to THR118, ALA113 to THR153, ALA113 to THR157, ALA113 to TRP192, ALA113 to TYR149, ALA115 to ASN150, ALA115 to ASN86, ALA115 to GLY82, ALA115 to ILE146, ALA115 to LEU110, ALA115 to LEU83, ALA115 to MET90, ALA115 to PHE87, ALA115 to SER329, ALA115 to THR120, ALA117 to ASN150, ALA117 to ASP147, ALA117 to GLN124, ALA117 to ILE146, ALA117 to LEU112, ALA117 to LEU83, ALA117 to MET151, ALA117 to PRO122, ALA117 to SER154, ALA117 to SER329, ALA117 to TYR326, ALA168 to ALA175, ALA168 to ARG179, ALA168 to LEU275, ALA168 to PHE178, ALA168 to VAL163, ALA168 to VAL173, ALA175 to ASP164, ALA175 to ILE167, ALA175 to THR180, ALA175 to VAL169, ALA184 to ARG179, ALA184 to ASP164, ALA184 to ILE105, ALA184 to PHE178, ALA184 to THR101, ALA184 to THR103, ALA184 to THR160, ALA184 to TYR106, ALA184 to VAL189, ALA197 to TRP192, ALA197 to TYR149, ALA197 to VAL202, ALA206 to ASN137, ALA206 to CYS140, ALA206 to CYS217, ALA206 to ILE142, ALA206 to ILE144, ALA206 to LEU219, ALA206 to LYS141, ALA206 to PRO201, ALA206 to SER145, ALA206 to THR218, ALA206 to THR220, ALA240 to CYS235, ALA240 to HIS297, ALA240 to ILE155, ALA240 to ILE234, ALA240 to MET151, ALA240 to PHE152, ALA240 to PHE156, ALA240 to PHE289, ALA240 to TRP293, ALA240 to VAL245, ALA287 to CYS292, ALA287 to ILE248, ALA287 to TYR252, ALA287 to VAL282, ALA304 to ASN230, ALA304 to GLU229, ALA304 to LYS233, ALA304 to TYR299, ALA323 to ASN328, ALA323 to CYS292, ALA323 to ILE296, ALA323 to ILE71, ALA323 to LEU121, ALA323 to LEU74, ALA323 to TRP318, ALA323 to TYR75, ALA323 to VAL78, ALA337 to ARG345, ALA337 to ASN332, ALA337 to ASN342, ALA337 to ILE107, ALA337 to ILE93, ALA337 to LEU110, ALA337 to LEU331, ALA337 to LYS344, ALA337 to MET161, ALA337 to MET281, ALA337 to PHE343, ALA337 to PHE347, ALA337 to VAL89, ALA68 to ALA73, ALA68 to LEU129, ALA68 to LEU74, ALA68 to SER125, ALA68 to TYR128, ALA68 to VAL316, ALA73 to VAL78, ARG165 to ARG179, ARG165 to ARG276, ARG165 to ARG280, ARG165 to ASN274, ARG165 to ASP340, ARG165 to CYS170, ARG165 to CYS251, ARG165 to ILE278, ARG165 to LEU158, ARG165 to LEU275, ARG165 to LEU283, ARG165 to LEU335, ARG165 to LEU339, ARG165 to MET255, ARG165 to MET281, ARG165 to PHE178, ARG165 to THR103, ARG165 to THR160, ARG165 to THR279, ARG165 to TYR106, ARG165 to TYR252, ARG165 to TYR336, ARG165 to VAL282, ARG165 to VAL285, ARG179 to ASP164, ARG179 to HIS171, ARG179 to ILE167, ARG179 to ILE278, ARG179 to LYS174, ARG179 to MET161, ARG179 to THR101, ARG179 to THR103, ARG179 to TYR106, ARG179 to VAL169, ARG182 to ILE105, ARG182 to VAL187, ARG211 to ASP216, ARG211 to THR132, ARG258 to CYS170, ARG258 to GLY253, ARG258 to HIS171, ARG258 to PRO172, ARG258 to TYR166, ARG258 to VAL169, ARG273 to ARG280, ARG273 to ILE278, ARG276 to LYS185, ARG276 to MET281, ARG276 to VAL169, ARG277 to ASP340, ARG277 to GLU341, ARG277 to LEU339, ARG277 to LYS344, ARG277 to VAL282, ARG280 to GLU341, ARG280 to ILE256, ARG280 to LEU275, ARG280 to LEU339, ARG280 to PHE338, ARG280 to VAL285, ARG345 to ASP340, ARG345 to LYS98, ARG345 to PHE338, ARG95 to LYS100, ARG95 to MET90, ASN104 to ASN109, ASN104 to ASN342, ASN104 to ASP340, ASN104 to ILE93, ASN104 to LYS98, ASN104 to MET281, ASN104 to MET99, ASN104 to PHE343, ASN104 to THR97, ASN104 to VAL89, ASN109 to ASN150, ASN109 to ASN188, ASN109 to ASN191, ASN109 to ASP114, ASN109 to ILE93, ASN109 to MET90, ASN109 to MET99, ASN109 to PHE156, ASN109 to SER154, ASN109 to THR153, ASN109 to THR157, ASN109 to THR160, ASN109 to TRP192, ASN109 to VAL187, ASN109 to VAL189, ASN127 to ASP216, ASN127 to CYS217, ASN127 to HIS319, ASN127 to ILE215, ASN127 to PHE135, ASN127 to PRO122, ASN127 to PRO134, ASN127 to THR132, ASN127 to TRP133, ASN137 to CYS217, ASN137 to ILE142, ASN137 to LYS209, ASN137 to THR207, ASN137 to THR208, ASN150 to ASP114, ASN150 to GLY325, ASN150 to ILE155, ASN150 to LEU110, ASN150 to LEU112, ASN150 to LEU116, ASN150 to PHE289, ASN150 to SER145, ASN150 to SER195, ASN150 to SER329, ASN150 to THR120, ASN150 to TRP192, ASN150 to TRP293, ASN150 to TYR326, ASN183 to ASN188, ASN183 to ASP177, ASN183 to ILE105, ASN183 to LEU176, ASN183 to PHE178, ASN183 to TYR106, ASN188 to ILE105, ASN188 to ILE107, ASN188 to ILE193, ASN188 to LEU110, ASN188 to PHE108, ASN188 to THR153, ASN188 to THR157, ASN188 to THR160, ASN188 to TYR106, ASN191 to ILE155, ASN191 to ILE186, ASN191 to LEU158, ASN191 to PHE152, ASN191 to PHE156, ASN191 to SER154, ASN191 to SER196, ASN191 to THR153, ASN191 to THR157, ASN191 to THR160, ASN191 to TYR106, ASN191 to TYR149, ASN230 to CYS235, ASN230 to LEU305, ASN230 to PHE221, ASN230 to THR225, ASN274 to GLU341, ASN274 to THR279, ASN328 to ASP114, ASN328 to CYS292, ASN328 to ILE155, ASN328 to ILE290, ASN328 to LEU110, ASN328 to LEU158, ASN328 to LEU335, ASN328 to PHE289, ASN328 to PRO333, ASN328 to SER154, ASN328 to TRP293, ASN328 to TYR336, ASN328 to VAL285, ASN328 to VAL288, ASN328 to VAL291, ASN328 to VAL78, ASN332 to ASN86, ASN332 to ASP114, ASN332 to ILE107, ASN332 to ILE155, ASN332 to LEU110, ASN332 to LEU158, ASN332 to PHE289, ASN332 to PHE338, ASN332 to SER154, ASN332 to THR327, ASN332 to TRP293, ASN332 to VAL285, ASN332 to VAL288, ASN332 to VAL89, ASN342 to LYS98, ASN342 to MET99, ASN342 to PHE347, ASN342 to THR101, ASN342 to THR103, ASN342 to THR97, ASN342 to TYR336, ASN342 to VAL92, ASN86 to ASP114, ASN86 to CYS330, ASN86 to ILE107, ASN86 to LEU110, ASN86 to LEU112, ASN86 to LEU116, ASN86 to LEU331, ASN86 to PHE338, ASN86 to PRO333, ASN86 to SER329, ASN86 to THR118, ASN86 to TYR336, ASN86 to TYR91, ASN86 to VAL81, ASP114 to CYS330, ASP114 to GLY82, ASP114 to ILE155, ASP114 to LEU158, ASP114 to LEU331, ASP114 to LEU83, ASP114 to PRO333, ASP114 to SER119, ASP114 to SER154, ASP114 to SER329, ASP114 to THR153, ASP114 to TYR326, ASP114 to TYR336, ASP147 to GLN124, ASP147 to ILE142, ASP147 to LEU116, ASP147 to LEU121, ASP147 to PHE152, ASP147 to THR118, ASP147 to THR120, ASP147 to TRP293, ASP147 to TYR326, ASP164 to CYS159, ASP164 to CYS251, ASP164 to PHE178, ASP164 to THR103, ASP164 to THR180, ASP164 to TYR106, ASP164 to VAL169, ASP177 to PRO172, ASP216 to CYS140, ASP216 to GLY131, ASP216 to LYS209, ASP216 to THR132, ASP216 to THR207, ASP216 to THR208, ASP216 to TRP133, ASP216 to TYR210, ASP340 to ILE107, ASP340 to ILE278, ASP340 to LEU335, ASP340 to MET161, ASP340 to MET281, ASP340 to MET99, ASP340 to PRO333, ASP340 to THR103, ASP340 to VAL334, CYS140 to CYS217, CYS140 to ILE146, CYS140 to LEU219, CYS140 to PHE135, CYS140 to SER145, CYS140 to THR207, CYS140 to THR208, CYS140 to THR218, CYS140 to TRP133, CYS140 to VAL202, CYS159 to CYS251, CYS159 to ILE247, CYS159 to ILE248, CYS159 to MET243, CYS159 to PHE239, CYS159 to PHE289, CYS159 to PRO244, CYS159 to SER154, CYS159 to TYR252, CYS159 to TYR336, CYS159 to VAL245, CYS159 to VAL286, CYS170 to CYS251, CYS170 to ILE256, CYS170 to LEU254, CYS170 to LEU257, CYS170 to LEU259, CYS170 to LEU275, CYS170 to MET255, CYS190 to LYS185, CYS190 to PHE156, CYS190 to SER195, CYS190 to SER196, CYS217 to GLY136, CYS217 to ILE144, CYS217 to LEU139, CYS217 to LYS141, CYS217 to LYS209, CYS217 to THR132, CYS217 to THR207, CYS217 to THR208, CYS217 to TRP133, CYS217 to VAL143, CYS235 to ILE198, CYS235 to PHE152, CYS235 to PHE241, CYS251 to ILE256, CYS251 to LEU246, CYS251 to SER162, CYS251 to TYR166, CYS251 to VAL163, CYS292 to CYS321, CYS292 to GLY325, CYS292 to HIS297, CYS292 to ILE322, CYS292 to LEU324, CYS292 to LEU331, CYS292 to SER329, CYS292 to THR327, CYS292 to TYR326, CYS321 to HIS297, CYS321 to ILE296, CYS321 to LEU74, CYS321 to PRO295, CYS321 to TRP293, CYS321 to TYR299, CYS321 to TYR326, CYS321 to VAL316, CYS330 to CYS79, CYS330 to GLY325, CYS330 to GLY82, CYS330 to GLY85, CYS330 to ILE77, CYS330 to LEU121, CYS330 to LEU335, CYS330 to LEU83, CYS330 to THR118, CYS330 to VAL78, CYS330 to VAL80, CYS330 to VAL81, CYS346 to GLU341, CYS346 to LEU88, CYS346 to LYS98, CYS346 to MET99, CYS346 to PHE338, CYS346 to THR97, CYS346 to TYR96, CYS346 to VAL92, CYS79 to LEU121, CYS79 to LEU74, CYS79 to PHE84, CYS79 to PRO122, CYS79 to SER119, CYS79 to THR118, CYS79 to THR120, CYS79 to TYR326, GLN124 to HIS319, GLN124 to ILE322, GLN124 to LEU129, GLN124 to PHE135, GLN124 to TRP133, GLN124 to TYR326, GLN124 to TYR75, GLN124 to VAL143, GLN314 to HIS319, GLN314 to ILE308, GLN314 to LYS303, GLN314 to PRO309, GLN314 to THR307, GLN314 to TYR299, GLU229 to ILE234, GLU229 to LEU219, GLU229 to PHE221, GLU229 to PRO224, GLU229 to SER222, GLU229 to THR218, GLU310 to THR315, GLU341 to TYR336, GLY131 to GLY213, GLY131 to ILE215, GLY131 to SER125, GLY131 to SER214, GLY131 to VAL126, GLY136 to LYS141, GLY136 to THR207, GLY136 to THR208, GLY199 to ILE144, GLY199 to ILE146, GLY199 to LEU194, GLY199 to LYS141, GLY199 to PHE152, GLY199 to PHE204, GLY199 to SER145, GLY199 to TYR148, GLY199 to TYR149, GLY213 to THR132, GLY253 to ILE247, GLY253 to ILE248, GLY253 to VAL282, GLY325 to ILE296, GLY325 to PHE320, GLY325 to TRP293, GLY325 to VAL291, GLY325 to VAL78, GLY82 to ILE77, GLY82 to LEU331, GLY82 to LEU88, GLY82 to PHE87, GLY82 to PRO333, GLY82 to SER329, GLY82 to SER76, GLY82 to THR118, GLY82 to TYR326, GLY85 to MET90, GLY85 to PHE338, GLY85 to PRO333, GLY85 to SER329, GLY85 to TYR336, GLY85 to VAL334, GLY85 to VAL80, HIS171 to LEU176, HIS171 to PHE178, HIS171 to TYR166, HIS223 to TRP228, HIS297 to ILE155, HIS297 to ILE238, HIS297 to ILE302, HIS297 to LYS233, HIS297 to MET151, HIS297 to PHE237, HIS297 to PHE241, HIS297 to PHE289, HIS297 to VAL236, HIS319 to ILE71, HIS319 to LEU324, HIS319 to LEU74, HIS319 to THR67, HIS319 to TYR128, HIS319 to TYR299, HIS319 to TYR75, ILE105 to ILE186, ILE105 to ILE93, ILE105 to LEU110, ILE105 to LYS100, ILE105 to LYS185, ILE105 to MET99, ILE105 to PRO181, ILE105 to THR157, ILE105 to THR180, ILE107 to ILE93, ILE107 to LEU112, ILE107 to MET161, ILE107 to MET281, ILE107 to MET90, ILE107 to PHE338, ILE107 to PHE343, ILE107 to THR157, ILE107 to TYR336, ILE107 to VAL282, ILE107 to VAL89, ILE138 to MET203, ILE138 to THR208, ILE138 to TRP133, ILE138 to VAL143, ILE142 to MET203, ILE142 to THR120, ILE142 to TYR149, ILE144 to LEU139, ILE144 to LEU219, ILE144 to MET203, ILE144 to THR120, ILE144 to THR207, ILE144 to THR218, ILE144 to TRP133, ILE144 to TYR149, ILE144 to VAL202, ILE146 to LEU116, ILE146 to LYS141, ILE146 to MET151, ILE146 to MET203, ILE146 to SER119, ILE146 to THR118, ILE146 to THR120, ILE146 to THR153, ILE146 to VAL202, ILE155 to ILE242, ILE155 to ILE248, ILE155 to ILE290, ILE155 to LEU110, ILE155 to MET243, ILE155 to PHE239, ILE155 to PHE241, ILE155 to PHE289, ILE155 to PRO244, ILE155 to THR160, ILE155 to TRP293, ILE155 to VAL245, ILE167 to LEU176, ILE167 to LYS174, ILE167 to MET255, ILE167 to PHE178, ILE167 to PRO172, ILE167 to SER162, ILE167 to VAL173, ILE186 to PRO181, ILE193 to ILE198, ILE193 to THR153, ILE193 to TYR149, ILE198 to LEU232, ILE198 to MET151, ILE198 to MET203, ILE198 to MET205, ILE198 to PHE152, ILE198 to PHE239, ILE198 to SER145, ILE198 to TYR148, ILE198 to TYR149, ILE198 to VAL236, ILE215 to LYS209, ILE215 to PRO134, ILE215 to THR132, ILE215 to THR208, ILE215 to TRP133, ILE215 to TYR210, ILE234 to ILE242, ILE234 to ILE301, ILE234 to PHE239, ILE238 to LEU231, ILE238 to LYS233, ILE238 to MET243, ILE238 to PHE152, ILE238 to PRO244, ILE242 to ILE247, ILE242 to PHE237, ILE242 to PHE289, ILE242 to VAL236, ILE247 to LEU158, ILE247 to SER162, ILE247 to THR160, ILE247 to TYR252, ILE247 to VAL163, ILE248 to ILE290, ILE248 to LEU158, ILE248 to MET243, ILE248 to MET255, ILE248 to PHE289, ILE248 to SER162, ILE248 to THR160, ILE248 to TYR336, ILE248 to VAL163, ILE248 to VAL282, ILE248 to VAL285, ILE248 to VAL286, ILE256 to ILE278, ILE256 to LEU275, ILE256 to LEU283, ILE256 to THR279, ILE256 to VAL169, ILE256 to VAL282, ILE278 to LEU259, ILE278 to LEU283, ILE278 to LEU339, ILE278 to MET255, ILE278 to THR101, ILE278 to THR103, ILE290 to LEU158, ILE290 to PHE241, ILE290 to PRO295, ILE290 to THR249, ILE290 to VAL245, ILE290 to VAL285, ILE296 to ILE301, ILE296 to ILE322, ILE296 to LEU324, ILE296 to MET151, ILE296 to TRP318, ILE296 to VAL291, ILE298 to LYS303, ILE298 to PHE237, ILE298 to PHE241, ILE298 to TRP293, ILE301 to ILE306, ILE301 to LYS233, ILE301 to PHE237, ILE301 to VAL236, ILE302 to ILE308, ILE302 to THR307, ILE308 to LYS303, ILE308 to TRP318, ILE308 to TYR299, ILE322 to LEU121, ILE322 to PRO295, ILE322 to SER317, ILE322 to THR327, ILE322 to TRP293, ILE322 to TYR128, ILE322 to TYR75, ILE322 to VAL300, ILE322 to VAL78, ILE69 to LEU129, ILE69 to LEU74, ILE69 to TYR128, ILE71 to LEU129, ILE71 to PHE320, ILE71 to SER125, ILE71 to SER317, ILE71 to SER76, ILE71 to THR312, ILE71 to THR315, ILE71 to TYR128, ILE71 to VAL316, ILE71 to VAL66, ILE77 to LEU121, ILE77 to LEU83, ILE77 to MET72, ILE93 to LEU88, ILE93 to LYS100, ILE93 to LYS98, ILE93 to MET99, ILE93 to PHE108, ILE93 to PHE343, ILE93 to THR101, ILE93 to THR103, ILE93 to TYR106, LEU110 to LEU158, LEU110 to MET161, LEU110 to PHE289, LEU110 to PRO333, LEU110 to SER154, LEU110 to SER329, LEU110 to THR153, LEU110 to THR157, LEU110 to TYR336, LEU110 to VAL285, LEU112 to MET90, LEU112 to SER119, LEU112 to THR153, LEU112 to TRP192, LEU116 to LEU121, LEU116 to LEU83, LEU116 to MET90, LEU116 to PHE87, LEU116 to TRP192, LEU116 to TYR149, LEU116 to TYR326, LEU121 to LEU74, LEU121 to SER76, LEU121 to TYR128, LEU121 to TYR326, LEU121 to TYR75, LEU121 to VAL126, LEU121 to VAL143, LEU121 to VAL78, LEU121 to VAL80, LEU129 to MET65, LEU129 to MET72, LEU139 to PHE123, LEU139 to TRP133, LEU158 to PHE289, LEU158 to PRO244, LEU158 to THR153, LEU158 to TRP293, LEU158 to TYR252, LEU158 to TYR336, LEU158 to VAL163, LEU158 to VAL282, LEU158 to VAL285, LEU158 to VAL286, LEU194 to MET243, LEU194 to PHE152, LEU194 to PHE156, LEU194 to PHE239, LEU194 to TYR149, LEU194 to VAL189, LEU200 to MET205, LEU200 to SER145, LEU200 to SER195, LEU200 to TRP192, LEU200 to TYR149, LEU219 to LEU232, LEU219 to LYS209, LEU219 to MET203, LEU219 to MET205, LEU219 to PHE204, LEU219 to PRO201, LEU219 to THR207, LEU219 to THR225, LEU219 to TYR148, LEU219 to VAL202, LEU231 to THR225, LEU231 to TRP226, LEU231 to VAL236, LEU232 to MET205, LEU232 to PHE221, LEU232 to PHE237, LEU232 to TYR148, LEU232 to TYR227, LEU232 to VAL202, LEU246 to PHE241, LEU254 to LEU259, LEU254 to THR249, LEU254 to TYR166, LEU254 to VAL169, LEU257 to LEU275, LEU257 to TYR252, LEU259 to LEU275, LEU259 to VAL169, LEU275 to MET255, LEU275 to PRO172, LEU275 to VAL169, LEU283 to LEU339, LEU283 to MET161, LEU283 to MET255, LEU283 to SER162, LEU283 to TYR252, LEU283 to VAL288, LEU305 to VAL300, LEU324 to LEU331, LEU324 to LEU74, LEU324 to PRO295, LEU324 to SER329, LEU324 to THR294, LEU324 to TRP293, LEU324 to TYR75, LEU324 to VAL288, LEU324 to VAL291, LEU324 to VAL78, LEU331 to TYR326, LEU331 to TYR336, LEU331 to VAL288, LEU331 to VAL78, LEU331 to VAL81, LEU335 to MET161, LEU335 to MET281, LEU335 to PHE289, LEU335 to VAL284, LEU335 to VAL285, LEU335 to VAL286, LEU335 to VAL288, LEU339 to LYS344, LEU339 to MET281, LEU339 to PRO333, LEU339 to VAL282, LEU339 to VAL284, LEU339 to VAL285, LEU339 to VAL334, LEU74 to PHE320, LEU74 to THR327, LEU74 to VAL316, LEU83 to LEU88, LEU83 to MET90, LEU83 to PRO122, LEU83 to SER119, LEU83 to SER329, LEU83 to THR118, LEU83 to THR120, LEU83 to VAL78, LEU88 to PHE338, LEU88 to PHE343, LEU88 to PHE347, LYS100 to PRO181, LYS100 to THR180, LYS100 to VAL92, LYS100 to VAL94, LYS141 to MET203, LYS141 to MET205, LYS141 to PHE204, LYS141 to PRO201, LYS141 to THR207, LYS141 to THR208, LYS141 to TRP133, LYS141 to VAL202, LYS185 to MET99, LYS185 to THR180, LYS185 to TYR106, LYS209 to SER214, LYS209 to THR218, LYS209 to THR220, LYS233 to LYS303, LYS233 to PHE221, LYS233 to TRP228, LYS233 to TRP318, LYS233 to TYR148, LYS233 to VAL300, LYS303 to TRP318, LYS344 to PHE338, LYS344 to TYR336, LYS98 to VAL92, MET130 to PHE135, MET130 to SER125, MET130 to SER214, MET151 to PHE156, MET151 to PHE241, MET151 to PHE289, MET151 to SER195, MET151 to TRP293, MET151 to VAL236, MET161 to MET281, MET161 to PHE156, MET161 to THR103, MET161 to TYR106, MET161 to TYR166, MET161 to TYR252, MET161 to TYR336, MET161 to VAL282, MET161 to VAL285, MET161 to VAL286, MET203 to SER145, MET203 to TYR149, MET203 to VAL143, MET205 to PHE221, MET205 to SER222, MET205 to THR218, MET205 to THR220, MET243 to PHE156, MET243 to PHE237, MET255 to SER162, MET255 to THR249, MET255 to THR279, MET255 to TYR166, MET255 to VAL163, MET255 to VAL169, MET255 to VAL250, MET255 to VAL282, MET281 to PHE343, MET281 to THR103, MET281 to TYR252, MET281 to TYR336, MET281 to VAL286, MET281 to VAL334, MET65 to THR70, MET72 to SER125, MET72 to THR67, MET72 to TYR128, MET72 to VAL126, MET72 to VAL66, MET90 to PHE108, MET90 to PHE343, MET99 to PHE108, MET99 to PHE343, MET99 to PRO181, MET99 to TYR106, MET99 to VAL89, MET99 to VAL92, MET99 to VAL94, PHE108 to THR103, PHE108 to THR157, PHE108 to TYR336, PHE108 to TYR91, PHE108 to VAL89, PHE108 to VAL94, PHE123 to PHE135, PHE123 to PRO134, PHE123 to THR132, PHE123 to TRP133, PHE123 to TYR128, PHE123 to VAL143, PHE135 to PRO122, PHE135 to THR208, PHE135 to VAL126, PHE135 to VAL143, PHE152 to PHE237, PHE152 to PHE239, PHE152 to PHE241, PHE152 to SER195, PHE152 to SER196, PHE152 to THR157, PHE152 to TRP293, PHE152 to VAL236, PHE156 to PHE239, PHE156 to PHE241, PHE156 to PRO244, PHE156 to SER195, PHE156 to SER196, PHE156 to TRP192, PHE156 to VAL187, PHE178 to THR160, PHE178 to TYR106, PHE178 to VAL163, PHE178 to VAL173, PHE178 to VAL187, PHE204 to THR220, PHE221 to TRP226, PHE221 to TRP228, PHE237 to PRO244, PHE237 to THR294, PHE239 to PRO244, PHE241 to PHE289, PHE241 to PRO295, PHE241 to THR294, PHE241 to TRP293, PHE241 to VAL236, PHE289 to PRO244, PHE289 to PRO295, PHE289 to SER154, PHE289 to THR294, PHE289 to TYR336, PHE289 to VAL245, PHE289 to VAL284, PHE313 to TRP318, PHE313 to TYR299, PHE320 to PRO295, PHE320 to THR315, PHE320 to THR327, PHE320 to TYR75, PHE338 to PHE343, PHE338 to PHE84, PHE338 to PRO333, PHE338 to VAL89, PHE338 to VAL92, PHE343 to PRO333, PHE343 to THR97, PHE343 to TYR336, PHE343 to VAL89, PHE343 to VAL92, PHE347 to PHE84, PHE347 to TYR96, PHE347 to VAL92, PHE84 to PRO333, PHE84 to THR118, PHE84 to VAL89, PHE87 to PRO333, PHE87 to SER119, PHE87 to THR118, PHE87 to VAL92, PRO122 to TYR75, PRO134 to VAL126, PRO172 to TYR166, PRO181 to THR101, PRO181 to THR103, PRO201 to SER195, PRO201 to SER196, PRO201 to TYR149, PRO244 to THR249, PRO295 to VAL300, PRO309 to THR315, PRO333 to THR327, PRO333 to VAL81, PRO333 to VAL89, SER119 to TYR326, SER119 to VAL143, SER125 to SER76, SER125 to THR120, SER125 to TYR75, SER145 to VAL202, SER154 to SER195, SER154 to SER329, SER154 to TRP293, SER154 to TYR149, SER162 to THR157, SER162 to THR249, SER162 to TYR106, SER162 to TYR252, SER162 to TYR336, SER162 to VAL250, SER162 to VAL282, SER162 to VAL286, SER195 to THR153, SER195 to TYR148, SER195 to TYR149, SER196 to THR153, SER196 to TYR149, SER196 to VAL189, SER196 to VAL202, SER214 to THR132, SER214 to TRP133, SER222 to TRP228, SER222 to TYR227, SER317 to THR312, SER317 to TYR299, SER329 to THR118, SER329 to TRP293, SER329 to VAL78, SER329 to VAL81, SER76 to THR70, SER76 to VAL81, THR101 to THR180, THR101 to TYR106, THR103 to THR180, THR103 to TYR336, THR103 to VAL282, THR118 to THR327, THR118 to TYR326, THR118 to TYR75, THR118 to VAL78, THR118 to VAL80, THR118 to VAL81, THR120 to TRP133, THR120 to TYR326, THR120 to VAL143, THR132 to VAL126, THR153 to TRP192, THR153 to TYR148, THR157 to TRP192, THR157 to TYR106, THR160 to TYR106, THR160 to VAL187, THR180 to TYR106, THR207 to THR218, THR207 to THR220, THR207 to VAL202, THR208 to THR218, THR208 to THR220, THR208 to TRP133, THR218 to VAL202, THR220 to THR225, THR249 to VAL282, THR249 to VAL286, THR279 to TYR252, THR279 to VAL169, THR279 to VAL284, THR294 to TYR299, THR294 to VAL245, THR311 to VAL316, THR312 to THR67, THR312 to TRP318, THR315 to THR67, THR315 to TYR128, THR315 to TYR299, THR327 to TYR75, THR327 to VAL288, THR327 to VAL78, THR67 to TYR128, THR67 to VAL316, THR70 to TYR75, THR70 to VAL316, THR97 to TYR91, THR97 to VAL89, THR97 to VAL92, TRP133 to VAL126, TRP133 to VAL143, TRP192 to TYR149, TRP192 to VAL187, TRP293 to TYR326, TRP293 to VAL288, TRP318 to TYR128, TRP318 to TYR299, TRP318 to TYR75, TRP318 to VAL300, TYR106 to TYR336, TYR106 to VAL187, TYR128 to TYR326, TYR128 to TYR75, TYR148 to VAL143, TYR148 to VAL202, TYR148 to VAL236, TYR149 to VAL202, TYR166 to TYR252, TYR166 to VAL250, TYR252 to TYR336, TYR252 to VAL163, TYR252 to VAL282, TYR252 to VAL284, TYR252 to VAL285, TYR252 to VAL286, TYR299 to VAL316, TYR326 to TYR75, TYR326 to VAL143, TYR326 to VAL78, TYR336 to VAL285, TYR336 to VAL286, TYR336 to VAL89, TYR75 to VAL80, TYR91 to TYR96, VAL236 to VAL300, VAL245 to VAL250, VAL245 to VAL286, VAL286 to VAL291, VAL334 to VAL81, VAL334 to VAL89, VAL89 to VAL94, ALA102_CA to ALA184_CA, ALA102_CA to ARG165_CA, ALA102_CA to ARG179_CA, ALA102_CA to ARG182_CA, ALA102_CA to ASN183_CA, ALA102_CA to ASN188_CA, ALA102_CA to ASP164_CA, ALA102_CA to ILE107_CA, ALA102_CA to LYS185_CA, ALA102_CA to MET161_CA, ALA102_CA to PHE178_CA, ALA102_CA to PRO181_CA, ALA102_CA to THR180_CA, ALA111_CA to ASN332_CA, ALA111_CA to ASN86_CA, ALA111_CA to GLY82_CA, ALA111_CA to GLY85_CA, ALA111_CA to ILE93_CA, ALA111_CA to LEU116_CA, ALA111_CA to MET90_CA, ALA111_CA to PHE87_CA, ALA111_CA to PRO333_CA, ALA111_CA to THR118_CA, ALA111_CA to THR157_CA, ALA111_CA to TYR106_CA, ALA111_CA to TYR336_CA, ALA111_CA to VAL89_CA, ALA113_CA to ASN150_CA, ALA113_CA to ASN86_CA, ALA113_CA to ILE146_CA, ALA113_CA to ILE155_CA, ALA113_CA to MET151_CA, ALA113_CA to MET90_CA, ALA113_CA to PHE108_CA, ALA113_CA to PHE152_CA, ALA113_CA to SER154_CA, ALA113_CA to SER329_CA, ALA113_CA to THR118_CA, ALA113_CA to THR153_CA, ALA113_CA to THR157_CA, ALA113_CA to TRP192_CA, ALA113_CA to TYR149_CA, ALA115_CA to ASN150_CA, ALA115_CA to ASN86_CA, ALA115_CA to GLY82_CA, ALA115_CA to ILE146_CA, ALA115_CA to LEU110_CA, ALA115_CA to LEU83_CA, ALA115_CA to MET90_CA, ALA115_CA to PHE87_CA, ALA115_CA to SER329_CA, ALA115_CA to THR120_CA, ALA117_CA to ASN150_CA, ALA117_CA to ASP147_CA, ALA117_CA to GLN124_CA, ALA117_CA to ILE146_CA, ALA117_CA to LEU112_CA, ALA117_CA to LEU83_CA, ALA117_CA to MET151_CA, ALA117_CA to PRO122_CA, ALA117_CA to SER154_CA, ALA117_CA to SER329_CA, ALA117_CA to TYR326_CA, ALA168_CA to ALA175_CA, ALA168_CA to ARG179_CA, ALA168_CA to LEU275_CA, ALA168_CA to PHE178_CA, ALA168_CA to VAL163_CA, ALA168_CA to VAL173_CA, ALA175_CA to ASP164_CA, ALA175_CA to ILE167_CA, ALA175_CA to THR180_CA, ALA175_CA to VAL169_CA, ALA184_CA to ARG179_CA, ALA184_CA to ASP164_CA, ALA184_CA to ILE105_CA, ALA184_CA to PHE178_CA, ALA184_CA to THR101_CA, ALA184_CA to THR103_CA, ALA184_CA to THR160_CA, ALA184_CA to TYR106_CA, ALA184_CA to VAL189_CA, ALA197_CA to TRP192_CA, ALA197_CA to TYR149_CA, ALA197_CA to VAL202_CA, ALA206_CA to ASN137_CA, ALA206_CA to CYS140_CA, ALA206_CA to CYS217_CA, ALA206_CA to ILE142_CA, ALA206_CA to ILE144_CA, ALA206_CA to LEU219_CA, ALA206_CA to LYS141_CA, ALA206_CA to PRO201_CA, ALA206_CA to SER145_CA, ALA206_CA to THR218_CA, ALA206_CA to THR220_CA, ALA240_CA to CYS235_CA, ALA240_CA to HIS297_CA, ALA240_CA to ILE155_CA, ALA240_CA to ILE234_CA, ALA240_CA to MET151_CA, ALA240_CA to PHE152_CA, ALA240_CA to PHE156_CA, ALA240_CA to PHE289_CA, ALA240_CA to TRP293_CA, ALA240_CA to VAL245_CA, ALA287_CA to CYS292_CA, ALA287_CA to ILE248_CA, ALA287_CA to TYR252_CA, ALA287_CA to VAL282_CA, ALA304_CA to ASN230_CA, ALA304_CA to GLU229_CA, ALA304_CA to LYS233_CA, ALA304_CA to TYR299_CA, ALA323_CA to ASN328_CA, ALA323_CA to CYS292_CA, ALA323_CA to ILE296_CA, ALA323_CA to ILE71_CA, ALA323_CA to LEU121_CA, ALA323_CA to LEU74_CA, ALA323_CA to TRP318_CA, ALA323_CA to TYR75_CA, ALA323_CA to VAL78_CA, ALA337_CA to ARG345_CA, ALA337_CA to ASN332_CA, ALA337_CA to ASN342_CA, ALA337_CA to ILE107_CA, ALA337_CA to ILE93_CA, ALA337_CA to LEU110_CA, ALA337_CA to LEU331_CA, ALA337_CA to LYS344_CA, ALA337_CA to MET161_CA, ALA337_CA to MET281_CA, ALA337_CA to PHE343_CA, ALA337_CA to PHE347_CA, ALA337_CA to VAL89_CA, ALA68_CA to ALA73_CA, ALA68_CA to LEU129_CA, ALA68_CA to LEU74_CA, ALA68_CA to SER125_CA, ALA68_CA to TYR128_CA, ALA68_CA to VAL316_CA, ALA73_CA to VAL78_CA, ARG165_CA to ARG179_CA, ARG165_CA to ARG276_CA, ARG165_CA to ARG280_CA, ARG165_CA to ASN274_CA, ARG165_CA to ASP340_CA, ARG165_CA to CYS170_CA, ARG165_CA to CYS251_CA, ARG165_CA to ILE278_CA, ARG165_CA to LEU158_CA, ARG165_CA to LEU275_CA, ARG165_CA to LEU283_CA, ARG165_CA to LEU335_CA, ARG165_CA to LEU339_CA, ARG165_CA to MET255_CA, ARG165_CA to MET281_CA, ARG165_CA to PHE178_CA, ARG165_CA to THR103_CA, ARG165_CA to THR160_CA, ARG165_CA to THR279_CA, ARG165_CA to TYR106_CA, ARG165_CA to TYR252_CA, ARG165_CA to TYR336_CA, ARG165_CA to VAL282_CA, ARG165_CA to VAL285_CA, ARG179_CA to ASP164_CA, ARG179_CA to HIS171_CA, ARG179_CA to ILE167_CA, ARG179_CA to ILE278_CA, ARG179_CA to LYS174_CA, ARG179_CA to MET161_CA, ARG179_CA to THR101_CA, ARG179_CA to THR103_CA, ARG179_CA to TYR106_CA, ARG179_CA to VAL169_CA, ARG182_CA to ILE105_CA, ARG182_CA to VAL187_CA, ARG211_CA to ASP216_CA, ARG211_CA to THR132_CA, ARG258_CA to CYS170_CA, ARG258_CA to GLY253_CA, ARG258_CA to HIS171_CA, ARG258_CA to PRO172_CA, ARG258_CA to TYR166_CA, ARG258_CA to VAL169_CA, ARG273_CA to ARG280_CA, ARG273_CA to ILE278_CA, ARG276_CA to LYS185_CA, ARG276_CA to MET281_CA, ARG276_CA to VAL169_CA, ARG277_CA to ASP340_CA, ARG277_CA to GLU341_CA, ARG277_CA to LEU339_CA, ARG277_CA to LYS344_CA, ARG277_CA to VAL282_CA, ARG280_CA to GLU341_CA, ARG280_CA to ILE256_CA, ARG280_CA to LEU275_CA, ARG280_CA to LEU339_CA, ARG280_CA to PHE338_CA, ARG280_CA to VAL285_CA, ARG345_CA to ASP340_CA, ARG345_CA to LYS98_CA, ARG345_CA to PHE338_CA, ARG95_CA to LYS100_CA, ARG95_CA to MET90_CA, ASN104_CA to ASN109_CA, ASN104_CA to ASN342_CA, ASN104_CA to ASP340_CA, ASN104_CA to ILE93_CA, ASN104_CA to LYS98_CA, ASN104_CA to MET281_CA, ASN104_CA to MET99_CA, ASN104_CA to PHE343_CA, ASN104_CA to THR97_CA, ASN104_CA to VAL89_CA, ASN109_CA to ASN150_CA, ASN109_CA to ASN188_CA, ASN109_CA to ASN191_CA, ASN109_CA to ASP114_CA, ASN109_CA to ILE93_CA, ASN109_CA to MET90_CA, ASN109_CA to MET99_CA, ASN109_CA to PHE156_CA, ASN109_CA to SER154_CA, ASN109_CA to THR153_CA, ASN109_CA to THR157_CA, ASN109_CA to THR160_CA, ASN109_CA to TRP192_CA, ASN109_CA to VAL187_CA, ASN109_CA to VAL189_CA, ASN127_CA to ASP216_CA, ASN127_CA to CYS217_CA, ASN127_CA to HIS319_CA, ASN127_CA to ILE215_CA, ASN127_CA to PHE135_CA, ASN127_CA to PRO122_CA, ASN127_CA to PRO134_CA, ASN127_CA to THR132_CA, ASN127_CA to TRP133_CA, ASN137_CA to CYS217_CA, ASN137_CA to ILE142_CA, ASN137_CA to LYS209_CA, ASN137_CA to THR207_CA, ASN137_CA to THR208_CA, ASN150_CA to ASP114_CA, ASN150_CA to GLY325_CA, ASN150_CA to ILE155_CA, ASN150_CA to LEU110_CA, ASN150_CA to LEU112_CA, ASN150_CA to LEU116_CA, ASN150_CA to PHE289_CA, ASN150_CA to SER145_CA, ASN150_CA to SER195_CA, ASN150_CA to SER329_CA, ASN150_CA to THR120_CA, ASN150_CA to TRP192_CA, ASN150_CA to TRP293_CA, ASN150_CA to TYR326_CA, ASN183_CA to ASN188_CA, ASN183_CA to ASP177_CA, ASN183_CA to ILE105_CA, ASN183_CA to LEU176_CA, ASN183_CA to PHE178_CA, ASN183_CA to TYR106_CA, ASN188_CA to ILE105_CA, ASN188_CA to ILE107_CA, ASN188_CA to ILE193_CA, ASN188_CA to LEU110_CA, ASN188_CA to PHE108_CA, ASN188_CA to THR153_CA, ASN188_CA to THR157_CA, ASN188_CA to THR160_CA, ASN188_CA to TYR106_CA, ASN191_CA to ILE155_CA, ASN191_CA to ILE186_CA, ASN191_CA to LEU158_CA, ASN191_CA to PHE152_CA, ASN191_CA to PHE156_CA, ASN191_CA to SER154_CA, ASN191_CA to SER196_CA, ASN191_CA to THR153_CA, ASN191_CA to THR157_CA, ASN191_CA to THR160_CA, ASN191_CA to TYR106_CA, ASN191_CA to TYR149_CA, ASN230_CA to CYS235_CA, ASN230_CA to LEU305_CA, ASN230_CA to PHE221_CA, ASN230_CA to THR225_CA, ASN274_CA to GLU341_CA, ASN274_CA to THR279_CA, ASN328_CA to ASP114_CA, ASN328_CA to CYS292_CA, ASN328_CA to ILE155_CA, ASN328_CA to ILE290_CA, ASN328_CA to LEU110_CA, ASN328_CA to LEU158_CA, ASN328_CA to LEU335_CA, ASN328_CA to PHE289_CA, ASN328_CA to PRO333_CA, ASN328_CA to SER154_CA, ASN328_CA to TRP293_CA, ASN328_CA to TYR336_CA, ASN328_CA to VAL285_CA, ASN328_CA to VAL288_CA, ASN328_CA to VAL291_CA, ASN328_CA to VAL78_CA, ASN332_CA to ASN86_CA, ASN332_CA to ASP114_CA, ASN332_CA to ILE107_CA, ASN332_CA to ILE155_CA, ASN332_CA to LEU110_CA, ASN332_CA to LEU158_CA, ASN332_CA to PHE289_CA, ASN332_CA to PHE338_CA, ASN332_CA to SER154_CA, ASN332_CA to THR327_CA, ASN332_CA to TRP293_CA, ASN332_CA to VAL285_CA, ASN332_CA to VAL288_CA, ASN332_CA to VAL89_CA, ASN342_CA to LYS98_CA, ASN342_CA to MET99_CA, ASN342_CA to PHE347_CA, ASN342_CA to THR101_CA, ASN342_CA to THR103_CA, ASN342_CA to THR97_CA, ASN342_CA to TYR336_CA, ASN342_CA to VAL92_CA, ASN86_CA to ASP114_CA, ASN86_CA to CYS330_CA, ASN86_CA to ILE107_CA, ASN86_CA to LEU110_CA, ASN86_CA to LEU112_CA, ASN86_CA to LEU116_CA, ASN86_CA to LEU331_CA, ASN86_CA to PHE338_CA, ASN86_CA to PRO333_CA, ASN86_CA to SER329_CA, ASN86_CA to THR118_CA, ASN86_CA to TYR336_CA, ASN86_CA to TYR91_CA, ASN86_CA to VAL81_CA, ASP114_CA to CYS330_CA, ASP114_CA to GLY82_CA, ASP114_CA to ILE155_CA, ASP114_CA to LEU158_CA, ASP114_CA to LEU331_CA, ASP114_CA to LEU83_CA, ASP114_CA to PRO333_CA, ASP114_CA to SER119_CA, ASP114_CA to SER154_CA, ASP114_CA to SER329_CA, ASP114_CA to THR153_CA, ASP114_CA to TYR326_CA, ASP114_CA to TYR336_CA, ASP147_CA to GLN124_CA, ASP147_CA to ILE142_CA, ASP147_CA to LEU116_CA, ASP147_CA to LEU121_CA, ASP147_CA to PHE152_CA, ASP147_CA to THR118_CA, ASP147_CA to THR120_CA, ASP147_CA to TRP293_CA, ASP147_CA to TYR326_CA, ASP164_CA to CYS159_CA, ASP164_CA to CYS251_CA, ASP164_CA to PHE178_CA, ASP164_CA to THR103_CA, ASP164_CA to THR180_CA, ASP164_CA to TYR106_CA, ASP164_CA to VAL169_CA, ASP177_CA to PRO172_CA, ASP216_CA to CYS140_CA, ASP216_CA to GLY131_CA, ASP216_CA to LYS209_CA, ASP216_CA to THR132_CA, ASP216_CA to THR207_CA, ASP216_CA to THR208_CA, ASP216_CA to TRP133_CA, ASP216_CA to TYR210_CA, ASP340_CA to ILE107_CA, ASP340_CA to ILE278_CA, ASP340_CA to LEU335_CA, ASP340_CA to MET161_CA, ASP340_CA to MET281_CA, ASP340_CA to MET99_CA, ASP340_CA to PRO333_CA, ASP340_CA to THR103_CA, ASP340_CA to VAL334_CA, CYS140_CA to CYS217_CA, CYS140_CA to ILE146_CA, CYS140_CA to LEU219_CA, CYS140_CA to PHE135_CA, CYS140_CA to SER145_CA, CYS140_CA to THR207_CA, CYS140_CA to THR208_CA, CYS140_CA to THR218_CA, CYS140_CA to TRP133_CA, CYS140_CA to VAL202_CA, CYS159_CA to CYS251_CA, CYS159_CA to ILE247_CA, CYS159_CA to ILE248_CA, CYS159_CA to MET243_CA, CYS159_CA to PHE239_CA, CYS159_CA to PHE289_CA, CYS159_CA to PRO244_CA, CYS159_CA to SER154_CA, CYS159_CA to TYR252_CA, CYS159_CA to TYR336_CA, CYS159_CA to VAL245_CA, CYS159_CA to VAL286_CA, CYS170_CA to CYS251_CA, CYS170_CA to ILE256_CA, CYS170_CA to LEU254_CA, CYS170_CA to LEU257_CA, CYS170_CA to LEU259_CA, CYS170_CA to LEU275_CA, CYS170_CA to MET255_CA, CYS190_CA to LYS185_CA, CYS190_CA to PHE156_CA, CYS190_CA to SER195_CA, CYS190_CA to SER196_CA, CYS217_CA to GLY136_CA, CYS217_CA to ILE144_CA, CYS217_CA to LEU139_CA, CYS217_CA to LYS141_CA, CYS217_CA to LYS209_CA, CYS217_CA to THR132_CA, CYS217_CA to THR207_CA, CYS217_CA to THR208_CA, CYS217_CA to TRP133_CA, CYS217_CA to VAL143_CA, CYS235_CA to ILE198_CA, CYS235_CA to PHE152_CA, CYS235_CA to PHE241_CA, CYS251_CA to ILE256_CA, CYS251_CA to LEU246_CA, CYS251_CA to SER162_CA, CYS251_CA to TYR166_CA, CYS251_CA to VAL163_CA, CYS292_CA to CYS321_CA, CYS292_CA to GLY325_CA, CYS292_CA to HIS297_CA, CYS292_CA to ILE322_CA, CYS292_CA to LEU324_CA, CYS292_CA to LEU331_CA, CYS292_CA to SER329_CA, CYS292_CA to THR327_CA, CYS292_CA to TYR326_CA, CYS321_CA to HIS297_CA, CYS321_CA to ILE296_CA, CYS321_CA to LEU74_CA, CYS321_CA to PRO295_CA, CYS321_CA to TRP293_CA, CYS321_CA to TYR299_CA, CYS321_CA to TYR326_CA, CYS321_CA to VAL316_CA, CYS330_CA to CYS79_CA, CYS330_CA to GLY325_CA, CYS330_CA to GLY82_CA, CYS330_CA to GLY85_CA, CYS330_CA to ILE77_CA, CYS330_CA to LEU121_CA, CYS330_CA to LEU335_CA, CYS330_CA to LEU83_CA, CYS330_CA to THR118_CA, CYS330_CA to VAL78_CA, CYS330_CA to VAL80_CA, CYS330_CA to VAL81_CA, CYS346_CA to GLU341_CA, CYS346_CA to LEU88_CA, CYS346_CA to LYS98_CA, CYS346_CA to MET99_CA, CYS346_CA to PHE338_CA, CYS346_CA to THR97_CA, CYS346_CA to TYR96_CA, CYS346_CA to VAL92_CA, CYS79_CA to LEU121_CA, CYS79_CA to LEU74_CA, CYS79_CA to PHE84_CA, CYS79_CA to PRO122_CA, CYS79_CA to SER119_CA, CYS79_CA to THR118_CA, CYS79_CA to THR120_CA, CYS79_CA to TYR326_CA, GLN124_CA to HIS319_CA, GLN124_CA to ILE322_CA, GLN124_CA to LEU129_CA, GLN124_CA to PHE135_CA, GLN124_CA to TRP133_CA, GLN124_CA to TYR326_CA, GLN124_CA to TYR75_CA, GLN124_CA to VAL143_CA, GLN314_CA to HIS319_CA, GLN314_CA to ILE308_CA, GLN314_CA to LYS303_CA, GLN314_CA to PRO309_CA, GLN314_CA to THR307_CA, GLN314_CA to TYR299_CA, GLU229_CA to ILE234_CA, GLU229_CA to LEU219_CA, GLU229_CA to PHE221_CA, GLU229_CA to PRO224_CA, GLU229_CA to SER222_CA, GLU229_CA to THR218_CA, GLU310_CA to THR315_CA, GLU341_CA to TYR336_CA, GLY131_CA to GLY213_CA, GLY131_CA to ILE215_CA, GLY131_CA to SER125_CA, GLY131_CA to SER214_CA, GLY131_CA to VAL126_CA, GLY136_CA to LYS141_CA, GLY136_CA to THR207_CA, GLY136_CA to THR208_CA, GLY199_CA to ILE144_CA, GLY199_CA to ILE146_CA, GLY199_CA to LEU194_CA, GLY199_CA to LYS141_CA, GLY199_CA to PHE152_CA, GLY199_CA to PHE204_CA, GLY199_CA to SER145_CA, GLY199_CA to TYR148_CA, GLY199_CA to TYR149_CA, GLY213_CA to THR132_CA, GLY253_CA to ILE247_CA, GLY253_CA to ILE248_CA, GLY253_CA to VAL282_CA, GLY325_CA to ILE296_CA, GLY325_CA to PHE320_CA, GLY325_CA to TRP293_CA, GLY325_CA to VAL291_CA, GLY325_CA to VAL78_CA, GLY82_CA to ILE77_CA, GLY82_CA to LEU331_CA, GLY82_CA to LEU88_CA, GLY82_CA to PHE87_CA, GLY82_CA to PRO333_CA, GLY82_CA to SER329_CA, GLY82_CA to SER76_CA, GLY82_CA to THR118_CA, GLY82_CA to TYR326_CA, GLY85_CA to MET90_CA, GLY85_CA to PHE338_CA, GLY85_CA to PRO333_CA, GLY85_CA to SER329_CA, GLY85_CA to TYR336_CA, GLY85_CA to VAL334_CA, GLY85_CA to VAL80_CA, HIS171_CA to LEU176_CA, HIS171_CA to PHE178_CA, HIS171_CA to TYR166_CA, HIS223_CA to TRP228_CA, HIS297_CA to ILE155_CA, HIS297_CA to ILE238_CA, HIS297_CA to ILE302_CA, HIS297_CA to LYS233_CA, HIS297_CA to MET151_CA, HIS297_CA to PHE237_CA, HIS297_CA to PHE241_CA, HIS297_CA to PHE289_CA, HIS297_CA to VAL236_CA, HIS319_CA to ILE71_CA, HIS319_CA to LEU324_CA, HIS319_CA to LEU74_CA, HIS319_CA to THR67_CA, HIS319_CA to TYR128_CA, HIS319_CA to TYR299_CA, HIS319_CA to TYR75_CA, ILE105_CA to ILE186_CA, ILE105_CA to ILE93_CA, ILE105_CA to LEU110_CA, ILE105_CA to LYS100_CA, ILE105_CA to LYS185_CA, ILE105_CA to MET99_CA, ILE105_CA to PRO181_CA, ILE105_CA to THR157_CA, ILE105_CA to THR180_CA, ILE107_CA to ILE93_CA, ILE107_CA to LEU112_CA, ILE107_CA to MET161_CA, ILE107_CA to MET281_CA, ILE107_CA to MET90_CA, ILE107_CA to PHE338_CA, ILE107_CA to PHE343_CA, ILE107_CA to THR157_CA, ILE107_CA to TYR336_CA, ILE107_CA to VAL282_CA, ILE107_CA to VAL89_CA, ILE138_CA to MET203_CA, ILE138_CA to THR208_CA, ILE138_CA to TRP133_CA, ILE138_CA to VAL143_CA, ILE142_CA to MET203_CA, ILE142_CA to THR120_CA, ILE142_CA to TYR149_CA, ILE144_CA to LEU139_CA, ILE144_CA to LEU219_CA, ILE144_CA to MET203_CA, ILE144_CA to THR120_CA, ILE144_CA to THR207_CA, ILE144_CA to THR218_CA, ILE144_CA to TRP133_CA, ILE144_CA to TYR149_CA, ILE144_CA to VAL202_CA, ILE146_CA to LEU116_CA, ILE146_CA to LYS141_CA, ILE146_CA to MET151_CA, ILE146_CA to MET203_CA, ILE146_CA to SER119_CA, ILE146_CA to THR118_CA, ILE146_CA to THR120_CA, ILE146_CA to THR153_CA, ILE146_CA to VAL202_CA, ILE155_CA to ILE242_CA, ILE155_CA to ILE248_CA, ILE155_CA to ILE290_CA, ILE155_CA to LEU110_CA, ILE155_CA to MET243_CA, ILE155_CA to PHE239_CA, ILE155_CA to PHE241_CA, ILE155_CA to PHE289_CA, ILE155_CA to PRO244_CA, ILE155_CA to THR160_CA, ILE155_CA to TRP293_CA, ILE155_CA to VAL245_CA, ILE167_CA to LEU176_CA, ILE167_CA to LYS174_CA, ILE167_CA to MET255_CA, ILE167_CA to PHE178_CA, ILE167_CA to PRO172_CA, ILE167_CA to SER162_CA, ILE167_CA to VAL173_CA, ILE186_CA to PRO181_CA, ILE193_CA to ILE198_CA, ILE193_CA to THR153_CA, ILE193_CA to TYR149_CA, ILE198_CA to LEU232_CA, ILE198_CA to MET151_CA, ILE198_CA to MET203_CA, ILE198_CA to MET205_CA, ILE198_CA to PHE152_CA, ILE198_CA to PHE239_CA, ILE198_CA to SER145_CA, ILE198_CA to TYR148_CA, ILE198_CA to TYR149_CA, ILE198_CA to VAL236_CA, ILE215_CA to LYS209_CA, ILE215_CA to PRO134_CA, ILE215_CA to THR132_CA, ILE215_CA to THR208_CA, ILE215_CA to TRP133_CA, ILE215_CA to TYR210_CA, ILE234_CA to ILE242_CA, ILE234_CA to ILE301_CA, ILE234_CA to PHE239_CA, ILE238_CA to LEU231_CA, ILE238_CA to LYS233_CA, ILE238_CA to MET243_CA, ILE238_CA to PHE152_CA, ILE238_CA to PRO244_CA, ILE242_CA to ILE247_CA, ILE242_CA to PHE237_CA, ILE242_CA to PHE289_CA, ILE242_CA to VAL236_CA, ILE247_CA to LEU158_CA, ILE247_CA to SER162_CA, ILE247_CA to THR160_CA, ILE247_CA to TYR252_CA, ILE247_CA to VAL163_CA, ILE248_CA to ILE290_CA, ILE248_CA to LEU158_CA, ILE248_CA to MET243_CA, ILE248_CA to MET255_CA, ILE248_CA to PHE289_CA, ILE248_CA to SER162_CA, ILE248_CA to THR160_CA, ILE248_CA to TYR336_CA, ILE248_CA to VAL163_CA, ILE248_CA to VAL282_CA, ILE248_CA to VAL285_CA, ILE248_CA to VAL286_CA, ILE256_CA to ILE278_CA, ILE256_CA to LEU275_CA, ILE256_CA to LEU283_CA, ILE256_CA to THR279_CA, ILE256_CA to VAL169_CA, ILE256_CA to VAL282_CA, ILE278_CA to LEU259_CA, ILE278_CA to LEU283_CA, ILE278_CA to LEU339_CA, ILE278_CA to MET255_CA, ILE278_CA to THR101_CA, ILE278_CA to THR103_CA, ILE290_CA to LEU158_CA, ILE290_CA to PHE241_CA, ILE290_CA to PRO295_CA, ILE290_CA to THR249_CA, ILE290_CA to VAL245_CA, ILE290_CA to VAL285_CA, ILE296_CA to ILE301_CA, ILE296_CA to ILE322_CA, ILE296_CA to LEU324_CA, ILE296_CA to MET151_CA, ILE296_CA to TRP318_CA, ILE296_CA to VAL291_CA, ILE298_CA to LYS303_CA, ILE298_CA to PHE237_CA, ILE298_CA to PHE241_CA, ILE298_CA to TRP293_CA, ILE301_CA to ILE306_CA, ILE301_CA to LYS233_CA, ILE301_CA to PHE237_CA, ILE301_CA to VAL236_CA, ILE302_CA to ILE308_CA, ILE302_CA to THR307_CA, ILE308_CA to LYS303_CA, ILE308_CA to TRP318_CA, ILE308_CA to TYR299_CA, ILE322_CA to LEU121_CA, ILE322_CA to PRO295_CA, ILE322_CA to SER317_CA, ILE322_CA to THR327_CA, ILE322_CA to TRP293_CA, ILE322_CA to TYR128_CA, ILE322_CA to TYR75_CA, ILE322_CA to VAL300_CA, ILE322_CA to VAL78_CA, ILE69_CA to LEU129_CA, ILE69_CA to LEU74_CA, ILE69_CA to TYR128_CA, ILE71_CA to LEU129_CA, ILE71_CA to PHE320_CA, ILE71_CA to SER125_CA, ILE71_CA to SER317_CA, ILE71_CA to SER76_CA, ILE71_CA to THR312_CA, ILE71_CA to THR315_CA, ILE71_CA to TYR128_CA, ILE71_CA to VAL316_CA, ILE71_CA to VAL66_CA, ILE77_CA to LEU121_CA, ILE77_CA to LEU83_CA, ILE77_CA to MET72_CA, ILE93_CA to LEU88_CA, ILE93_CA to LYS100_CA, ILE93_CA to LYS98_CA, ILE93_CA to MET99_CA, ILE93_CA to PHE108_CA, ILE93_CA to PHE343_CA, ILE93_CA to THR101_CA, ILE93_CA to THR103_CA, ILE93_CA to TYR106_CA, LEU110_CA to LEU158_CA, LEU110_CA to MET161_CA, LEU110_CA to PHE289_CA, LEU110_CA to PRO333_CA, LEU110_CA to SER154_CA, LEU110_CA to SER329_CA, LEU110_CA to THR153_CA, LEU110_CA to THR157_CA, LEU110_CA to TYR336_CA, LEU110_CA to VAL285_CA, LEU112_CA to MET90_CA, LEU112_CA to SER119_CA, LEU112_CA to THR153_CA, LEU112_CA to TRP192_CA, LEU116_CA to LEU121_CA, LEU116_CA to LEU83_CA, LEU116_CA to MET90_CA, LEU116_CA to PHE87_CA, LEU116_CA to TRP192_CA, LEU116_CA to TYR149_CA, LEU116_CA to TYR326_CA, LEU121_CA to LEU74_CA, LEU121_CA to SER76_CA, LEU121_CA to TYR128_CA, LEU121_CA to TYR326_CA, LEU121_CA to TYR75_CA, LEU121_CA to VAL126_CA, LEU121_CA to VAL143_CA, LEU121_CA to VAL78_CA, LEU121_CA to VAL80_CA, LEU129_CA to MET65_CA, LEU129_CA to MET72_CA, LEU139_CA to PHE123_CA, LEU139_CA to TRP133_CA, LEU158_CA to PHE289_CA, LEU158_CA to PRO244_CA, LEU158_CA to THR153_CA, LEU158_CA to TRP293_CA, LEU158_CA to TYR252_CA, LEU158_CA to TYR336_CA, LEU158_CA to VAL163_CA, LEU158_CA to VAL282_CA, LEU158_CA to VAL285_CA, LEU158_CA to VAL286_CA, LEU194_CA to MET243_CA, LEU194_CA to PHE152_CA, LEU194_CA to PHE156_CA, LEU194_CA to PHE239_CA, LEU194_CA to TYR149_CA, LEU194_CA to VAL189_CA, LEU200_CA to MET205_CA, LEU200_CA to SER145_CA, LEU200_CA to SER195_CA, LEU200_CA to TRP192_CA, LEU200_CA to TYR149_CA, LEU219_CA to LEU232_CA, LEU219_CA to LYS209_CA, LEU219_CA to MET203_CA, LEU219_CA to MET205_CA, LEU219_CA to PHE204_CA, LEU219_CA to PRO201_CA, LEU219_CA to THR207_CA, LEU219_CA to THR225_CA, LEU219_CA to TYR148_CA, LEU219_CA to VAL202_CA, LEU231_CA to THR225_CA, LEU231_CA to TRP226_CA, LEU231_CA to VAL236_CA, LEU232_CA to MET205_CA, LEU232_CA to PHE221_CA, LEU232_CA to PHE237_CA, LEU232_CA to TYR148_CA, LEU232_CA to TYR227_CA, LEU232_CA to VAL202_CA, LEU246_CA to PHE241_CA, LEU254_CA to LEU259_CA, LEU254_CA to THR249_CA, LEU254_CA to TYR166_CA, LEU254_CA to VAL169_CA, LEU257_CA to LEU275_CA, LEU257_CA to TYR252_CA, LEU259_CA to LEU275_CA, LEU259_CA to VAL169_CA, LEU275_CA to MET255_CA, LEU275_CA to PRO172_CA, LEU275_CA to VAL169_CA, LEU283_CA to LEU339_CA, LEU283_CA to MET161_CA, LEU283_CA to MET255_CA, LEU283_CA to SER162_CA, LEU283_CA to TYR252_CA, LEU283_CA to VAL288_CA, LEU305_CA to VAL300_CA, LEU324_CA to LEU331_CA, LEU324_CA to LEU74_CA, LEU324_CA to PRO295_CA, LEU324_CA to SER329_CA, LEU324_CA to THR294_CA, LEU324_CA to TRP293_CA, LEU324_CA to TYR75_CA, LEU324_CA to VAL288_CA, LEU324_CA to VAL291_CA, LEU324_CA to VAL78_CA, LEU331_CA to TYR326_CA, LEU331_CA to TYR336_CA, LEU331_CA to VAL288_CA, LEU331_CA to VAL78_CA, LEU331_CA to VAL81_CA, LEU335_CA to MET161_CA, LEU335_CA to MET281_CA, LEU335_CA to PHE289_CA, LEU335_CA to VAL284_CA, LEU335_CA to VAL285_CA, LEU335_CA to VAL286_CA, LEU335_CA to VAL288_CA, LEU339_CA to LYS344_CA, LEU339_CA to MET281_CA, LEU339_CA to PRO333_CA, LEU339_CA to VAL282_CA, LEU339_CA to VAL284_CA, LEU339_CA to VAL285_CA, LEU339_CA to VAL334_CA, LEU74_CA to PHE320_CA, LEU74_CA to THR327_CA, LEU74_CA to VAL316_CA, LEU83_CA to LEU88_CA, LEU83_CA to MET90_CA, LEU83_CA to PRO122_CA, LEU83_CA to SER119_CA, LEU83_CA to SER329_CA, LEU83_CA to THR118_CA, LEU83_CA to THR120_CA, LEU83_CA to VAL78_CA, LEU88_CA to PHE338_CA, LEU88_CA to PHE343_CA, LEU88_CA to PHE347_CA, LYS100_CA to PRO181_CA, LYS100_CA to THR180_CA, LYS100_CA to VAL92_CA, LYS100_CA to VAL94_CA, LYS141_CA to MET203_CA, LYS141_CA to MET205_CA, LYS141_CA to PHE204_CA, LYS141_CA to PRO201_CA, LYS141_CA to THR207_CA, LYS141_CA to THR208_CA, LYS141_CA to TRP133_CA, LYS141_CA to VAL202_CA, LYS185_CA to MET99_CA, LYS185_CA to THR180_CA, LYS185_CA to TYR106_CA, LYS209_CA to SER214_CA, LYS209_CA to THR218_CA, LYS209_CA to THR220_CA, LYS233_CA to LYS303_CA, LYS233_CA to PHE221_CA, LYS233_CA to TRP228_CA, LYS233_CA to TRP318_CA, LYS233_CA to TYR148_CA, LYS233_CA to VAL300_CA, LYS303_CA to TRP318_CA, LYS344_CA to PHE338_CA, LYS344_CA to TYR336_CA, LYS98_CA to VAL92_CA, MET130_CA to PHE135_CA, MET130_CA to SER125_CA, MET130_CA to SER214_CA, MET151_CA to PHE156_CA, MET151_CA to PHE241_CA, MET151_CA to PHE289_CA, MET151_CA to SER195_CA, MET151_CA to TRP293_CA, MET151_CA to VAL236_CA, MET161_CA to MET281_CA, MET161_CA to PHE156_CA, MET161_CA to THR103_CA, MET161_CA to TYR106_CA, MET161_CA to TYR166_CA, MET161_CA to TYR252_CA, MET161_CA to TYR336_CA, MET161_CA to VAL282_CA, MET161_CA to VAL285_CA, MET161_CA to VAL286_CA, MET203_CA to SER145_CA, MET203_CA to TYR149_CA, MET203_CA to VAL143_CA, MET205_CA to PHE221_CA, MET205_CA to SER222_CA, MET205_CA to THR218_CA, MET205_CA to THR220_CA, MET243_CA to PHE156_CA, MET243_CA to PHE237_CA, MET255_CA to SER162_CA, MET255_CA to THR249_CA, MET255_CA to THR279_CA, MET255_CA to TYR166_CA, MET255_CA to VAL163_CA, MET255_CA to VAL169_CA, MET255_CA to VAL250_CA, MET255_CA to VAL282_CA, MET281_CA to PHE343_CA, MET281_CA to THR103_CA, MET281_CA to TYR252_CA, MET281_CA to TYR336_CA, MET281_CA to VAL286_CA, MET281_CA to VAL334_CA, MET65_CA to THR70_CA, MET72_CA to SER125_CA, MET72_CA to THR67_CA, MET72_CA to TYR128_CA, MET72_CA to VAL126_CA, MET72_CA to VAL66_CA, MET90_CA to PHE108_CA, MET90_CA to PHE343_CA, MET99_CA to PHE108_CA, MET99_CA to PHE343_CA, MET99_CA to PRO181_CA, MET99_CA to TYR106_CA, MET99_CA to VAL89_CA, MET99_CA to VAL92_CA, MET99_CA to VAL94_CA, PHE108_CA to THR103_CA, PHE108_CA to THR157_CA, PHE108_CA to TYR336_CA, PHE108_CA to TYR91_CA, PHE108_CA to VAL89_CA, PHE108_CA to VAL94_CA, PHE123_CA to PHE135_CA, PHE123_CA to PRO134_CA, PHE123_CA to THR132_CA, PHE123_CA to TRP133_CA, PHE123_CA to TYR128_CA, PHE123_CA to VAL143_CA, PHE135_CA to PRO122_CA, PHE135_CA to THR208_CA, PHE135_CA to VAL126_CA, PHE135_CA to VAL143_CA, PHE152_CA to PHE237_CA, PHE152_CA to PHE239_CA, PHE152_CA to PHE241_CA, PHE152_CA to SER195_CA, PHE152_CA to SER196_CA, PHE152_CA to THR157_CA, PHE152_CA to TRP293_CA, PHE152_CA to VAL236_CA, PHE156_CA to PHE239_CA, PHE156_CA to PHE241_CA, PHE156_CA to PRO244_CA, PHE156_CA to SER195_CA, PHE156_CA to SER196_CA, PHE156_CA to TRP192_CA, PHE156_CA to VAL187_CA, PHE178_CA to THR160_CA, PHE178_CA to TYR106_CA, PHE178_CA to VAL163_CA, PHE178_CA to VAL173_CA, PHE178_CA to VAL187_CA, PHE204_CA to THR220_CA, PHE221_CA to TRP226_CA, PHE221_CA to TRP228_CA, PHE237_CA to PRO244_CA, PHE237_CA to THR294_CA, PHE239_CA to PRO244_CA, PHE241_CA to PHE289_CA, PHE241_CA to PRO295_CA, PHE241_CA to THR294_CA, PHE241_CA to TRP293_CA, PHE241_CA to VAL236_CA, PHE289_CA to PRO244_CA, PHE289_CA to PRO295_CA, PHE289_CA to SER154_CA, PHE289_CA to THR294_CA, PHE289_CA to TYR336_CA, PHE289_CA to VAL245_CA, PHE289_CA to VAL284_CA, PHE313_CA to TRP318_CA, PHE313_CA to TYR299_CA, PHE320_CA to PRO295_CA, PHE320_CA to THR315_CA, PHE320_CA to THR327_CA, PHE320_CA to TYR75_CA, PHE338_CA to PHE343_CA, PHE338_CA to PHE84_CA, PHE338_CA to PRO333_CA, PHE338_CA to VAL89_CA, PHE338_CA to VAL92_CA, PHE343_CA to PRO333_CA, PHE343_CA to THR97_CA, PHE343_CA to TYR336_CA, PHE343_CA to VAL89_CA, PHE343_CA to VAL92_CA, PHE347_CA to PHE84_CA, PHE347_CA to TYR96_CA, PHE347_CA to VAL92_CA, PHE84_CA to PRO333_CA, PHE84_CA to THR118_CA, PHE84_CA to VAL89_CA, PHE87_CA to PRO333_CA, PHE87_CA to SER119_CA, PHE87_CA to THR118_CA, PHE87_CA to VAL92_CA, PRO122_CA to TYR75_CA, PRO134_CA to VAL126_CA, PRO172_CA to TYR166_CA, PRO181_CA to THR101_CA, PRO181_CA to THR103_CA, PRO201_CA to SER195_CA, PRO201_CA to SER196_CA, PRO201_CA to TYR149_CA, PRO244_CA to THR249_CA, PRO295_CA to VAL300_CA, PRO309_CA to THR315_CA, PRO333_CA to THR327_CA, PRO333_CA to VAL81_CA, PRO333_CA to VAL89_CA, SER119_CA to TYR326_CA, SER119_CA to VAL143_CA, SER125_CA to SER76_CA, SER125_CA to THR120_CA, SER125_CA to TYR75_CA, SER145_CA to VAL202_CA, SER154_CA to SER195_CA, SER154_CA to SER329_CA, SER154_CA to TRP293_CA, SER154_CA to TYR149_CA, SER162_CA to THR157_CA, SER162_CA to THR249_CA, SER162_CA to TYR106_CA, SER162_CA to TYR252_CA, SER162_CA to TYR336_CA, SER162_CA to VAL250_CA, SER162_CA to VAL282_CA, SER162_CA to VAL286_CA, SER195_CA to THR153_CA, SER195_CA to TYR148_CA, SER195_CA to TYR149_CA, SER196_CA to THR153_CA, SER196_CA to TYR149_CA, SER196_CA to VAL189_CA, SER196_CA to VAL202_CA, SER214_CA to THR132_CA, SER214_CA to TRP133_CA, SER222_CA to TRP228_CA, SER222_CA to TYR227_CA, SER317_CA to THR312_CA, SER317_CA to TYR299_CA, SER329_CA to THR118_CA, SER329_CA to TRP293_CA, SER329_CA to VAL78_CA, SER329_CA to VAL81_CA, SER76_CA to THR70_CA, SER76_CA to VAL81_CA, THR101_CA to THR180_CA, THR101_CA to TYR106_CA, THR103_CA to THR180_CA, THR103_CA to TYR336_CA, THR103_CA to VAL282_CA, THR118_CA to THR327_CA, THR118_CA to TYR326_CA, THR118_CA to TYR75_CA, THR118_CA to VAL78_CA, THR118_CA to VAL80_CA, THR118_CA to VAL81_CA, THR120_CA to TRP133_CA, THR120_CA to TYR326_CA, THR120_CA to VAL143_CA, THR132_CA to VAL126_CA, THR153_CA to TRP192_CA, THR153_CA to TYR148_CA, THR157_CA to TRP192_CA, THR157_CA to TYR106_CA, THR160_CA to TYR106_CA, THR160_CA to VAL187_CA, THR180_CA to TYR106_CA, THR207_CA to THR218_CA, THR207_CA to THR220_CA, THR207_CA to VAL202_CA, THR208_CA to THR218_CA, THR208_CA to THR220_CA, THR208_CA to TRP133_CA, THR218_CA to VAL202_CA, THR220_CA to THR225_CA, THR249_CA to VAL282_CA, THR249_CA to VAL286_CA, THR279_CA to TYR252_CA, THR279_CA to VAL169_CA, THR279_CA to VAL284_CA, THR294_CA to TYR299_CA, THR294_CA to VAL245_CA, THR311_CA to VAL316_CA, THR312_CA to THR67_CA, THR312_CA to TRP318_CA, THR315_CA to THR67_CA, THR315_CA to TYR128_CA, THR315_CA to TYR299_CA, THR327_CA to TYR75_CA, THR327_CA to VAL288_CA, THR327_CA to VAL78_CA, THR67_CA to TYR128_CA, THR67_CA to VAL316_CA, THR70_CA to TYR75_CA, THR70_CA to VAL316_CA, THR97_CA to TYR91_CA, THR97_CA to VAL89_CA, THR97_CA to VAL92_CA, TRP133_CA to VAL126_CA, TRP133_CA to VAL143_CA, TRP192_CA to TYR149_CA, TRP192_CA to VAL187_CA, TRP293_CA to TYR326_CA, TRP293_CA to VAL288_CA, TRP318_CA to TYR128_CA, TRP318_CA to TYR299_CA, TRP318_CA to TYR75_CA, TRP318_CA to VAL300_CA, TYR106_CA to TYR336_CA, TYR106_CA to VAL187_CA, TYR128_CA to TYR326_CA, TYR128_CA to TYR75_CA, TYR148_CA to VAL143_CA, TYR148_CA to VAL202_CA, TYR148_CA to VAL236_CA, TYR149_CA to VAL202_CA, TYR166_CA to TYR252_CA, TYR166_CA to VAL250_CA, TYR252_CA to TYR336_CA, TYR252_CA to VAL163_CA, TYR252_CA to VAL282_CA, TYR252_CA to VAL284_CA, TYR252_CA to VAL285_CA, TYR252_CA to VAL286_CA, TYR299_CA to VAL316_CA, TYR326_CA to TYR75_CA, TYR326_CA to VAL143_CA, TYR326_CA to VAL78_CA, TYR336_CA to VAL285_CA, TYR336_CA to VAL286_CA, TYR336_CA to VAL89_CA, TYR75_CA to VAL80_CA, TYR91_CA to TYR96_CA, VAL236_CA to VAL300_CA, VAL245_CA to VAL250_CA, VAL245_CA to VAL286_CA, VAL286_CA to VAL291_CA, VAL334_CA to VAL81_CA, VAL334_CA to VAL89_CA, VAL89_CA to VAL94_CA]\n",
      "Completed featurizing\n"
     ]
    }
   ],
   "source": [
    "import custom_featurizer\n",
    "reload(custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "\n",
    "featurize_contacts_custom(ref_receptors_dir, features_dir = ref_features_dir, traj_ext = \".pdb\", contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes, within_turn=False, binarize=None, redo=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 124,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/phi_psi_chi2_allprot_tica_coords.h5\"...\n",
      "None\n",
      "None\n",
      "['/home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/4dkl_R_for_conformation.dataset', '/home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/5c1m.dataset']\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/5c1m.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/4dkl_R_for_conformation.dataset\n"
     ]
    }
   ],
   "source": [
    "transform(existing_model = projection_operator_dir, features_directory = ref_features_dir, tica_dir = ref_tica_dir, normalizer=compat_verboseload(\"%s/normalizer.h5\" %features_dir))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_tica\n",
    "reload(custom_tica)\n",
    "from custom_tica import *\n",
    "transform_to_h5(projection_operator_dir, features_dir, projected_features_dir, worker_pool=None, parallel=True, normalizer=compat_verboseload(\"%s/normalizer.h5\" %features_dir))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_object = compat_verboseload(projection_operator_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "with open(projection_operator_dir, 'rb') as f:\n",
    "    tica_object = pickle.load(f, encoding='latin1') "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#all_tica = compat_verboseload(projected_features_dir)\n",
    "#all_tica = [x[:,range(1,10)] for x in all_tica]\n",
    "#print(all_tica[0].shape)\n",
    "#print(len(all_tica))\n",
    "#verbosedump(all_tica, projected_features_dir)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#n_components=9"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 1655.96224959,  1078.68106057,   797.08171757,   716.45590377,\n",
       "         658.99925169,   454.42244334,   372.47408422,   370.3421338 ,\n",
       "         365.56500232,   353.28358375])"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tica_object.timescales_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_columns(tica_dir, projected_features_dir, titles = [\"tIC%d\" %j for j in range(1,11)], tICA = True, scale = 1.0, refcoords_file = None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "feature_indices = []\n",
    "traj_basenames = get_trajectory_files(traj_dir, \".h5\")\n",
    "traj_basenames = [os.path.splitext(os.path.basename(t))[0] for t in traj_basenames]\n",
    "feature_basenames = get_trajectory_files(features_dir, \".dataset\")\n",
    "feature_basenames = [os.path.splitext(os.path.basename(t))[0] for t in feature_basenames]\n",
    "for i, traj_basename in enumerate(traj_basenames):\n",
    "    if traj_basename in feature_basenames:\n",
    "        feature_indices.append(int(i))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_coords = compat_verboseload(projected_features_dir)\n",
    "pnas_coords = compat_verboseload(user_defined_features_file)\n",
    "pnas_coords = [pnas_coords[i] for i in feature_indices]\n",
    "tica_names = [\"tIC.%d\" %i for i in range(1,n_components+1)]\n",
    "pnas_names = sorted(feature_name_residues_dict.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(755979, 10)\n",
      "(738927, 15)\n"
     ]
    }
   ],
   "source": [
    "print(np.concatenate(tica_coords).shape)\n",
    "print(np.concatenate(pnas_coords).shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from plots import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_data_vs_data(np.concatenate(tica_coords), np.concatenate(pnas_coords), tica_names, pnas_names, analysis_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "subsampled_features_dir = os.path.join(tica_dir, \"subsampled_features\")\n",
    "if not os.path.exists(subsampled_features_dir): os.makedirs(subsampled_features_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "feature_names = compat_verboseload(feature_residues_pkl)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/4dkl_R_for_conformation.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/5c1m.dataset\n",
      "2\n",
      "(1, 2408)\n",
      "(1, 2408)\n",
      "2408\n"
     ]
    }
   ],
   "source": [
    "ref_features = [load_file(f) for f in get_trajectory_files(ref_features_dir, \".dataset\")]\n",
    "print(len(ref_features))\n",
    "print(ref_features[0].shape)\n",
    "print(ref_features[1].shape)\n",
    "print(len(feature_names))\n",
    "ref_features = pd.DataFrame(ref_features[0], columns=[str(f) for f in feature_names])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Interpreting tIC 1\n",
      "feature_importances_df.shape\n",
      "(10, 5)\n",
      "residue_importances_df.shape\n",
      "(12, 2)\n",
      "             feature_name      res_i      res_j  importance  \\\n",
      "7  Lys233_Ca To Lys303_Ca  Lys233_Ca  Lys303_Ca   -0.380112   \n",
      "1  Ala304_Ca To Asn230_Ca  Ala304_Ca  Asn230_Ca    0.325877   \n",
      "2  Ala304_Ca To Lys233_Ca  Ala304_Ca  Lys233_Ca    0.306402   \n",
      "6  Ile308_Ca To Tyr299_Ca  Ile308_Ca  Tyr299_Ca    0.290794   \n",
      "5  Ile308_Ca To Trp318_Ca  Ile308_Ca  Trp318_Ca   -0.284625   \n",
      "3  Ala304_Ca To Tyr299_Ca  Ala304_Ca  Tyr299_Ca   -0.282444   \n",
      "0        Leu339 To Val334     Leu339     Val334    0.251023   \n",
      "9  Val236_Ca To Val300_Ca  Val236_Ca  Val300_Ca    0.222654   \n",
      "4  Ile301_Ca To Val236_Ca  Ile301_Ca  Val236_Ca   -0.214483   \n",
      "8  Lys303_Ca To Trp318_Ca  Lys303_Ca  Trp318_Ca    0.171570   \n",
      "\n",
      "                  feature  \n",
      "7  LYS233_CA to LYS303_CA  \n",
      "1  ALA304_CA to ASN230_CA  \n",
      "2  ALA304_CA to LYS233_CA  \n",
      "6  ILE308_CA to TYR299_CA  \n",
      "5  ILE308_CA to TRP318_CA  \n",
      "3  ALA304_CA to TYR299_CA  \n",
      "0        LEU339 to VAL334  \n",
      "9  VAL236_CA to VAL300_CA  \n",
      "4  ILE301_CA to VAL236_CA  \n",
      "8  LYS303_CA to TRP318_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Asn230_Ca  Asn230_Ca    0.325877\n",
      "Ala304_Ca  Ala304_Ca    0.323930\n",
      "Lys233_Ca  Lys233_Ca    0.272077\n",
      "Tyr299_Ca  Tyr299_Ca    0.262132\n",
      "Ile308_Ca  Ile308_Ca    0.262023\n",
      "Val334        Val334    0.251023\n",
      "Leu339        Leu339    0.251023\n",
      "Val300_Ca  Val300_Ca    0.222654\n",
      "Ile301_Ca  Ile301_Ca   -0.214483\n",
      "Val236_Ca  Val236_Ca    0.200797\n",
      "Trp318_Ca  Trp318_Ca    0.148760\n",
      "Lys303_Ca  Lys303_Ca    0.143986\n",
      "Using dark_background\n",
      "Interpreting tIC 2\n",
      "feature_importances_df.shape\n",
      "(8, 5)\n",
      "residue_importances_df.shape\n",
      "(16, 2)\n",
      "             feature_name      res_i      res_j  importance  \\\n",
      "0         Leu88 To Phe338      Leu88     Phe338    0.434772   \n",
      "2  Ala304_Ca To Asn230_Ca  Ala304_Ca  Asn230_Ca   -0.296001   \n",
      "4  Leu339_Ca To Val334_Ca  Leu339_Ca  Val334_Ca    0.232692   \n",
      "6   Phe338_Ca To Phe84_Ca  Phe338_Ca   Phe84_Ca    0.142109   \n",
      "3  Asn328_Ca To Ile155_Ca  Asn328_Ca  Ile155_Ca    0.110870   \n",
      "5  Phe289_Ca To Tyr336_Ca  Phe289_Ca  Tyr336_Ca    0.097682   \n",
      "1  Ala111_Ca To Asn332_Ca  Ala111_Ca  Asn332_Ca    0.068724   \n",
      "7   Ser329_Ca To Val81_Ca  Ser329_Ca   Val81_Ca    0.062663   \n",
      "\n",
      "                  feature  \n",
      "0         LEU88 to PHE338  \n",
      "2  ALA304_CA to ASN230_CA  \n",
      "4  LEU339_CA to VAL334_CA  \n",
      "6   PHE338_CA to PHE84_CA  \n",
      "3  ASN328_CA to ILE155_CA  \n",
      "5  PHE289_CA to TYR336_CA  \n",
      "1  ALA111_CA to ASN332_CA  \n",
      "7   SER329_CA to VAL81_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Phe338        Phe338    0.434772\n",
      "Leu88          Leu88    0.434772\n",
      "Asn230_Ca  Asn230_Ca   -0.296001\n",
      "Ala304_Ca  Ala304_Ca   -0.296001\n",
      "Val334_Ca  Val334_Ca    0.232692\n",
      "Leu339_Ca  Leu339_Ca    0.232692\n",
      "Phe84_Ca    Phe84_Ca    0.142109\n",
      "Phe338_Ca  Phe338_Ca    0.142109\n",
      "Ile155_Ca  Ile155_Ca    0.110870\n",
      "Asn328_Ca  Asn328_Ca    0.110870\n",
      "Tyr336_Ca  Tyr336_Ca    0.097682\n",
      "Phe289_Ca  Phe289_Ca    0.097682\n",
      "Asn332_Ca  Asn332_Ca    0.068724\n",
      "Ala111_Ca  Ala111_Ca    0.068724\n",
      "Val81_Ca    Val81_Ca    0.062663\n",
      "Ser329_Ca  Ser329_Ca    0.062663\n",
      "Using dark_background\n",
      "Interpreting tIC 3\n",
      "feature_importances_df.shape\n",
      "(15, 5)\n",
      "residue_importances_df.shape\n",
      "(21, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "0         Ala304 To Asn230     Ala304     Asn230    0.430344   \n",
      "4   Ala304_Ca To Glu229_Ca  Ala304_Ca  Glu229_Ca   -0.361428   \n",
      "8   Ile301_Ca To Val236_Ca  Ile301_Ca  Val236_Ca   -0.352829   \n",
      "7   Ile301_Ca To Phe237_Ca  Ile301_Ca  Phe237_Ca    0.317058   \n",
      "14  Val236_Ca To Val300_Ca  Val236_Ca  Val300_Ca   -0.290237   \n",
      "3         Lys233 To Val300     Lys233     Val300    0.252101   \n",
      "9   Leu232_Ca To Phe237_Ca  Leu232_Ca  Phe237_Ca   -0.233917   \n",
      "6   Arg280_Ca To Phe338_Ca  Arg280_Ca  Phe338_Ca   -0.225227   \n",
      "11  Lys233_Ca To Val300_Ca  Lys233_Ca  Val300_Ca    0.198210   \n",
      "5   Ala304_Ca To Tyr299_Ca  Ala304_Ca  Tyr299_Ca    0.141234   \n",
      "10  Lys233_Ca To Lys303_Ca  Lys233_Ca  Lys303_Ca    0.136402   \n",
      "1         Ala304 To Lys233     Ala304     Lys233    0.122657   \n",
      "12   Pro333_Ca To Val81_Ca  Pro333_Ca   Val81_Ca    0.118268   \n",
      "2         Leu305 To Val300     Leu305     Val300   -0.114106   \n",
      "13  Tyr336_Ca To Val285_Ca  Tyr336_Ca  Val285_Ca    0.111286   \n",
      "\n",
      "                   feature  \n",
      "0         ALA304 to ASN230  \n",
      "4   ALA304_CA to GLU229_CA  \n",
      "8   ILE301_CA to VAL236_CA  \n",
      "7   ILE301_CA to PHE237_CA  \n",
      "14  VAL236_CA to VAL300_CA  \n",
      "3         LYS233 to VAL300  \n",
      "9   LEU232_CA to PHE237_CA  \n",
      "6   ARG280_CA to PHE338_CA  \n",
      "11  LYS233_CA to VAL300_CA  \n",
      "5   ALA304_CA to TYR299_CA  \n",
      "10  LYS233_CA to LYS303_CA  \n",
      "1         ALA304 to LYS233  \n",
      "12   PRO333_CA to VAL81_CA  \n",
      "2         LEU305 to VAL300  \n",
      "13  TYR336_CA to VAL285_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Asn230        Asn230    0.430344\n",
      "Ala304        Ala304    0.414960\n",
      "Glu229_Ca  Glu229_Ca   -0.361428\n",
      "Val236_Ca  Val236_Ca   -0.293366\n",
      "Phe237_Ca  Phe237_Ca    0.289509\n",
      "Ile301_Ca  Ile301_Ca    0.283564\n",
      "Lys233        Lys233    0.245629\n",
      "Leu232_Ca  Leu232_Ca   -0.233917\n",
      "Val300        Val300    0.233791\n",
      "Phe338_Ca  Phe338_Ca   -0.225227\n",
      "Arg280_Ca  Arg280_Ca   -0.225227\n",
      "Lys233_Ca  Lys233_Ca    0.195119\n",
      "Val300_Ca  Val300_Ca    0.173787\n",
      "Tyr299_Ca  Tyr299_Ca    0.141234\n",
      "Lys303_Ca  Lys303_Ca    0.136402\n",
      "Pro333_Ca  Pro333_Ca    0.118268\n",
      "Val81_Ca    Val81_Ca    0.118268\n",
      "Ala304_Ca  Ala304_Ca    0.116101\n",
      "Leu305        Leu305   -0.114106\n",
      "Tyr336_Ca  Tyr336_Ca    0.111286\n",
      "Val285_Ca  Val285_Ca    0.111286\n",
      "Using dark_background\n",
      "Interpreting tIC 4\n",
      "feature_importances_df.shape\n",
      "(18, 5)\n",
      "residue_importances_df.shape\n",
      "(30, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "9   Asp340_Ca To Ile278_Ca  Asp340_Ca  Ile278_Ca   -0.300659   \n",
      "1         Cys159 To Tyr336     Cys159     Tyr336   -0.277281   \n",
      "6   Arg277_Ca To Asp340_Ca  Arg277_Ca  Asp340_Ca    0.252329   \n",
      "7   Arg280_Ca To Glu341_Ca  Arg280_Ca  Glu341_Ca    0.196026   \n",
      "11   His319_Ca To Tyr75_Ca  His319_Ca   Tyr75_Ca   -0.181141   \n",
      "5         Phe289 To Tyr336     Phe289     Tyr336   -0.165437   \n",
      "12   Ile71_Ca To Phe320_Ca   Ile71_Ca  Phe320_Ca   -0.161613   \n",
      "4          Ile71 To Tyr128      Ile71     Tyr128    0.141940   \n",
      "17   Tyr326_Ca To Val78_Ca  Tyr326_Ca   Val78_Ca    0.135542   \n",
      "3          Gly82 To Tyr326      Gly82     Tyr326   -0.130659   \n",
      "13  Leu158_Ca To Val285_Ca  Leu158_Ca  Val285_Ca    0.120677   \n",
      "14  Ser119_Ca To Tyr326_Ca  Ser119_Ca  Tyr326_Ca    0.117934   \n",
      "16  Trp293_Ca To Val288_Ca  Trp293_Ca  Val288_Ca    0.093417   \n",
      "2          Cys79 To Tyr326      Cys79     Tyr326   -0.088631   \n",
      "8    Asn86_Ca To Ser329_Ca   Asn86_Ca  Ser329_Ca    0.082114   \n",
      "0         Asp147 To Tyr326     Asp147     Tyr326    0.081705   \n",
      "15   Ser329_Ca To Val81_Ca  Ser329_Ca   Val81_Ca    0.076892   \n",
      "10   Cys330_Ca To Gly82_Ca  Cys330_Ca   Gly82_Ca    0.071798   \n",
      "\n",
      "                   feature  \n",
      "9   ASP340_CA to ILE278_CA  \n",
      "1         CYS159 to TYR336  \n",
      "6   ARG277_CA to ASP340_CA  \n",
      "7   ARG280_CA to GLU341_CA  \n",
      "11   HIS319_CA to TYR75_CA  \n",
      "5         PHE289 to TYR336  \n",
      "12   ILE71_CA to PHE320_CA  \n",
      "4          ILE71 to TYR128  \n",
      "17   TYR326_CA to VAL78_CA  \n",
      "3          GLY82 to TYR326  \n",
      "13  LEU158_CA to VAL285_CA  \n",
      "14  SER119_CA to TYR326_CA  \n",
      "16  TRP293_CA to VAL288_CA  \n",
      "2          CYS79 to TYR326  \n",
      "8    ASN86_CA to SER329_CA  \n",
      "0         ASP147 to TYR326  \n",
      "15   SER329_CA to VAL81_CA  \n",
      "10   CYS330_CA to GLY82_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Ile278_Ca  Ile278_Ca   -0.300659\n",
      "Cys159        Cys159   -0.277281\n",
      "Arg277_Ca  Arg277_Ca    0.252329\n",
      "Asp340_Ca  Asp340_Ca    0.224679\n",
      "Arg280_Ca  Arg280_Ca    0.196026\n",
      "Glu341_Ca  Glu341_Ca    0.196026\n",
      "Tyr75_Ca    Tyr75_Ca   -0.181141\n",
      "His319_Ca  His319_Ca   -0.181141\n",
      "Tyr336        Tyr336   -0.171029\n",
      "Phe289        Phe289   -0.165437\n",
      "Phe320_Ca  Phe320_Ca   -0.161613\n",
      "Ile71_Ca    Ile71_Ca   -0.161613\n",
      "Tyr128        Tyr128    0.141940\n",
      "Ile71          Ile71    0.141940\n",
      "Val78_Ca    Val78_Ca    0.135542\n",
      "Tyr326_Ca  Tyr326_Ca    0.134661\n",
      "Gly82          Gly82   -0.130659\n",
      "Leu158_Ca  Leu158_Ca    0.120677\n",
      "Val285_Ca  Val285_Ca    0.120677\n",
      "Ser119_Ca  Ser119_Ca    0.117934\n",
      "Val288_Ca  Val288_Ca    0.093417\n",
      "Trp293_Ca  Trp293_Ca    0.093417\n",
      "Cys79          Cys79   -0.088631\n",
      "Asn86_Ca    Asn86_Ca    0.082114\n",
      "Ser329_Ca  Ser329_Ca    0.081853\n",
      "Asp147        Asp147    0.081705\n",
      "Val81_Ca    Val81_Ca    0.076892\n",
      "Cys330_Ca  Cys330_Ca    0.071798\n",
      "Gly82_Ca    Gly82_Ca    0.071798\n",
      "Tyr326        Tyr326    0.064672\n",
      "Using dark_background\n",
      "Interpreting tIC 5\n",
      "feature_importances_df.shape\n",
      "(19, 5)\n",
      "residue_importances_df.shape\n",
      "(30, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "18  Tyr336_Ca To Val286_Ca  Tyr336_Ca  Val286_Ca    1.011800   \n",
      "12  Leu158_Ca To Val285_Ca  Leu158_Ca  Val285_Ca    0.739674   \n",
      "17  Tyr336_Ca To Val285_Ca  Tyr336_Ca  Val285_Ca   -0.673830   \n",
      "13  Leu158_Ca To Val286_Ca  Leu158_Ca  Val286_Ca   -0.475162   \n",
      "16  Tyr252_Ca To Val286_Ca  Tyr252_Ca  Val286_Ca    0.446082   \n",
      "3   Ala287_Ca To Tyr252_Ca  Ala287_Ca  Tyr252_Ca   -0.341441   \n",
      "5   Arg280_Ca To Phe338_Ca  Arg280_Ca  Phe338_Ca    0.263789   \n",
      "6   Cys159_Ca To Tyr336_Ca  Cys159_Ca  Tyr336_Ca   -0.258376   \n",
      "15  Thr279_Ca To Val284_Ca  Thr279_Ca  Val284_Ca   -0.217152   \n",
      "4   Arg280_Ca To Leu339_Ca  Arg280_Ca  Leu339_Ca   -0.214627   \n",
      "9   Ile155_Ca To Ile290_Ca  Ile155_Ca  Ile290_Ca   -0.207729   \n",
      "10  Ile278_Ca To Leu283_Ca  Ile278_Ca  Leu283_Ca   -0.177243   \n",
      "8    His319_Ca To Thr67_Ca  His319_Ca   Thr67_Ca    0.168867   \n",
      "0         Arg280 To Val285     Arg280     Val285    0.152716   \n",
      "1         Asp114 To Tyr336     Asp114     Tyr336    0.135257   \n",
      "2         Trp293 To Tyr326     Trp293     Tyr326   -0.127651   \n",
      "14  Met161_Ca To Val282_Ca  Met161_Ca  Val282_Ca   -0.104470   \n",
      "7   Glu229_Ca To Leu219_Ca  Glu229_Ca  Leu219_Ca    0.100676   \n",
      "11   Ile322_Ca To Val78_Ca  Ile322_Ca   Val78_Ca    0.078645   \n",
      "\n",
      "                   feature  \n",
      "18  TYR336_CA to VAL286_CA  \n",
      "12  LEU158_CA to VAL285_CA  \n",
      "17  TYR336_CA to VAL285_CA  \n",
      "13  LEU158_CA to VAL286_CA  \n",
      "16  TYR252_CA to VAL286_CA  \n",
      "3   ALA287_CA to TYR252_CA  \n",
      "5   ARG280_CA to PHE338_CA  \n",
      "6   CYS159_CA to TYR336_CA  \n",
      "15  THR279_CA to VAL284_CA  \n",
      "4   ARG280_CA to LEU339_CA  \n",
      "9   ILE155_CA to ILE290_CA  \n",
      "10  ILE278_CA to LEU283_CA  \n",
      "8    HIS319_CA to THR67_CA  \n",
      "0         ARG280 to VAL285  \n",
      "1         ASP114 to TYR336  \n",
      "2         TRP293 to TYR326  \n",
      "14  MET161_CA to VAL282_CA  \n",
      "7   GLU229_CA to LEU219_CA  \n",
      "11   ILE322_CA to VAL78_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Val286_Ca  Val286_Ca    0.955228\n",
      "Tyr336_Ca  Tyr336_Ca    0.884782\n",
      "Leu158_Ca  Leu158_Ca    0.678933\n",
      "Val285_Ca  Val285_Ca    0.668999\n",
      "Tyr252_Ca  Tyr252_Ca    0.406706\n",
      "Ala287_Ca  Ala287_Ca   -0.341441\n",
      "Phe338_Ca  Phe338_Ca    0.263789\n",
      "Cys159_Ca  Cys159_Ca   -0.258376\n",
      "Arg280_Ca  Arg280_Ca    0.239868\n",
      "Thr279_Ca  Thr279_Ca   -0.217152\n",
      "Val284_Ca  Val284_Ca   -0.217152\n",
      "Leu339_Ca  Leu339_Ca   -0.214627\n",
      "Ile290_Ca  Ile290_Ca   -0.207729\n",
      "Ile155_Ca  Ile155_Ca   -0.207729\n",
      "Ile278_Ca  Ile278_Ca   -0.177243\n",
      "Leu283_Ca  Leu283_Ca   -0.177243\n",
      "Thr67_Ca    Thr67_Ca    0.168867\n",
      "His319_Ca  His319_Ca    0.168867\n",
      "Val285        Val285    0.152716\n",
      "Arg280        Arg280    0.152716\n",
      "Tyr336        Tyr336    0.135257\n",
      "Asp114        Asp114    0.135257\n",
      "Tyr326        Tyr326   -0.127651\n",
      "Trp293        Trp293   -0.127651\n",
      "Met161_Ca  Met161_Ca   -0.104470\n",
      "Val282_Ca  Val282_Ca   -0.104470\n",
      "Glu229_Ca  Glu229_Ca    0.100676\n",
      "Leu219_Ca  Leu219_Ca    0.100676\n",
      "Ile322_Ca  Ile322_Ca    0.078645\n",
      "Val78_Ca    Val78_Ca    0.078645\n",
      "Using dark_background\n",
      "Interpreting tIC 6\n",
      "feature_importances_df.shape\n",
      "(23, 5)\n",
      "residue_importances_df.shape\n",
      "(37, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "16  Leu158_Ca To Val285_Ca  Leu158_Ca  Val285_Ca   -0.290031   \n",
      "17  Leu158_Ca To Val286_Ca  Leu158_Ca  Val286_Ca    0.256093   \n",
      "14   Ile71_Ca To Thr312_Ca   Ile71_Ca  Thr312_Ca    0.251472   \n",
      "12   His319_Ca To Tyr75_Ca  His319_Ca   Tyr75_Ca   -0.213358   \n",
      "13  Ile146_Ca To Met203_Ca  Ile146_Ca  Met203_Ca    0.190060   \n",
      "21   Pro333_Ca To Val81_Ca  Pro333_Ca   Val81_Ca   -0.183692   \n",
      "10  Asp340_Ca To Pro333_Ca  Asp340_Ca  Pro333_Ca   -0.178046   \n",
      "4         Phe135 To Thr208     Phe135     Thr208    0.174408   \n",
      "20  Met203_Ca To Tyr149_Ca  Met203_Ca  Tyr149_Ca   -0.166275   \n",
      "15   Leu121_Ca To Tyr75_Ca  Leu121_Ca   Tyr75_Ca    0.163256   \n",
      "0          Ala68 To Tyr128      Ala68     Tyr128    0.159714   \n",
      "3          Ile71 To Tyr128      Ile71     Tyr128    0.159333   \n",
      "7         Ser317 To Thr312     Ser317     Thr312    0.157976   \n",
      "8          Trp318 To Tyr75     Trp318      Tyr75    0.157397   \n",
      "6         Ser162 To Tyr336     Ser162     Tyr336    0.131901   \n",
      "11  Cys217_Ca To Thr208_Ca  Cys217_Ca  Thr208_Ca    0.119780   \n",
      "22   Tyr326_Ca To Val78_Ca  Tyr326_Ca   Val78_Ca    0.115754   \n",
      "19  Lys233_Ca To Tyr148_Ca  Lys233_Ca  Tyr148_Ca   -0.111157   \n",
      "18  Leu231_Ca To Val236_Ca  Leu231_Ca  Val236_Ca   -0.110378   \n",
      "2          Cys79 To Tyr326      Cys79     Tyr326   -0.106886   \n",
      "5          Pro122 To Tyr75     Pro122      Tyr75   -0.098548   \n",
      "9   Asp114_Ca To Pro333_Ca  Asp114_Ca  Pro333_Ca    0.096611   \n",
      "1          Cys79 To Pro122      Cys79     Pro122    0.089013   \n",
      "\n",
      "                   feature  \n",
      "16  LEU158_CA to VAL285_CA  \n",
      "17  LEU158_CA to VAL286_CA  \n",
      "14   ILE71_CA to THR312_CA  \n",
      "12   HIS319_CA to TYR75_CA  \n",
      "13  ILE146_CA to MET203_CA  \n",
      "21   PRO333_CA to VAL81_CA  \n",
      "10  ASP340_CA to PRO333_CA  \n",
      "4         PHE135 to THR208  \n",
      "20  MET203_CA to TYR149_CA  \n",
      "15   LEU121_CA to TYR75_CA  \n",
      "0          ALA68 to TYR128  \n",
      "3          ILE71 to TYR128  \n",
      "7         SER317 to THR312  \n",
      "8          TRP318 to TYR75  \n",
      "6         SER162 to TYR336  \n",
      "11  CYS217_CA to THR208_CA  \n",
      "22   TYR326_CA to VAL78_CA  \n",
      "19  LYS233_CA to TYR148_CA  \n",
      "18  LEU231_CA to VAL236_CA  \n",
      "2          CYS79 to TYR326  \n",
      "5          PRO122 to TYR75  \n",
      "9   ASP114_CA to PRO333_CA  \n",
      "1          CYS79 to PRO122  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Val285_Ca  Val285_Ca   -0.290031\n",
      "Val286_Ca  Val286_Ca    0.256093\n",
      "Thr312_Ca  Thr312_Ca    0.251472\n",
      "Ile71_Ca    Ile71_Ca    0.251472\n",
      "Leu158_Ca  Leu158_Ca    0.228787\n",
      "His319_Ca  His319_Ca   -0.213358\n",
      "Ile146_Ca  Ile146_Ca    0.190060\n",
      "Val81_Ca    Val81_Ca   -0.183692\n",
      "Asp340_Ca  Asp340_Ca   -0.178046\n",
      "Phe135        Phe135    0.174408\n",
      "Thr208        Thr208    0.174408\n",
      "Met203_Ca  Met203_Ca    0.172243\n",
      "Tyr149_Ca  Tyr149_Ca   -0.166275\n",
      "Leu121_Ca  Leu121_Ca    0.163256\n",
      "Ala68          Ala68    0.159714\n",
      "Tyr128        Tyr128    0.159695\n",
      "Ile71          Ile71    0.159333\n",
      "Thr312        Thr312    0.157976\n",
      "Ser317        Ser317    0.157976\n",
      "Trp318        Trp318    0.157397\n",
      "Tyr75          Tyr75    0.144599\n",
      "Tyr75_Ca    Tyr75_Ca    0.144425\n",
      "Ser162        Ser162    0.131901\n",
      "Tyr336        Tyr336    0.131901\n",
      "Thr208_Ca  Thr208_Ca    0.119780\n",
      "Cys217_Ca  Cys217_Ca    0.119780\n",
      "Tyr326_Ca  Tyr326_Ca    0.115754\n",
      "Val78_Ca    Val78_Ca    0.115754\n",
      "Lys233_Ca  Lys233_Ca   -0.111157\n",
      "Tyr148_Ca  Tyr148_Ca   -0.111157\n",
      "Leu231_Ca  Leu231_Ca   -0.110378\n",
      "Val236_Ca  Val236_Ca   -0.110378\n",
      "Tyr326        Tyr326   -0.106886\n",
      "Asp114_Ca  Asp114_Ca    0.096611\n",
      "Pro122        Pro122    0.079635\n",
      "Cys79          Cys79    0.079218\n",
      "Pro333_Ca  Pro333_Ca    0.069145\n",
      "Using dark_background\n",
      "Interpreting tIC 7\n",
      "feature_importances_df.shape\n",
      "(30, 5)\n",
      "residue_importances_df.shape\n",
      "(50, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "3          Gly82 To Tyr326      Gly82     Tyr326    0.450765   \n",
      "15   Gly82_Ca To Tyr326_Ca   Gly82_Ca  Tyr326_Ca   -0.362602   \n",
      "19  Ile301_Ca To Val236_Ca  Ile301_Ca  Val236_Ca   -0.284568   \n",
      "5         Phe289 To Pro244     Phe289     Pro244    0.272065   \n",
      "18  Ile301_Ca To Phe237_Ca  Ile301_Ca  Phe237_Ca    0.262713   \n",
      "10  Asn230_Ca To Cys235_Ca  Asn230_Ca  Cys235_Ca    0.258898   \n",
      "27   Pro333_Ca To Val81_Ca  Pro333_Ca   Val81_Ca    0.243900   \n",
      "25  Phe289_Ca To Pro244_Ca  Phe289_Ca  Pro244_Ca   -0.211463   \n",
      "20   Ile71_Ca To Phe320_Ca   Ile71_Ca  Phe320_Ca   -0.210253   \n",
      "9   Asn150_Ca To Ser329_Ca  Asn150_Ca  Ser329_Ca   -0.195692   \n",
      "2         Gln314 To Tyr299     Gln314     Tyr299    0.191163   \n",
      "21  Leu231_Ca To Val236_Ca  Leu231_Ca  Val236_Ca    0.180551   \n",
      "26  Pro309_Ca To Thr315_Ca  Pro309_Ca  Thr315_Ca   -0.167726   \n",
      "24  Met281_Ca To Thr103_Ca  Met281_Ca  Thr103_Ca   -0.158102   \n",
      "28   Ser329_Ca To Val81_Ca  Ser329_Ca   Val81_Ca   -0.142810   \n",
      "8   Asn150_Ca To Ser145_Ca  Asn150_Ca  Ser145_Ca   -0.142653   \n",
      "29  Tyr336_Ca To Val286_Ca  Tyr336_Ca  Val286_Ca   -0.141577   \n",
      "6   Ala113_Ca To Asn150_Ca  Ala113_Ca  Asn150_Ca    0.131244   \n",
      "17  Ile146_Ca To Met151_Ca  Ile146_Ca  Met151_Ca   -0.126516   \n",
      "7   Ala113_Ca To Met151_Ca  Ala113_Ca  Met151_Ca   -0.120281   \n",
      "14  Glu310_Ca To Thr315_Ca  Glu310_Ca  Thr315_Ca    0.119110   \n",
      "12  Cys217_Ca To Thr208_Ca  Cys217_Ca  Thr208_Ca    0.113860   \n",
      "13   Cys330_Ca To Gly82_Ca  Cys330_Ca   Gly82_Ca   -0.111805   \n",
      "22  Leu335_Ca To Val288_Ca  Leu335_Ca  Val288_Ca    0.102569   \n",
      "0         Ala117 To Asn150     Ala117     Asn150    0.099639   \n",
      "11  Asp216_Ca To Lys209_Ca  Asp216_Ca  Lys209_Ca    0.095681   \n",
      "1         Asp216 To Thr207     Asp216     Thr207    0.082960   \n",
      "4          Leu129 To Met72     Leu129      Met72    0.082044   \n",
      "16  His297_Ca To Lys233_Ca  His297_Ca  Lys233_Ca   -0.081567   \n",
      "23  Lys141_Ca To Thr207_Ca  Lys141_Ca  Thr207_Ca    0.071360   \n",
      "\n",
      "                   feature  \n",
      "3          GLY82 to TYR326  \n",
      "15   GLY82_CA to TYR326_CA  \n",
      "19  ILE301_CA to VAL236_CA  \n",
      "5         PHE289 to PRO244  \n",
      "18  ILE301_CA to PHE237_CA  \n",
      "10  ASN230_CA to CYS235_CA  \n",
      "27   PRO333_CA to VAL81_CA  \n",
      "25  PHE289_CA to PRO244_CA  \n",
      "20   ILE71_CA to PHE320_CA  \n",
      "9   ASN150_CA to SER329_CA  \n",
      "2         GLN314 to TYR299  \n",
      "21  LEU231_CA to VAL236_CA  \n",
      "26  PRO309_CA to THR315_CA  \n",
      "24  MET281_CA to THR103_CA  \n",
      "28   SER329_CA to VAL81_CA  \n",
      "8   ASN150_CA to SER145_CA  \n",
      "29  TYR336_CA to VAL286_CA  \n",
      "6   ALA113_CA to ASN150_CA  \n",
      "17  ILE146_CA to MET151_CA  \n",
      "7   ALA113_CA to MET151_CA  \n",
      "14  GLU310_CA to THR315_CA  \n",
      "12  CYS217_CA to THR208_CA  \n",
      "13   CYS330_CA to GLY82_CA  \n",
      "22  LEU335_CA to VAL288_CA  \n",
      "0         ALA117 to ASN150  \n",
      "11  ASP216_CA to LYS209_CA  \n",
      "1         ASP216 to THR207  \n",
      "4          LEU129 to MET72  \n",
      "16  HIS297_CA to LYS233_CA  \n",
      "23  LYS141_CA to THR207_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Tyr326        Tyr326    0.450765\n",
      "Gly82          Gly82    0.450765\n",
      "Tyr326_Ca  Tyr326_Ca   -0.362602\n",
      "Phe289        Phe289    0.272065\n",
      "Pro244        Pro244    0.272065\n",
      "Phe237_Ca  Phe237_Ca    0.262713\n",
      "Cys235_Ca  Cys235_Ca    0.258898\n",
      "Asn230_Ca  Asn230_Ca    0.258898\n",
      "Pro333_Ca  Pro333_Ca    0.243900\n",
      "Ile301_Ca  Ile301_Ca    0.235349\n",
      "Val81_Ca    Val81_Ca    0.224564\n",
      "Phe289_Ca  Phe289_Ca   -0.211463\n",
      "Pro244_Ca  Pro244_Ca   -0.211463\n",
      "Phe320_Ca  Phe320_Ca   -0.210253\n",
      "Ile71_Ca    Ile71_Ca   -0.210253\n",
      "Gln314        Gln314    0.191163\n",
      "Tyr299        Tyr299    0.191163\n",
      "Leu231_Ca  Leu231_Ca    0.180551\n",
      "Pro309_Ca  Pro309_Ca   -0.167726\n",
      "Met281_Ca  Met281_Ca   -0.158102\n",
      "Thr103_Ca  Thr103_Ca   -0.158102\n",
      "Val236_Ca  Val236_Ca    0.157295\n",
      "Ser329_Ca  Ser329_Ca   -0.145454\n",
      "Ser145_Ca  Ser145_Ca   -0.142653\n",
      "Tyr336_Ca  Tyr336_Ca   -0.141577\n",
      "Val286_Ca  Val286_Ca   -0.141577\n",
      "Ile146_Ca  Ile146_Ca   -0.126516\n",
      "Gly82_Ca    Gly82_Ca   -0.124345\n",
      "Met151_Ca  Met151_Ca   -0.120593\n",
      "Glu310_Ca  Glu310_Ca    0.119110\n",
      "Ala113_Ca  Ala113_Ca    0.118668\n",
      "Cys217_Ca  Cys217_Ca    0.113860\n",
      "Thr208_Ca  Thr208_Ca    0.113860\n",
      "Cys330_Ca  Cys330_Ca   -0.111805\n",
      "Thr315_Ca  Thr315_Ca    0.104768\n",
      "Asn150_Ca  Asn150_Ca    0.103854\n",
      "Leu335_Ca  Leu335_Ca    0.102569\n",
      "Val288_Ca  Val288_Ca    0.102569\n",
      "Asn150        Asn150    0.099639\n",
      "Ala117        Ala117    0.099639\n",
      "Lys209_Ca  Lys209_Ca    0.095681\n",
      "Asp216_Ca  Asp216_Ca    0.095681\n",
      "Thr207        Thr207    0.082960\n",
      "Asp216        Asp216    0.082960\n",
      "Met72          Met72    0.082044\n",
      "Leu129        Leu129    0.082044\n",
      "His297_Ca  His297_Ca   -0.081567\n",
      "Lys233_Ca  Lys233_Ca   -0.081567\n",
      "Lys141_Ca  Lys141_Ca    0.071360\n",
      "Thr207_Ca  Thr207_Ca    0.071360\n",
      "Using dark_background\n",
      "Interpreting tIC 8\n",
      "feature_importances_df.shape\n",
      "(17, 5)\n",
      "residue_importances_df.shape\n",
      "(24, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "16  Tyr336_Ca To Val286_Ca  Tyr336_Ca  Val286_Ca   -1.021619   \n",
      "15  Tyr336_Ca To Val285_Ca  Tyr336_Ca  Val285_Ca    0.652525   \n",
      "8   Arg280_Ca To Glu341_Ca  Arg280_Ca  Glu341_Ca   -0.571204   \n",
      "6   Arg277_Ca To Asp340_Ca  Arg277_Ca  Asp340_Ca   -0.558079   \n",
      "7   Arg277_Ca To Glu341_Ca  Arg277_Ca  Glu341_Ca    0.510331   \n",
      "13  Leu158_Ca To Val286_Ca  Leu158_Ca  Val286_Ca    0.508820   \n",
      "10  Asp340_Ca To Ile278_Ca  Asp340_Ca  Ile278_Ca    0.503623   \n",
      "12  Leu158_Ca To Val285_Ca  Leu158_Ca  Val285_Ca   -0.502696   \n",
      "5   Arg165_Ca To Thr279_Ca  Arg165_Ca  Thr279_Ca    0.390678   \n",
      "0          Asn86 To Tyr336      Asn86     Tyr336    0.366295   \n",
      "4   Arg165_Ca To Ile278_Ca  Arg165_Ca  Ile278_Ca   -0.312282   \n",
      "2         Leu335 To Phe289     Leu335     Phe289    0.193097   \n",
      "3         Ser317 To Thr312     Ser317     Thr312   -0.169266   \n",
      "14  Thr279_Ca To Val284_Ca  Thr279_Ca  Val284_Ca   -0.161332   \n",
      "9    Asn86_Ca To Ser329_Ca   Asn86_Ca  Ser329_Ca    0.154594   \n",
      "11  Cys321_Ca To Trp293_Ca  Cys321_Ca  Trp293_Ca    0.084349   \n",
      "1          Gly82 To Tyr326      Gly82     Tyr326   -0.066454   \n",
      "\n",
      "                   feature  \n",
      "16  TYR336_CA to VAL286_CA  \n",
      "15  TYR336_CA to VAL285_CA  \n",
      "8   ARG280_CA to GLU341_CA  \n",
      "6   ARG277_CA to ASP340_CA  \n",
      "7   ARG277_CA to GLU341_CA  \n",
      "13  LEU158_CA to VAL286_CA  \n",
      "10  ASP340_CA to ILE278_CA  \n",
      "12  LEU158_CA to VAL285_CA  \n",
      "5   ARG165_CA to THR279_CA  \n",
      "0          ASN86 to TYR336  \n",
      "4   ARG165_CA to ILE278_CA  \n",
      "2         LEU335 to PHE289  \n",
      "3         SER317 to THR312  \n",
      "14  THR279_CA to VAL284_CA  \n",
      "9    ASN86_CA to SER329_CA  \n",
      "11  CYS321_CA to TRP293_CA  \n",
      "1          GLY82 to TYR326  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Val285_Ca  Val285_Ca    0.594764\n",
      "Arg280_Ca  Arg280_Ca   -0.571204\n",
      "Tyr336_Ca  Tyr336_Ca    0.568817\n",
      "Ile278_Ca  Ile278_Ca    0.462828\n",
      "Leu158_Ca  Leu158_Ca    0.458244\n",
      "Arg277_Ca  Arg277_Ca    0.456910\n",
      "Glu341_Ca  Glu341_Ca    0.456254\n",
      "Asp340_Ca  Asp340_Ca    0.450538\n",
      "Val286_Ca  Val286_Ca    0.432298\n",
      "Asn86          Asn86    0.366295\n",
      "Tyr336        Tyr336    0.366295\n",
      "Thr279_Ca  Thr279_Ca    0.363077\n",
      "Arg165_Ca  Arg165_Ca    0.355530\n",
      "Phe289        Phe289    0.193097\n",
      "Leu335        Leu335    0.193097\n",
      "Thr312        Thr312   -0.169266\n",
      "Ser317        Ser317   -0.169266\n",
      "Val284_Ca  Val284_Ca   -0.161332\n",
      "Ser329_Ca  Ser329_Ca    0.154594\n",
      "Asn86_Ca    Asn86_Ca    0.154594\n",
      "Trp293_Ca  Trp293_Ca    0.084349\n",
      "Cys321_Ca  Cys321_Ca    0.084349\n",
      "Tyr326        Tyr326   -0.066454\n",
      "Gly82          Gly82   -0.066454\n",
      "Using dark_background\n",
      "Interpreting tIC 9\n",
      "feature_importances_df.shape\n",
      "(20, 5)\n",
      "residue_importances_df.shape\n",
      "(32, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "14  Glu229_Ca To Thr218_Ca  Glu229_Ca  Thr218_Ca    0.475962   \n",
      "13  Glu229_Ca To Leu219_Ca  Glu229_Ca  Leu219_Ca   -0.320567   \n",
      "0         Ala113 To Trp192     Ala113     Trp192    0.251497   \n",
      "11  Cys140_Ca To Leu219_Ca  Cys140_Ca  Leu219_Ca   -0.227881   \n",
      "4         His297 To Ile155     His297     Ile155   -0.222910   \n",
      "1         Arg280 To Phe338     Arg280     Phe338    0.215920   \n",
      "2         Asn150 To Phe289     Asn150     Phe289    0.208837   \n",
      "19   Thr315_Ca To Thr67_Ca  Thr315_Ca   Thr67_Ca    0.191768   \n",
      "6         His297 To Val236     His297     Val236   -0.176726   \n",
      "17  Phe123_Ca To Phe135_Ca  Phe123_Ca  Phe135_Ca   -0.166705   \n",
      "15  Ile256_Ca To Leu275_Ca  Ile256_Ca  Leu275_Ca    0.155848   \n",
      "16   Ile71_Ca To Thr312_Ca   Ile71_Ca  Thr312_Ca    0.144888   \n",
      "18   Pro333_Ca To Val81_Ca  Pro333_Ca   Val81_Ca    0.136917   \n",
      "10  Asp114_Ca To Pro333_Ca  Asp114_Ca  Pro333_Ca   -0.130924   \n",
      "3         Asp114 To Tyr336     Asp114     Tyr336    0.125096   \n",
      "9   Arg280_Ca To Ile256_Ca  Arg280_Ca  Ile256_Ca   -0.115556   \n",
      "7         Phe289 To Pro244     Phe289     Pro244    0.112876   \n",
      "5         His297 To Phe289     His297     Phe289   -0.089113   \n",
      "8   Ala113_Ca To Ile146_Ca  Ala113_Ca  Ile146_Ca   -0.068007   \n",
      "12  Cys321_Ca To Tyr299_Ca  Cys321_Ca  Tyr299_Ca   -0.061691   \n",
      "\n",
      "                   feature  \n",
      "14  GLU229_CA to THR218_CA  \n",
      "13  GLU229_CA to LEU219_CA  \n",
      "0         ALA113 to TRP192  \n",
      "11  CYS140_CA to LEU219_CA  \n",
      "4         HIS297 to ILE155  \n",
      "1         ARG280 to PHE338  \n",
      "2         ASN150 to PHE289  \n",
      "19   THR315_CA to THR67_CA  \n",
      "6         HIS297 to VAL236  \n",
      "17  PHE123_CA to PHE135_CA  \n",
      "15  ILE256_CA to LEU275_CA  \n",
      "16   ILE71_CA to THR312_CA  \n",
      "18   PRO333_CA to VAL81_CA  \n",
      "10  ASP114_CA to PRO333_CA  \n",
      "3         ASP114 to TYR336  \n",
      "9   ARG280_CA to ILE256_CA  \n",
      "7         PHE289 to PRO244  \n",
      "5         HIS297 to PHE289  \n",
      "8   ALA113_CA to ILE146_CA  \n",
      "12  CYS321_CA to TYR299_CA  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Thr218_Ca  Thr218_Ca    0.475962\n",
      "Glu229_Ca  Glu229_Ca    0.436135\n",
      "Ala113        Ala113    0.251497\n",
      "Trp192        Trp192    0.251497\n",
      "Leu219_Ca  Leu219_Ca   -0.232515\n",
      "Cys140_Ca  Cys140_Ca   -0.227881\n",
      "Ile155        Ile155   -0.222910\n",
      "Arg280        Arg280    0.215920\n",
      "Phe338        Phe338    0.215920\n",
      "Asn150        Asn150    0.208837\n",
      "Phe289        Phe289    0.199241\n",
      "Thr315_Ca  Thr315_Ca    0.191768\n",
      "Thr67_Ca    Thr67_Ca    0.191768\n",
      "Val236        Val236   -0.176726\n",
      "Phe135_Ca  Phe135_Ca   -0.166705\n",
      "Phe123_Ca  Phe123_Ca   -0.166705\n",
      "Leu275_Ca  Leu275_Ca    0.155848\n",
      "Thr312_Ca  Thr312_Ca    0.144888\n",
      "Ile71_Ca    Ile71_Ca    0.144888\n",
      "Ile256_Ca  Ile256_Ca    0.142278\n",
      "Val81_Ca    Val81_Ca    0.136917\n",
      "Asp114_Ca  Asp114_Ca   -0.130924\n",
      "Tyr336        Tyr336    0.125096\n",
      "Asp114        Asp114    0.125096\n",
      "Pro333_Ca  Pro333_Ca    0.123525\n",
      "Arg280_Ca  Arg280_Ca   -0.115556\n",
      "Pro244        Pro244    0.112876\n",
      "His297        His297   -0.097874\n",
      "Ala113_Ca  Ala113_Ca   -0.068007\n",
      "Ile146_Ca  Ile146_Ca   -0.068007\n",
      "Tyr299_Ca  Tyr299_Ca   -0.061691\n",
      "Cys321_Ca  Cys321_Ca   -0.061691\n",
      "Using dark_background\n",
      "Interpreting tIC 10\n",
      "feature_importances_df.shape\n",
      "(15, 5)\n",
      "residue_importances_df.shape\n",
      "(25, 2)\n",
      "              feature_name      res_i      res_j  importance  \\\n",
      "5         Tyr128 To Tyr326     Tyr128     Tyr326    0.992651   \n",
      "1         Ala240 To Trp293     Ala240     Trp293    0.428114   \n",
      "14  Tyr128_Ca To Tyr326_Ca  Tyr128_Ca  Tyr326_Ca   -0.409725   \n",
      "7   Ala240_Ca To Phe289_Ca  Ala240_Ca  Phe289_Ca   -0.298209   \n",
      "11  Leu339_Ca To Val282_Ca  Leu339_Ca  Val282_Ca    0.226152   \n",
      "3         Asp147 To Tyr326     Asp147     Tyr326    0.183398   \n",
      "12  Phe289_Ca To Thr294_Ca  Phe289_Ca  Thr294_Ca    0.183260   \n",
      "8   Arg280_Ca To Leu339_Ca  Arg280_Ca  Leu339_Ca   -0.178134   \n",
      "9    His319_Ca To Leu74_Ca  His319_Ca   Leu74_Ca    0.158605   \n",
      "4         Gln314 To Tyr299     Gln314     Tyr299    0.114364   \n",
      "13  Thr279_Ca To Val284_Ca  Thr279_Ca  Val284_Ca    0.111921   \n",
      "0         Ala117 To Tyr326     Ala117     Tyr326    0.089910   \n",
      "10  Ile256_Ca To Leu275_Ca  Ile256_Ca  Leu275_Ca    0.088965   \n",
      "6   Ala240_Ca To His297_Ca  Ala240_Ca  His297_Ca   -0.087478   \n",
      "2          Ala323 To Tyr75     Ala323      Tyr75    0.080185   \n",
      "\n",
      "                   feature  \n",
      "5         TYR128 to TYR326  \n",
      "1         ALA240 to TRP293  \n",
      "14  TYR128_CA to TYR326_CA  \n",
      "7   ALA240_CA to PHE289_CA  \n",
      "11  LEU339_CA to VAL282_CA  \n",
      "3         ASP147 to TYR326  \n",
      "12  PHE289_CA to THR294_CA  \n",
      "8   ARG280_CA to LEU339_CA  \n",
      "9    HIS319_CA to LEU74_CA  \n",
      "4         GLN314 to TYR299  \n",
      "13  THR279_CA to VAL284_CA  \n",
      "0         ALA117 to TYR326  \n",
      "10  ILE256_CA to LEU275_CA  \n",
      "6   ALA240_CA to HIS297_CA  \n",
      "2          ALA323 to TYR75  \n",
      "Using dark_background\n",
      "             residue  importance\n",
      "Tyr128        Tyr128    0.992651\n",
      "Tyr326        Tyr326    0.911725\n",
      "Ala240        Ala240    0.428114\n",
      "Trp293        Trp293    0.428114\n",
      "Tyr326_Ca  Tyr326_Ca   -0.409725\n",
      "Tyr128_Ca  Tyr128_Ca   -0.409725\n",
      "Val282_Ca  Val282_Ca    0.226152\n",
      "Leu339_Ca  Leu339_Ca    0.205937\n",
      "Asp147        Asp147    0.183398\n",
      "Thr294_Ca  Thr294_Ca    0.183260\n",
      "Arg280_Ca  Arg280_Ca   -0.178134\n",
      "Phe289_Ca  Phe289_Ca    0.159187\n",
      "His319_Ca  His319_Ca    0.158605\n",
      "Leu74_Ca    Leu74_Ca    0.158605\n",
      "Tyr299        Tyr299    0.114364\n",
      "Gln314        Gln314    0.114364\n",
      "Thr279_Ca  Thr279_Ca    0.111921\n",
      "Val284_Ca  Val284_Ca    0.111921\n",
      "Ala240_Ca  Ala240_Ca   -0.098015\n",
      "Ala117        Ala117    0.089910\n",
      "Ile256_Ca  Ile256_Ca    0.088965\n",
      "Leu275_Ca  Leu275_Ca    0.088965\n",
      "His297_Ca  His297_Ca   -0.087478\n",
      "Tyr75          Tyr75    0.080185\n",
      "Ala323        Ala323    0.080185\n",
      "Using dark_background\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fd533ec2550>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#import interpret_tICs\n",
    "#reload(interpret_tICs)\n",
    "#from interpret_tICs import *\n",
    "tic_components_dir = tica_dir\n",
    "important_contact_features = interpret_tIC_components(projection_operator_dir, tic_components_dir, feature_residues_pkl, n_tica_components=n_components, percentile=95)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import interpret_tICs\n",
    "reload(interpret_tICs)\n",
    "from interpret_tICs import *\n",
    "tic_subsampled_features_file = \"%s/features_subsampled.pkl\" % tica_dir\n",
    "subsampled_features_dir = os.path.join(tica_dir, \"subsampled_features\")\n",
    "if not os.path.exists(subsampled_features_dir): os.makedirs(subsampled_features_dir)\n",
    "important_contact_features_pruned, important_contact_features_indices = find_non_zero_features(important_contact_features[0], feature_names)\n",
    "if not os.path.exists(tic_subsampled_features_file):\n",
    "    subsample_features(features_dir, important_contact_features_indices, important_contact_features_pruned, tic_subsampled_features_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/features_subsampled.pkl'"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tic_subsampled_features_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/features_subsampled.pkl\n"
     ]
    }
   ],
   "source": [
    "protein_top_features = load_file(tic_subsampled_features_file)\n",
    "protein_top_features_concat = pd.concat(protein_top_features)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.scatter(protein_top_features_concat[\"LEU158_CA to VAL285_CA\"].values[::1000], protein_top_features_concat[\"PHE289 to TYR336\"].values[::1000])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from ipyparallel import Client\n",
    "rc = Client()\n",
    "dview = rc[:]\n",
    "dview.map(os.chdir, ['/home/enf/b2ar_analysis/conformation']*len(rc.ids))\n",
    "\n",
    "print(len(rc.ids))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/user_defined_features.h5\n"
     ]
    }
   ],
   "source": [
    "bu72_trajs = []\n",
    "apo_trajs = []\n",
    "oxy_trajs = []\n",
    "suf_trajs = []\n",
    "trv_trajs = []\n",
    "f338a_trajs = []\n",
    "trajs = get_trajectory_files(traj_dir, \".h5\")\n",
    "#trajs = [t for t in get_trajectory_files(traj_dir, traj_ext) if \"apo_reimaged\" not in t and \"oxy\" not in t]\n",
    "for i, traj in enumerate(trajs):\n",
    "    if \"bu72\" in traj or \"CO\" in traj or \"Co\" in traj:\n",
    "        bu72_trajs.append(i)\n",
    "    elif \"apo\" in traj:\n",
    "        apo_trajs.append(i)\n",
    "    elif \"oxy\" in traj:\n",
    "        oxy_trajs.append(i)\n",
    "    elif \"suf\" in traj:\n",
    "        suf_trajs.append(i)\n",
    "    elif \"trv\" in traj:\n",
    "        trv_trajs.append(i)\n",
    "    elif \"f338a\" in traj:\n",
    "        f338a_trajs.append(i)\n",
    "\n",
    "user_defined_coords = load_file(user_defined_features_file)\n",
    "\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "58"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(f338a_trajs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "bu72_pnas = [user_defined_coords[i] for i in bu72_trajs]\n",
    "apo_pnas = [user_defined_coords[i] for i in apo_trajs]\n",
    "oxy_pnas = [user_defined_coords[i] for i in oxy_trajs]\n",
    "suf_pnas = [user_defined_coords[i] for i in suf_trajs]\n",
    "f338a_pnas = [user_defined_coords[i] for i in f338a_trajs]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_pnas_file = \"%s/bu72.h5\" % whole_trajectory_pnas\n",
    "apo_pnas_file = \"%s/apo.h5\" % whole_trajectory_pnas\n",
    "#oxy_pnas_file = \"%s/oxy.h5\" % whole_trajectory_pnas\n",
    "suf_pnas_file = \"%s/suf.h5\" % whole_trajectory_pnas\n",
    "f338a_pnas_file = \"%s/f338a.h5\" % whole_trajectory_pnas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(248499, 15)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/bu72.h5\"... (<class 'list'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/apo.h5\"... (<class 'list'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/suf.h5\"... (<class 'list'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/f338a.h5\"... (<class 'list'>)\n"
     ]
    }
   ],
   "source": [
    "from imp import reload\n",
    "import analysis\n",
    "reload(analysis)\n",
    "from analysis import *\n",
    "import seaborn as sns\n",
    "bu72_pnas_concatenated = np.concatenate(bu72_pnas)\n",
    "print(np.shape(bu72_pnas_concatenated))\n",
    "apo_pnas_concatenated = np.concatenate(apo_pnas)\n",
    "#oxy_pnas_concatenated = np.concatenate(oxy_pnas)\n",
    "suf_pnas_concatenated = np.concatenate(suf_pnas)\n",
    "f338a_pnas_concatenated = np.concatenate(f338a_pnas)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "verbosedump(bu72_pnas, bu72_pnas_file)\n",
    "verbosedump(apo_pnas, apo_pnas_file)\n",
    "#verbosedump(oxy_pnas, oxy_pnas_file)\n",
    "verbosedump(suf_pnas, suf_pnas_file)\n",
    "verbosedump(f338a_pnas, f338a_pnas_file)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "columns=sorted(feature_name_residues_dict.keys())\n",
    "#plot_columns(whole_trajectory_pnas, bu72_pnas_file, titles=columns, main = \"BU72\", tICA = False, scale = 1.0, refcoords_file = None)\n",
    "#plot_columns(whole_trajectory_pnas, apo_pnas_file, titles=columns, main = \"Apo\", tICA = False, scale = 1.0, refcoords_file = None)\n",
    "\n",
    "#df = pd.DataFrame(bu72_pnas_concatenated, columns=sorted(feature_name_residues_dict.keys()))\n",
    "#sns.jointplot(x=\"tm6_tm3_dist\", y=\"rmsd_npxxy_inactive\", data=df, kind=\"kde\")\n",
    "#plt.hexbin(bu72_pnas_concatenated[:,0], bu72_pnas_concatenated[:,2], cmap=plt.cm.YlOrRd_r)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#oxy_tica_file = \"%s/oxy_tica.h5\" % tica_dir\n",
    "bu72_tica_file = \"%s/bu72_tica.h5\" % tica_dir\n",
    "apo_tica_file = \"%s/apo_tica.h5\" % tica_dir\n",
    "suf_tica_file = \"%s/suf_tica.h5\" % tica_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_tica.h5\"... (<class 'list'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/apo_tica.h5\"... (<class 'list'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_tica.h5\"... (<class 'list'>)\n"
     ]
    }
   ],
   "source": [
    "tica_coords = compat_verboseload(projected_features_dir)\n",
    "#oxy_tica = [tica_coords[i] for i in oxy_trajs]\n",
    "bu72_tica = [tica_coords[i] for i in bu72_trajs]\n",
    "apo_tica = [tica_coords[i] for i in apo_trajs]\n",
    "suf_tica = [tica_coords[i] for i in suf_trajs]\n",
    "\n",
    "\n",
    "#verbosedump(oxy_tica, oxy_tica_file)\n",
    "verbosedump(bu72_tica, bu72_tica_file)\n",
    "verbosedump(apo_tica, apo_tica_file)\n",
    "verbosedump(suf_tica, suf_tica_file)\n",
    "\n",
    "\n",
    "\n",
    "columns = [\"tIC%d\" %i for i in range(1,n_components+1)]\n",
    "#plot_columns(tica_dir, bu72_tica_file, titles=columns, main = \"BU72\", tICA = False, scale = 1.0, refcoords_file = None)\n",
    "#plot_columns(tica_dir, apo_tica_file, titles=columns, main = \"Apo\", tICA = False, scale = 1.0, refcoords_file = None)\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(235459, 10)\n",
      "(248499, 10)\n",
      "(272021, 10)\n"
     ]
    }
   ],
   "source": [
    "#print(np.concatenate(oxy_tica).shape)\n",
    "print(np.concatenate(apo_tica).shape)\n",
    "print(np.concatenate(bu72_tica).shape)\n",
    "print(np.concatenate(suf_tica).shape)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Clustering by KMeans\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/phi_psi_chi2_allprot_projected.h5\"...\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/clusterer_100clusters.h5\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "n_clusters = 100\n",
    "clusterer_dir = \"%s/clusterer_%dclusters.h5\" %(tica_dir, n_clusters)\n",
    "if not os.path.exists(clusterer_dir):\n",
    "    cluster_minikmeans(tica_dir, projected_features_dir, traj_dir, n_clusters=n_clusters, clusterer_dir=clusterer_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/clusterer_100clusters.h5\n"
     ]
    }
   ],
   "source": [
    "print(clusterer_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "oxy_clusterer_file = \"%s/oxy_clusterer%d.h5\" %(tica_dir, n_clusters)\n",
    "bu72_clusterer_file = \"%s/bu72_clusterer%d.h5\" %(tica_dir, n_clusters)\n",
    "apo_clusterer_file = \"%s/apo_clusterer%d.h5\" %(tica_dir, n_clusters)\n",
    "suf_clusterer_file = \"%s/suf_clusterer%d.h5\" %(tica_dir, n_clusters)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_clusterer100.h5\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/apo_clusterer100.h5\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_clusterer100.h5\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n"
     ]
    }
   ],
   "source": [
    "clusterer = compat_verboseload(clusterer_dir)\n",
    "cluster_labels = clusterer.labels_\n",
    "#oxy_clusters = [cluster_labels[i] for i in oxy_trajs]\n",
    "bu72_clusters = [cluster_labels[i] for i in bu72_trajs]\n",
    "apo_clusters = [cluster_labels[i] for i in apo_trajs]\n",
    "suf_clusters = [cluster_labels[i] for i in suf_trajs]\n",
    "\n",
    "\n",
    "\n",
    "bu72_clusterer = copy.deepcopy(clusterer)\n",
    "bu72_clusterer.labels_ = bu72_clusters\n",
    "#if not os.path.exists(bu72_clusterer_file):\n",
    "verbosedump(bu72_clusterer, bu72_clusterer_file)\n",
    "\n",
    "apo_clusterer = copy.deepcopy(clusterer)\n",
    "apo_clusterer.labels_ = apo_clusters\n",
    "    \n",
    "#if not os.path.exists(apo_clusterer_file):\n",
    "verbosedump(apo_clusterer, apo_clusterer_file)\n",
    "\n",
    "#oxy_clusterer = copy.deepcopy(clusterer)\n",
    "#oxy_clusterer.labels_ = oxy_clusters\n",
    "    \n",
    "#if not os.path.exists(oxy_clusterer_file):\n",
    "#verbosedump(oxy_clusterer, oxy_clusterer_file)\n",
    "\n",
    "suf_clusterer = copy.deepcopy(clusterer)\n",
    "suf_clusterer.labels_ = suf_clusters\n",
    "    \n",
    "#if not os.path.exists(oxy_clusterer_file):\n",
    "verbosedump(suf_clusterer, suf_clusterer_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cluster_tica_averages = calculate_cluster_averages_per_feature(bu72_clusterer, bu72_tica)\n",
    "cluster_tica_averages = pd.DataFrame(cluster_tica_averages, columns=[\"tIC.%d\" %i for i in range(1, n_components+1)])\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>tIC.1</th>\n",
       "      <th>tIC.2</th>\n",
       "      <th>tIC.3</th>\n",
       "      <th>tIC.4</th>\n",
       "      <th>tIC.5</th>\n",
       "      <th>tIC.6</th>\n",
       "      <th>tIC.7</th>\n",
       "      <th>tIC.8</th>\n",
       "      <th>tIC.9</th>\n",
       "      <th>tIC.10</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [tIC.1, tIC.2, tIC.3, tIC.4, tIC.5, tIC.6, tIC.7, tIC.8, tIC.9, tIC.10]\n",
       "Index: []"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "intermediate_actives = cluster_tica_averages.loc[(cluster_tica_averages[\"tIC.2\"] > 0.7) & (cluster_tica_averages[\"tIC.2\"] < 1.2) & (cluster_tica_averages[\"tIC.5\"] > 0.) & (cluster_tica_averages[\"tIC.2\"] < 0.8)]\n",
    "intermediate_actives"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import custom_msm\n",
    "reload(custom_msm)\n",
    "from custom_msm import *\n",
    "from msm_resampled import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "2604\n",
      "496\n",
      "13087\n"
     ]
    }
   ],
   "source": [
    "apo_clusters_map = make_clusters_map(apo_clusterer)\n",
    "bu72_clusters_map = make_clusters_map(bu72_clusterer)\n",
    "#oxy_clusters_map = make_clusters_map(oxy_clusterer)\n",
    "suf_clusters_map = make_clusters_map(suf_clusterer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plot_timescales(apo_clusterer_file, n_clusters, tica_dir, main=\"Apo MSM Timescales\", lag_times=list(range(1,51,10)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "import custom_msm\n",
    "reload(custom_msm)\n",
    "from custom_msm import *\n",
    "plot_timescales(bu72_clusterer_file, n_clusters, tica_dir, main=\"BU72 MSM Timescales\", lag_times=[1,5,10,15,20])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plot_timescales(suf_clusterer_file, n_clusters, tica_dir, main=\"SUF MSM Timescales\", lag_times=list(range(1,51,10)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found number to sample per cluster based on equilibrium proporrtions.\n",
      "Obtained random (trajectory, frame) pairs based on equilibrium populations\n",
      "Rearranged equilibrium sampled frames based on trajectories\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/apo_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'dict'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/apo_pnas_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/apo_tica_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "import custom_msm\n",
    "import importlib\n",
    "importlib.reload(custom_msm)\n",
    "from custom_msm import *\n",
    "\n",
    "apo_lag_time=25.\n",
    "prior_counts = 1e-5\n",
    "ergodic_cutoff = 'off'\n",
    "apo_msm_dir = os.path.join(tica_dir, \"apo_msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(apo_lag_time, str(prior_counts), n_clusters))\n",
    "#if 1==1:\n",
    "if not os.path.exists(apo_msm_dir):\n",
    "    apo_msm = build_msm(apo_clusterer_file, apo_lag_time, apo_msm_dir, prior_counts, ergodic_cutoff)\n",
    "else:\n",
    "    apo_msm = compat_verboseload(apo_msm_dir)\n",
    "\n",
    "import msm_resampled\n",
    "reload(msm_resampled)\n",
    "from msm_resampled import *\n",
    "total_samples = 20000\n",
    "num_trajs = len(apo_trajs)\n",
    "apo_resampled_traj_to_frames_file = os.path.join(tica_dir, \"apo_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(apo_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "#if not os.path.exists(apo_resampled_traj_to_frames_file):\n",
    "apo_resampled_traj_to_frames = resample_by_msm(total_samples, apo_msm, apo_clusters_map, num_trajs, apo_resampled_traj_to_frames_file)\n",
    "#else:\n",
    "apo_resampled_traj_to_frames = compat_verboseload(apo_resampled_traj_to_frames_file)\n",
    "\n",
    "apo_pnas = compat_verboseload(apo_pnas_file)\n",
    "apo_pnas_resampled_file = os.path.join(tica_dir, \"apo_pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(apo_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(apo_pnas, apo_resampled_traj_to_frames, apo_pnas_resampled_file)\n",
    "apo_pnas_resampled = compat_verboseload(apo_pnas_resampled_file)\n",
    "\n",
    "tica_concatenated = np.concatenate(compat_verboseload(projected_features_dir))\n",
    "tica_axes = [(np.min(tica_concatenated[:,i]), np.max(tica_concatenated[:,i])) for i in range(0, np.shape(tica_concatenated)[1])]\n",
    "\n",
    "apo_tica = compat_verboseload(apo_tica_file)\n",
    "apo_tica_resampled_file = os.path.join(tica_dir, \"apo_tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(apo_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(apo_tica, apo_resampled_traj_to_frames, apo_tica_resampled_file)\n",
    "apo_tica_resampled = compat_verboseload(apo_tica_resampled_file)\n",
    "\n",
    "apo_clusterer = compat_verboseload(apo_clusterer_file)\n",
    "apo_msm = compat_verboseload(apo_msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = apo_msm.populations_\n",
    "\n",
    "for cluster_id in apo_msm.mapping_.keys():\n",
    "    state_id = apo_msm.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "\n",
    "#plot_all_tics_and_clusters(tica_dir, apo_tica_resampled_file, apo_clusterer_file, lag_time, tic_range=range(0,n_components), main = \"Apo_MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)\n",
    "\n",
    "#plot_columns(tica_dir, apo_tica_resampled_file, titles = [\"tIC.%d\" %i for i in range(1,n_components+1)], main = \"mOR_Apo_MSM_\", tICA = False, scale = 1.0, refcoords_file = ref_tica_coords, axes=tica_axes, concatenate=False, reshape=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "print(np.concatenate(suf_tica).shape)\n",
    "print(np.concatenate(suf_pnas).shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "sorted(feature_name_residues_dict.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.hexbin(apo_tica_resampled[:,2], apo_tica_resampled[:,9])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "apo_tica_resampled.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.scatter(bu72_tica_resampled[:,2], bu72_tica_resampled[:,9])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_msm.timescales_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 119,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(16398, 15)"
      ]
     },
     "execution_count": 119,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.concatenate(f338a_pnas).shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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nrmt6rL1HLYVWb8oGBtYw88J484NXSC+sFyF1EjB7eG9ffdtTPbhutTD3RfnF3gjLuGew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\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa666e40630>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(np.concatenate(f338a_pnas)[:,-3], bins=50, range=[8,16])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 121,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa65e23c358>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(np.concatenate(suf_pnas)[:,-7], bins=50, range=[0,3])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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o/Df6S8dx0TK9j3QZFwgE5PMdimrseKXrez2STOy7uLj4oh8TUzCZPHmySktLZbVaNW3a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\nAgAAjEEwAQAAxiCYAAAAYxBMAACAMf4fjP9mL0qU6DQAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa669be3828>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(suf_pnas_resampled[:,-3],bins=50, range=[8,16])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAiYAAAFtCAYAAAAzuaF0AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz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\neB5dZ8eaxmcAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa669c94908>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(bu72_pnas_resampled[:,-3],bins=50, range=[8,16])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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58uWT1TsAAEgzE7pi0tzcrAsvvFCStGPHDq1cuVLPPPOMZs+erZaWFg0NDam5uVmNjY1q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\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa669c63fd0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(apo_pnas_resampled[:,-3],bins=50, range=[8,16])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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o/Df6S8dx0TK9j3QZFwgE5PMdimrseKXrez2STOy7uLj4oh8TUzCZPHmySktLZbVaNW3a\nNDmdTtlsNgWDQdntdh09elQej0dut/usIyS9vb0qLS2Nej+xNJTKfD5fxvV8Rjr3PuQPSjoZcZzV\nGt3MarqMi5bpfaTLOIfDoeIr4/8eTOf3+oVkat+xiOkTZM6cOfrggw8UDod17NgxBQIBlZWVaffu\n3ZKkPXv2qLy8XDNnztRHH32koaEhffXVV+rq6tL1118/oQ0AAID0EdMRE4/Ho+9+97u69957ZbFY\ntHbtWl177bWqq6vTzp07VVhYqIULFyorK0s1NTVatWqVLBaLqqqq5HK5JroHAACQJmJex6SyslKV\nlZVnbdu0adM547xer7xeb6y7AQAAGYSVXwEAgDEIJgAAwBgEEwAAYAyCCQAAMAbBBAAAGINgAgAA\njEEwAQAAxiCYAAAAYxBMAACAMQgmAADAGAQTAABgDIIJAAAwBsEEAAAYg2ACAACMQTABAADGIJgA\nAABjEEwAAIAxCCYAAMAYBBMAAGAMggkAADAGwQQAABiDYAIAAIxhS3YBQKo6fGJEPYFQxHHBU+EE\nVAOMT5ZFOugPRjV2qsOqIhc/PhAfvLKAGPUEQlq991jEcY1lkxJQDTA+A8GQavcNRjV249w8Fbni\nXBAyFlM5AADAGAQTAABgDIIJAAAwBsEEAAAYg2ACAACMQTABAADGIJgAAABjEEwAAIAxCCYAAMAY\nBBMAAGAMggkAADAGwQQAABiDYAIAAIxBMAEAAMawJbsAwDSHT4yoJxCKOC54KpyAagAgsxBMgK/p\nCYS0eu+xiOMayyYloBoAyCwEE6S8aI9wTHVYVeTiJQ8AJuNTGikv2iMcG+fmqciVgIIAADHj5FcA\nAGAMggkAADAGwQQAABhjXOeYnDx5Uj/60Y+0fPlyzZ49W3V1dQqFQnK73aqvr5fNZlN7e7u2b98u\nq9WqyspKLVq0aKJqBwAAaWZcR0xaW1t12WWXSZK2bNmipUuX6oUXXtC0adPU1tam4eFhtba2qrm5\nWS0tLXr11Vd1/PjxCSkcAACkn5iDyaFDh3To0CHdcsstCofDOnDggCoqKiRJFRUV6ujoUHd3t0pK\nSuR0OpWdna1Zs2aps7NzwooHAADpJeZg8uyzz+qhhx5SOHx69ctAICCb7fTMUEFBgfx+v/r7+5Wf\nnz/6mPz8fPn9/nGWDAAA0lVMweStt97Sddddp8svv3zMr58JK9FuBwAAkGI8+fVvf/ubDh8+rHff\nfVe9vb265JJL5HQ6FQwGZbfbdfToUXk8Hrnd7rOOkPT29qq0tDTq/fh8vljKS2mZ2PMZsfYeyJkS\n3bhAQD7foQl7vlAo8mqzjBs/0/vItHFS9O+l88nUz7lM7Lu4uPiiHxNTMFm/fv3o31988UVdfvnl\n6urq0u7duzV//nzt2bNH5eXlmjlzptavX6+hoSFZrVZ1dXVpzZo1Ue8nloZSmc/ny7iezxhP70P+\noKSTEcc5HA4VXxl5H9E+n9Ua3QFHxo2P6X1k2jgp+vfSWDL1cy5T+47FuJekPzM987Of/Ux1dXXa\nuXOnCgsLtXDhQmVlZammpkarVq2SxWJRVVWVXC7WBEdyZFmkg/5gxHHcNRgAkmfcwaSqqmr075s2\nbTrn616vV16vd7y7QQaK9uZ80QaJgWBItfsGI47jrsEAkDzcxA/GivbmfAQJAEgfLEkPAACMwRET\nJNxYUzSBnCn/e9Lp/8e5HgCQeQgmSLjzT9GcfSUMUzQAkHmYygEAAMYgmAAAAGMQTAAAgDEIJgAA\nwBgEEwAAYAyCCQAAMAbBBAAAGINgAgAAjEEwAQAAxmDlVwDARcmySAe/dguJsUx1WFXk4scMLg6v\nGADARRkIhlS7bzDiuI1z81TkSkBBSCtM5QAAAGMQTAAAgDEIJgAAwBgEEwAAYAyCCQAAMAbBBAAA\nGIPLhTFhDp8YUU8gFHFc8FQ4AdUAAFIRwQQTpicQ0uq9xyKOayyblIBqAACpiKkcAABgDIIJAAAw\nBsEEAAAYg2ACAACMQTABAADGIJgAAABjEEwAAIAxCCYAAMAYBBMAAGAMggkAADAGwQQAABiDYAIA\nAIxBMAEAAMYgmAAAAGMQTAAAgDEIJgAAwBgEEwAAYAyCCQAAMAbBBAAAGMOW7AIAAOkpyyId9AfP\n2hbImaKhr22b6rCqyMWPI5zGKwEAEBcDwZBq9w2O8ZWTZ/1r49w8FbkSUxPMx1QOAAAwBsEEAAAY\nI+apnOeee06dnZ0KhUL6yU9+opKSEtXV1SkUCsntdqu+vl42m03t7e3avn27rFarKisrtWjRooms\nHwAApJGYgsn+/fv12WefqbW1VQMDA/rxj3+ssrIyLVmyRPPmzVNzc7Pa2tq0YMECtba2atu2bcrK\nytKyZcvk9XqVm5s70X0AAIA0ENNUzg033KANGzZIknJzcxUIBHTgwAHdeuutkqSKigp1dHSou7tb\nJSUlcjqdys7O1qxZs9TZ2Tlx1QMAgLQSUzCxWCzKycmRJLW1temWW25RIBCQzXb6AExBQYH8fr/6\n+/uVn58/+rj8/Hz5/f4JKBsAAKSjcZ38+s4776itrU1r1649a3s4HB5z/Pm2AwAASOM4+fW9997T\ntm3b9Nxzz8nlcsnpdCoYDMput+vo0aPyeDxyu91nHSHp7e1VaWlp1Pvw+XyxlpeyUrnnQM6UqMaF\nQiHGMS5qpveRaePi8ZyBQEA+36Go95+qUvnzPVbFxcUX/ZiYgsnQ0JA2bdqk5uZmXXrppZKksrIy\n7d69W/Pnz9eePXtUXl6umTNnav369RoaGpLValVXV5fWrFkT9X5iaSiV+Xy+lO759GqOJyOOs1qj\nO1DHuPQeFy3T+8i0cfF4TofDoeIrU/ezLxqp/vmeSDEFkz//+c8aHBzUo48+Orqtrq5OTzzxhHbu\n3KnCwkItXLhQWVlZqqmp0apVq2SxWFRVVSWXi+X9AADA2GIKJpWVlaqsrDxn+6ZNm87Z5vV65fV6\nY9kNDHH4xIh6ApEPyQZPcQ4RAGB8uFcOIuoJhLR677GI4xrLJiWgGgBAOmNJegAAYAyOmAAAkirL\nIh30ByOOm+qwqsjFj610x3cYAJBUA8GQavcNRhy3cW6eirh+Iu0xlQMAAIxBMAEAAMYgmAAAAGMQ\nTAAAgDEIJgAAwBgEEwAAYAyCCQAAMAbBBAAAGINgAgAAjEEwAQAAxiCYAAAAYxBMAACAMQgmAADA\nGAQTAABgDIIJAAAwBsEEAAAYg2ACAACMYUt2AQAARCPLIh30ByOOm+qwqsjFj7dUxXcOAJASBoIh\n1e4bjDhu49w8FbkSUBDigmCSwQ6fGFFPIBRxXPBUOAHVAABAMMloPYGQVu89FnFcY9mkBFQDAAAn\nvwIAAIMQTAAAgDEIJgAAwBgEEwAAYAxOfgUApBXWO0ltfEcAAGmF9U5SG1M5AADAGAQTAABgDIIJ\nAAAwBsEEAAAYg2ACAACMwVU5AICMxGXFZuJ/GgCQkbis2ExM5QAAAGMQTAAAgDGYygEA4AI4FyWx\n+B8EAOACOBclsQgmcXT4xIh6AqGI46JN2dE+36WXWDT0f8MRxwVPRR4DAEAiEUziqCcQ0uq9xyKO\nizZlR/t8jWWTokr3jWWTIu8UABCVC035BHKmaOh/v8aUz4XxP2OAMy/m/37hjoUjHABgrshTPicl\nMeUTCcHEAGe/mE+edxxHOAAA6S4hwWTjxo3q7u6W1WrV6tWrVVJSkojdAgBgnIm+ymeiz2dMtrhX\neODAAf373/9Wa2ur/vnPf6qxsVGtra3x3i0AAEaa6Kt8Jvp8xmSLezD54IMPdNttt0mSrrrqKg0N\nDemrr76S0+mM964BAEhZ0R5Zifb8w2ifL9orO+N1BCbuwaSvr0/XXnvt6L8vu+wy9fX1pXQwifaw\nGSerAgBiFe2RlWjPP7yY54tm3HO35KkncOGg8223Para/pvl2LFjcf3puWHDBn3nO99RRUWFJKmq\nqkrr1q3TlVdeGc/dAgCAFBT3e+W43W719fWN/tvv98vtdsd7twAAIAXFPZjMmTNHu3btkiR9/PHH\n8ng8cjgc8d4tAABIQXE/x+S6667TtddeqxUrVshqterhhx+O9y4BAECKivs5JgAAANGK+1QOAABA\ntAgmAADAGAQTAABgDGOCSSAQ0COPPKLq6mpVVVXp/fffT3ZJCRMOh7VhwwatWLFC1dXVOnToULJL\nirtPPvlEixcv1o4dOyRJPT09qq6u1sqVK/WrX/1KIyMjSa4wfr7euyS99tprmjt3roaHh5NYWXyN\n9T2vqanRfffdpwcffFD9/f1JrjB+vt57V1eXqqqqVF1drYceekjHjkVeTjxVjfV6l6T33ntPc+bM\nSVJV8ff1vhsaGnTPPfeourpa1dXV2rt3b5IrjJ+v9z4yMqLa2lr99Kc/VU1NjYaGhi74eGOCyZtv\nvqnp06erpaVFGzZs0DPPPJPskhLmnXfe0YkTJ/Tiiy/qscceU1NTU7JLiqvh4WE9/fTTKisrG922\nZcsWLV26VC+88IKmTZumtra2JFYYP2P1/tZbb6m/v18ejyeJlcXXWH1v3rxZixcv1ubNm3Xbbbfp\n97//fRIrjJ+xet++fbsaGhrU0tKib33rW/rTn/6UxArjZ6zeJSkYDOq3v/1t2r7mz9f3Aw88oJaW\nFrW0tGju3LlJqi6+xur9jTfeUH5+vl566SV973vf08GDBy/4HMYEk7y8PA0MDEiSBgYGlJeXl+SK\nEudf//rX6B2Xp02bpi+++ELhcPpeLGW329XU1HTWQnv79+8fXR24oqJCHR0dySovrsbq3ev1qrq6\nOolVxd9YfT/yyCPyer2STr//BwcjL4Gdisbq/cknn9Tll1+ucDis3t5eTZkyJYkVxs9YvUvSyy+/\nrCVLlshmM/9Ot7E4X9+ZYKze//rXv2r+/PmSpMrKytHP+vMxJpjccccd+uKLL3TXXXepurpaP//5\nz5NdUsJcffXVev/99xUKhXTo0CEdPnw4rQ/tWq1W2e1n3z9heHh49EOqoKDgrNWC08lYvWfCgoNj\n9Z2TkyOLxaJQKKQdO3bozjvvTFJ18TVW79LpqYwlS5aov79fP/jBD5JQWfyN1fuhQ4fk8/k0b968\ntP0F7Hzf8z/+8Y+6//779dhjj43+Ip5uxur9yJEj2rt3r6qrq/XYY4/p+PHjF36OeBZ4Mdrb21VY\nWKjXX39dzz//vJ566qlkl5Qw5eXlmjlzplauXKnXXntNV111Vdq+YaORyb1nmlAopMcff1xlZWWa\nPXt2sstJqPLycu3YsUPTp0/Xyy+/nOxyEubZZ5/VQw89lOwyEm7BggV64IEH1NzcrOLiYm3ZsiXZ\nJSVMOBzWVVddpZaWFs2YMUMvvfTSBccbE0w6Ozt18803S5KKi4vl9/sz6gfUypUrtXXrVj388MMa\nHBxUQUFBsktKKKfTqWDw9F0qjx49mpGHQC0WS7JLSLiGhgZNnz5dy5cvT3YpCfWXv/xl9O/z5s1T\nZ2dn8opJoN7eXn3++edat26d7r33XvX19aX9NOYZs2fPVnFxsSTp1ltv1aeffprkihJn8uTJ+va3\nvy1Juvnmm/XZZ59dcLwxweSKK65Qd3e3pNOHfZxOZ8Z8UPt8PjU2Nko6fXj3mmuuSXJFiVdWVqbd\nu3dLkvbs2aPy8vIkVxR/Xw/emRTEpdNHSe12u1asWJHsUhJu69at8vl8kqTu7m5Nnz49yRXFXzgc\nlsfj0euvv67W1lb95je/0eTJk9XS0pLs0hLil7/8pf7zn/9IOn1O3YwZM5JcUeKUl5frvffek3T6\nnnmRXu/GLEkfCATU2Nio/v5+nTp1StXV1brhhhuSXVZChMNhPfHEE/r000+VnZ2thoaGtD0ZTjr9\nwmxqatKRI0dks9nk8XjU2Nio+vp6BYNBFRYWat26dcrKykp2qRNurN7nzJmjv//97+ru7lZJSYlK\nS0tVU1OT7FIn1Fh9f/nll7Lb7XK5XJKkGTNmaO3atUmudOKN1fuDDz6oZ555RjabTdnZ2aqvr0/L\nE/7H6v2pp55Sbm6upNMnQr7xxhtJrnLijdX30qVLtW3bNjkcDjkcDq1bty5jvueNjY369a9/Lb/f\nL5fLpcfXiWeLAAAARElEQVQff1z5+fnnfQ5jggkAAIAxUzkAAAAEEwAAYAyCCQAAMAbBBAAAGINg\nAgAAjEEwAQAAxiCYAAAAYxBMAACAMf4fjP9mL0qU6DQAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fa63cdfc470>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.clf()\n",
    "plt.hist(suf_pnas_resampled[:,-3],bins=50, range=[8,16])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plt.hist(bu72_tica_resampled[:,-3],bins=50, range=4,6])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plt.hist(apo_tica_resampled[:,2],bins=50, range=[-4,6])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found number to sample per cluster based on equilibrium proporrtions.\n",
      "Obtained random (trajectory, frame) pairs based on equilibrium populations\n",
      "Rearranged equilibrium sampled frames based on trajectories\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'dict'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_pnas_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_tica_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "\n",
    "bu72_lag_time=25\n",
    "prior_counts = 1e-5\n",
    "ergodic_cutoff='off'\n",
    "bu72_msm_dir = os.path.join(tica_dir, \"bu72_msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters))\n",
    "#if 1==1:\n",
    "if not os.path.exists(bu72_msm_dir):\n",
    "    bu72_msm = build_msm(bu72_clusterer_file, bu72_lag_time, bu72_msm_dir, prior_counts, ergodic_cutoff)\n",
    "else:\n",
    "    bu72_msm = compat_verboseload(bu72_msm_dir)\n",
    "\n",
    "import msm_resampled\n",
    "reload(msm_resampled)\n",
    "from msm_resampled import *\n",
    "total_samples = 20000\n",
    "num_trajs = len(bu72_trajs)\n",
    "bu72_resampled_traj_to_frames_file = os.path.join(tica_dir, \"bu72_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "#if not os.path.exists(bu72_resampled_traj_to_frames_file):\n",
    "bu72_resampled_traj_to_frames = resample_by_msm(total_samples, bu72_msm, bu72_clusters_map, num_trajs, bu72_resampled_traj_to_frames_file)\n",
    "#else:\n",
    "bu72_resampled_traj_to_frames = compat_verboseload(bu72_resampled_traj_to_frames_file)\n",
    "\n",
    "bu72_pnas = compat_verboseload(bu72_pnas_file)\n",
    "bu72_pnas_resampled_file = os.path.join(tica_dir, \"bu72_pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(bu72_pnas, bu72_resampled_traj_to_frames, bu72_pnas_resampled_file)\n",
    "bu72_pnas_resampled = compat_verboseload(bu72_pnas_resampled_file)\n",
    "\n",
    "tica_concatenated = np.concatenate(compat_verboseload(projected_features_dir))\n",
    "tica_axes = [(np.min(tica_concatenated[:,i]), np.max(tica_concatenated[:,i])) for i in range(0, np.shape(tica_concatenated)[1])]\n",
    "\n",
    "bu72_tica = compat_verboseload(bu72_tica_file)\n",
    "bu72_tica_resampled_file = os.path.join(tica_dir, \"bu72_tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(bu72_tica, bu72_resampled_traj_to_frames, bu72_tica_resampled_file)\n",
    "bu72_tica_resampled = compat_verboseload(bu72_tica_resampled_file)\n",
    "\n",
    "bu72_clusterer = compat_verboseload(bu72_clusterer_file)\n",
    "bu72_msm = compat_verboseload(bu72_msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = bu72_msm.populations_\n",
    "\n",
    "for cluster_id in bu72_msm.mapping_.keys():\n",
    "    state_id = bu72_msm.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "    \n",
    "#plot_all_tics_and_clusters(tica_dir, bu72_tica_resampled_file, bu72_clusterer_file, lag_time, tic_range=range(0,n_components), main = \"bu72_MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)\n",
    "\n",
    "#plot_columns(tica_dir, bu72_tica_resampled_file, titles = [\"tIC.%d\" %i for i in range(1,n_components+1)], main = \"mOR_bu72_MSM_\", tICA = False, scale = 1.0, refcoords_file = ref_tica_coords, axes=tica_axes, concatenate=False, reshape=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plt.hist(np.concatenate(bu72_pnas)[:,8], bins=50)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_pnas_averages = calculate_cluster_averages_per_feature(bu72_clusterer, bu72_pnas)\n",
    "len(sorted(list(set(np.concatenate(bu72_clusterer.labels_)))))\n",
    "print(np.sum(bu72_msm.populations_[np.concatenate(bu72_msm.transform(np.where(bu72_pnas_averages[:,8] > 12.)[0]))]))\n",
    "print(np.sum(bu72_msm.populations_[np.concatenate(bu72_msm.transform(np.where(bu72_pnas_averages[:,8] < 12.)[0]))]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "apo_pnas_averages = calculate_cluster_averages_per_feature(apo_clusterer, apo_pnas)\n",
    "len(sorted(list(set(np.concatenate(apo_clusterer.labels_)))))\n",
    "print(np.sum(apo_msm.populations_[np.concatenate(apo_msm.transform(np.where(apo_pnas_averages[:,8] > 12.)[0]))]))\n",
    "print(np.sum(apo_msm.populations_[np.concatenate(apo_msm.transform(np.where(apo_pnas_averages[:,8] < 12.)[0]))]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "apo_pnas_averages = calculate_cluster_averages_per_feature(apo_clusterer, apo_pnas)\n",
    "sorted(list(set(np.concatenate(apo_clusterer.labels_))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "np.sum(apo_msm.populations_[np.concatenate(apo_msm.partial_transform(list(set(np.concatenate(apo_clusterer.labels_)))))])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "apo_msm.partial_transform(list(set(np.concatenate(apo_clusterer.labels_))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "apo_msm.partial_transform(np.array(list(set(np.concatenate(apo_clusterer.labels_)))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.clf()\n",
    "plt.hist(np.concatenate(apo_pnas)[:,8], bins=50, range=[6,18.])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "graph_file = \"%s/bu72_clusters_%d_msm_lag_time%d_graph.graphml\" % (tica_dir, n_clusters, bu72_lag_time)\n",
    "bu72_tica_averages = calculate_cluster_averages_per_feature(bu72_clusterer, bu72_tica)\n",
    "bu72_cluster_attributes = {}\n",
    "for i, title in enumerate([\"tIC.%d\" %i for i in range(1,n_components+1)]):\n",
    "    bu72_cluster_attributes[title] = bu72_tica_averages[:,i]\n",
    "\n",
    "bu72_msm_attributes = {'eq_pops' : bu72_msm.populations_}\n",
    "construct_graph(bu72_msm_dir, bu72_clusterer_file, n_clusters, 5, 5, graph_file, inactive = None, active = None, pnas_clusters_averages = None, tica_clusters_averages = None, docking=None, macrostate = None, cluster_attributes=bu72_cluster_attributes, msm_attributes=bu72_msm_attributes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "suf_msm_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found number to sample per cluster based on equilibrium proporrtions.\n",
      "Obtained random (trajectory, frame) pairs based on equilibrium populations\n",
      "Rearranged equilibrium sampled frames based on trajectories\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'dict'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_pnas_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_tica_msm_lag-time25_prior-counts1e-05_clusters1000_resampled_20000.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "suf_lag_time=25\n",
    "prior_counts = 1e-5\n",
    "ergodic_cutoff='off'\n",
    "suf_msm_dir = os.path.join(tica_dir, \"suf_msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(suf_lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(suf_msm_dir):\n",
    "    suf_msm = build_msm(suf_clusterer_file, suf_lag_time, suf_msm_dir, prior_counts, ergodic_cutoff)\n",
    "else:\n",
    "    suf_msm = compat_verboseload(suf_msm_dir)\n",
    "\n",
    "import msm_resampled\n",
    "reload(msm_resampled)\n",
    "from msm_resampled import *\n",
    "total_samples = 20000\n",
    "num_trajs = len(suf_trajs)\n",
    "suf_resampled_traj_to_frames_file = os.path.join(tica_dir, \"suf_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(suf_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "#if not os.path.exists(suf_resampled_traj_to_frames_file):\n",
    "suf_resampled_traj_to_frames = resample_by_msm(total_samples, suf_msm, suf_clusters_map, num_trajs, suf_resampled_traj_to_frames_file)\n",
    "#else:\n",
    "suf_resampled_traj_to_frames = compat_verboseload(suf_resampled_traj_to_frames_file)\n",
    "\n",
    "suf_pnas = compat_verboseload(suf_pnas_file)\n",
    "suf_pnas_resampled_file = os.path.join(tica_dir, \"suf_pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(suf_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(suf_pnas, suf_resampled_traj_to_frames, suf_pnas_resampled_file)\n",
    "suf_pnas_resampled = compat_verboseload(suf_pnas_resampled_file)\n",
    "\n",
    "tica_concatenated = np.concatenate(compat_verboseload(projected_features_dir))\n",
    "tica_axes = [(np.min(tica_concatenated[:,i]), np.max(tica_concatenated[:,i])) for i in range(0, np.shape(tica_concatenated)[1])]\n",
    "\n",
    "suf_tica = compat_verboseload(suf_tica_file)\n",
    "suf_tica_resampled_file = os.path.join(tica_dir, \"suf_tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(suf_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(suf_tica, suf_resampled_traj_to_frames, suf_tica_resampled_file)\n",
    "suf_tica_resampled = compat_verboseload(suf_tica_resampled_file)\n",
    "\n",
    "suf_clusterer = compat_verboseload(suf_clusterer_file)\n",
    "suf_msm = compat_verboseload(suf_msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = suf_msm.populations_\n",
    "\n",
    "for cluster_id in suf_msm.mapping_.keys():\n",
    "    state_id = suf_msm.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "    \n",
    "#plot_all_tics_and_clusters(tica_dir, suf_tica_resampled_file, suf_clusterer_file, lag_time, tic_range=range(0,n_components), main = \"suf_MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)\n",
    "\n",
    "#plot_columns(tica_dir, suf_tica_resampled_file, titles = [\"tIC.%d\" %i for i in range(1,n_components+1)], main = \"mOR_suf_MSM_\", tICA = False, scale = 1.0, refcoords_file = ref_tica_coords, axes=tica_axes, concatenate=False, reshape=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "suf_resampled_traj_to_frames_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_columns(tica_dir, apo_pnas_resampled_file, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_Apo_MSM_\", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=False, reshape=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "bu72_lag_time=25\n",
    "prior_counts = 0.0\n",
    "bu72_msm_dir = os.path.join(tica_dir, \"bu72_msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(bu72_msm_dir):\n",
    "    bu72_msm = build_msm(bu72_clusterer_file, bu72_lag_time, bu72_msm_dir, prior_counts)\n",
    "else:\n",
    "    bu72_msm = compat_verboseload(bu72_msm_dir)\n",
    "bu72_msm.timescales_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fixed_assignments = dict()\n",
    "for i, traj in enumerate(bu72_clusterer.labels_):\n",
    "    fixed_assignments[i] = bu72_msm.transform(traj)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fixed_assignments[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "print(\"hello\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def pop_vs_counts(msm_obj, fixed_assignments, ax,**kwargs):\n",
    "\n",
    "    pop_count_vect=[]\n",
    "    for i in range(msm_obj.n_states_):\n",
    "        pop_count_vect.append(np.sum([np.count_nonzero(fixed_assignments[j]==i)\n",
    "                                      for j in fixed_assignments.keys()]))\n",
    "    pop_count_vect = pop_count_vect/np.sum(pop_count_vect)\n",
    "    ax.errorbar(np.log10(msm_object.populations_),np.log10(pop_count_vect),**kwargs)\n",
    "    ax.plot([0,-6],[0,-6])\n",
    "    ax.set_ylim([-6,0])\n",
    "    ax.set_xlim([-6,0])\n",
    "    ax.set_xlabel(\" MSM Population\",size=16)\n",
    "    ax.set_ylabel(\"Counts Population\",size=16)\n",
    "    return pop_count_vect\n",
    "f=figure()\n",
    "ax=f.add_subplot(1,1,1)\n",
    "pop_count_vect = pop_vs_counts(bu72_msm, fixed_assignments, ax fmt='o', color='r',label=\"RCSB-ASP\")\n",
    "ax.legend(loc='best',prop={'size':12})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "total_samples = 20000\n",
    "num_trajs = len(bu72_trajs)\n",
    "bu72_resampled_traj_to_frames_file = os.path.join(tica_dir, \"bu72_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "if not os.path.exists(bu72_resampled_traj_to_frames_file):\n",
    "    bu72_resampled_traj_to_frames = resample_by_msm(total_samples, bu72_msm, bu72_clusters_map, num_trajs, bu72_resampled_traj_to_frames_file)\n",
    "else:\n",
    "    bu72_resampled_traj_to_frames = compat_verboseload(bu72_resampled_traj_to_frames_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_resampled_traj_to_frames_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_pnas = compat_verboseload(bu72_pnas_file)\n",
    "bu72_pnas_resampled_file = os.path.join(tica_dir, \"bu72_pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(bu72_pnas, bu72_resampled_traj_to_frames, bu72_pnas_resampled_file)\n",
    "bu72_pnas_resampled = compat_verboseload(bu72_pnas_resampled_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_tica = compat_verboseload(bu72_tica_file)\n",
    "bu72_tica_resampled_file = os.path.join(tica_dir, \"bu72_tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(bu72_lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(bu72_tica, bu72_resampled_traj_to_frames, bu72_tica_resampled_file)\n",
    "bu72_tica_resampled = compat_verboseload(bu72_tica_resampled_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "bu72_clusterer = compat_verboseload(bu72_clusterer_file)\n",
    "bu72_msm = compat_verboseload(bu72_msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = bu72_msm.populations_\n",
    "\n",
    "for cluster_id in bu72_msm.mapping_.keys():\n",
    "    state_id = bu72_msm.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "    \n",
    "plot_all_tics_and_clusters(tica_dir, bu72_tica_resampled_file, bu72_clusterer_file, lag_time, tic_range=range(0,10), main = \"bu72_MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_pnas_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "analysis_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_resampled = np.vstack([compat_verboseload(bu72_pnas_resampled_file)[::1,], compat_verboseload(apo_pnas_resampled_file)[::1,], compat_verboseload(suf_pnas_resampled_file)[::1,]])\n",
    "mins = np.min(tica_resampled, axis=0)\n",
    "maxs = np.max(tica_resampled, axis=0)\n",
    "stds = np.std(tica_resampled, axis=0)\n",
    "custom_lims = [[mins[i] - .5*stds[i], maxs[i] + .5*stds[i]] for i in range(0,len(mins))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pnas = load_file(\"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\")\n",
    "ref_pnas = np.hstack([np.array(x).T for x in ref_pnas])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/4dkl_R_for_conformation.dataset\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/featuresall_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far/reference_receptors/5c1m.dataset\n",
      "(2, 2408)\n",
      "loading /home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\n"
     ]
    }
   ],
   "source": [
    "def get_features(features_dir):\n",
    "    feature_files = get_trajectory_files(features_dir, \".dataset\")\n",
    "    features = np.vstack([load_file(f) for f in feature_files])\n",
    "    print(features.shape)\n",
    "    return features\n",
    "\n",
    "ref_pp_features = pd.DataFrame(get_features(ref_features_dir), columns=feature_names)\n",
    "\n",
    "ref_pp_tica = pd.read_csv(ref_tica_coords, header=None).values\n",
    "#ref_pp_tica.columns = [\"mOR tIC.%d\" %i for i in range(1,ref_pp_tica.shape[1])]\n",
    "\n",
    "ref_pnas = load_file(\"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\")\n",
    "ref_pnas = np.hstack([np.array(x).T for x in ref_pnas])\n",
    "\n",
    "#ref_pnas = pd.DataFrame(ref_pnas, columns=sorted(feature_name_residues_dict.keys()))\n",
    "\n",
    "#ref_features = pd.concat([ref_pp_features*10., ref_lp_features*10., ref_pp_tica, ref_lp_tica, ref_pnas], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "coords_bounds_dict = {\"tIC.4\": [(8.0, 10.), (12., 15.)]}\n",
    "all_traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "trajs_to_watch = reaction_coordinate_sampler([all_traj_files[i] for i in bu72_trajs], \".h5\", [t.values for t in all_traj_features], \n",
    "                            all_traj_features[0].columns.values.tolist(), coords_bounds_dict, \n",
    "                            \"%s/trajs_to_watch.csv\" %pp_tica_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pp_tica"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "jointplots(bu72_pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_BU72_MSM_%d_Clusters\" %n_clusters, refcoords = ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=15, n_pts=200j, parallel=True, remake=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pnas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "jointplots(apo_pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_APO_MSM_%d_Clusters\" %n_clusters, refcoords=ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=10, remake=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "jointplots(suf_pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_SUF_MSM_%d_Clusters\" %n_clusters, refcoords=ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=10, remake=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_resampled = np.vstack([compat_verboseload(bu72_tica_resampled_file)[::1,], compat_verboseload(apo_tica_resampled_file)[::1,], compat_verboseload(suf_tica_resampled_file)[::1,]])\n",
    "mins = np.min(tica_resampled, axis=0)\n",
    "maxs = np.max(tica_resampled, axis=0)\n",
    "stds = np.std(tica_resampled, axis=0)\n",
    "custom_lims = [[mins[i] - 1.*stds[i], maxs[i] + 1.*stds[i]] for i in range(0,len(mins))]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "custom_lims"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "print(custom_lims)\n",
    "print(custom_lims[3][1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Making delta G plots.\n",
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      "8\n",
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      "[[ 0.1997732  -0.86493743]\n",
      " [-0.27086734  0.67270475]]\n",
      "Done plotting columns\n",
      "Making delta G plots.\n",
      "1\n",
      "(2, 19998)\n",
      "Computed 2D KDE\n",
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      "[[ 0.1997732  -0.86493743]\n",
      " [-0.27086734  0.67270475]]\n",
      "Done plotting columns\n",
      "Making delta G plots.\n",
      "1\n",
      "(2, 19994)\n",
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      "Computed Density. Now plotting.\n",
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      "(0.0, 8.0)\n",
      "[[ 0.1997732  -0.86493743]\n",
      " [-0.27086734  0.67270475]]\n",
      "Done plotting columns\n"
     ]
    },
    {
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    },
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       "<matplotlib.figure.Figure at 0x7fd52c248748>"
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     "metadata": {},
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    },
    {
     "data": {
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       "<matplotlib.figure.Figure at 0x7fd5228c30f0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fd533ed54e0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fd522904a90>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fd5228fa1d0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fd52c0a29b0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "refcoords_jointplots_dir = \"%s/refcoords_jointplots\" %analysis_dir\n",
    "if not os.path.exists(refcoords_jointplots_dir):\n",
    "    os.makedirs(refcoords_jointplots_dir)\n",
    "jointplots(compat_verboseload(bu72_tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"BU72 MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=custom_lims, n_pts=200j, n_levels=15, remake=False, parallel=False, max_i=1)\n",
    "jointplots(compat_verboseload(apo_tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Apo MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=custom_lims, n_pts=200j, n_levels=15, remake=False, parallel=False, max_i=1)\n",
    "jointplots(compat_verboseload(suf_tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Sufentanil MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=custom_lims, n_pts=200j, n_levels=15, remake=False, parallel=False, max_i=1)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pp_tica"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "np.concatenate(bu72_tica).shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "np.concatenate(apo_tica).shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "jointplots(compat_verboseload(bu72_tica_resampled_file)[::1,:], analysis_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"BU72 MSM\", refcoords=None, axes=None, data_j=bu72_pnas_resampled, titles_j=sorted(feature_name_residues_dict.keys()), reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=None, remake=True)\n",
    "#jointplots(compat_verboseload(apo_tica_resampled_file)[::1,:], analysis_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Apo MSM\", refcoords=None, axes=None, data_j=apo_pnas_resampled, titles_j=sorted(feature_name_residues_dict.keys()), reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=None)\n",
    "#jointplots(compat_verboseload(suf_tica_resampled_file)[::1,:], analysis_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Sufentanil MSM\", refcoords=None, axes=None, data_j=bu72_pnas_resampled, titles_j=sorted(feature_name_residues_dict.keys()), reshape=False, max_tIC=10, min_density=None, max_diff=8., custom_lims=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import detect_intermediates\n",
    "reload(detect_intermediates)\n",
    "from detect_intermediates import *\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#sample_tIC_regions_silverman(np.concatenate(compat_verboseload(projected_features_dir))[::100,:], analysis_dir)\n",
    "#get_kde_mins_and_maxes(np.concatenate(compat_verboseload(projected_features_dir))[::100,:], analysis_dir)\n",
    "sample_kde_maxima(compat_verboseload(projected_features_dir), analysis_dir, trajs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "jointplots(compat_verboseload(apo_tica_resampled_file)[::1,:], analysis_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Apo MSM\", refcoords_file = None, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=5, min_density=None, max_diff=5., custom_lims=custom_lims)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_columns(tica_dir, bu72_pnas_resampled_file, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_BU72_MSM_\", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=False, reshape=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#bu72_tica = compat_verboseload(bu72_tica_file)\n",
    "#bu72_tica_resampled_file = os.path.join(tica_dir, \"bu72_tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled.h5\" %(lag_time, str(prior_counts), n_clusters))\n",
    "#resample_features_by_msm_equilibirum_pop(bu72_tica, bu72_resampled_traj_to_frames, bu72_tica_resampled_file)\n",
    "#bu72_tica_resampled = compat_verboseload(bu72_tica_resampled_file)\n",
    "plot_columns(tica_dir, bu72_tica_resampled_file, titles = [\"tIC.%d\" %i for i in range(1,n_components+1)], main = \"mOR_BU72_MSM_\", tICA = False, scale = 1.0, refcoords_file = ref_tica_coords, axes=tica_axes, concatenate=False, reshape=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "bu72_clusterer = compat_verboseload(bu72_clusterer_file)\n",
    "bu72_msm = compat_verboseload(bu72_msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = bu72_msm.populations_\n",
    "\n",
    "for cluster_id in bu72_msm.mapping_.keys():\n",
    "    state_id = bu72_msm.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "\n",
    "#plot_all_tics_and_clusters(tica_dir, bu72_tica_resampled_file, bu72_clusterer_file, lag_time, tic_range=[0,3], main = \"BU72_MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "len(dview)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 126,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_clusterer_1000clusters_1samples_samples_kdtree\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_clusterer1000.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_clusterer1000.h5\"...\n",
      "[[149 356]\n",
      " [379 392]\n",
      " [468 474]\n",
      " ..., \n",
      " [218 185]\n",
      " [375 365]\n",
      " [294 237]]\n",
      "1000\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/bu72_clusterer_1000clusters_1samples_samples_kdtree_indices.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters= 1000\n",
    "samples_dir = \"%s/bu72_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/bu72_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(bu72_clusterer_file, bu72_tica_file, [traj_files[i] for i in bu72_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=True, lig_name=\"LIG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_clusterer_1000clusters_1samples_samples_kdtree\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_clusterer1000.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_clusterer1000.h5\"...\n",
      "[[494 114]\n",
      " [218 323]\n",
      " [ 38 170]\n",
      " ..., \n",
      " [726 453]\n",
      " [714  48]\n",
      " [615 459]]\n",
      "1000\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/suf_clusterer_1000clusters_1samples_samples_kdtree_indices.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters= 1000\n",
    "samples_dir = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(suf_clusterer_file, suf_tica_file, [traj_files[i] for i in suf_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=True, lig_name=\"LIG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/all_clusterer_100clusters_1samples_samples_kdtree\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/clusterer_100clusters.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/phi_psi_chi2_allprot_projected.h5\"...\n",
      "loading \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/clusterer_100clusters.h5\"...\n",
      "[[ 965    5]\n",
      " [ 760  289]\n",
      " [1444   39]\n",
      " [1667  224]\n",
      " [ 485   54]\n",
      " [ 339  428]\n",
      " [ 669  179]\n",
      " [ 783  303]\n",
      " [  99   47]\n",
      " [ 835   30]\n",
      " [1027  332]\n",
      " [ 354  101]\n",
      " [1708    7]\n",
      " [1663  356]\n",
      " [1591   58]\n",
      " [ 222  135]\n",
      " [1560  160]\n",
      " [1357   23]\n",
      " [ 534  242]\n",
      " [1181  374]\n",
      " [ 323  535]\n",
      " [ 854  521]\n",
      " [ 419   70]\n",
      " [1770  172]\n",
      " [ 303  470]\n",
      " [1516   76]\n",
      " [ 896  148]\n",
      " [ 885  521]\n",
      " [ 335  218]\n",
      " [1178  225]\n",
      " [1543   64]\n",
      " [1669  513]\n",
      " [ 586  274]\n",
      " [ 379  461]\n",
      " [1628  372]\n",
      " [ 992  211]\n",
      " [ 271  551]\n",
      " [ 161   11]\n",
      " [1602  499]\n",
      " [1609  188]\n",
      " [ 343   74]\n",
      " [ 309  436]\n",
      " [ 284  366]\n",
      " [ 813  437]\n",
      " [  64  375]\n",
      " [1707  137]\n",
      " [1592  482]\n",
      " [ 338   95]\n",
      " [1051  262]\n",
      " [1726  371]\n",
      " [1112  266]\n",
      " [  92  148]\n",
      " [1528  241]\n",
      " [1741  274]\n",
      " [ 781  532]\n",
      " [1241   24]\n",
      " [1730  572]\n",
      " [ 127  293]\n",
      " [ 210  165]\n",
      " [1476   10]\n",
      " [ 971   19]\n",
      " [ 805  429]\n",
      " [1761  383]\n",
      " [ 274  543]\n",
      " [ 210  220]\n",
      " [ 809  200]\n",
      " [  66  367]\n",
      " [ 400  221]\n",
      " [ 316  102]\n",
      " [ 255  304]\n",
      " [1241  332]\n",
      " [1631    0]\n",
      " [ 714   32]\n",
      " [  10  231]\n",
      " [1647  270]\n",
      " [1556  263]\n",
      " [  26  460]\n",
      " [ 873  328]\n",
      " [1006  231]\n",
      " [1089    3]\n",
      " [ 321  171]\n",
      " [1549  270]\n",
      " [ 372  220]\n",
      " [1677   19]\n",
      " [ 980  426]\n",
      " [1078  179]\n",
      " [1084  404]\n",
      " [1184   30]\n",
      " [1519   15]\n",
      " [1747  249]\n",
      " [1368   66]\n",
      " [1610  223]\n",
      " [1015   58]\n",
      " [ 453   11]\n",
      " [1691  408]\n",
      " [1709  213]\n",
      " [ 292   14]\n",
      " [1637  473]\n",
      " [1708  526]\n",
      " [1248    8]]\n",
      "100\n",
      "()\n",
      "Converting to list\n",
      "[965, 5, 0, 0]\n",
      "965\n",
      "()\n",
      "Converting to list\n",
      "[760, 289, 1, 0]\n",
      "760\n",
      "()\n",
      "Converting to list\n",
      "[1444, 39, 2, 0]\n",
      "1444\n",
      "()\n",
      "Converting to list\n",
      "[1667, 224, 3, 0]\n",
      "1667\n",
      "()\n",
      "Converting to list\n",
      "[485, 54, 4, 0]\n",
      "485\n",
      "()\n",
      "Converting to list\n",
      "[339, 428, 5, 0]\n",
      "339\n",
      "()\n",
      "Converting to list\n",
      "[669, 179, 6, 0]\n",
      "669\n",
      "()\n",
      "Converting to list\n",
      "[783, 303, 7, 0]\n",
      "783\n",
      "()\n",
      "Converting to list\n",
      "[99, 47, 8, 0]\n",
      "99\n",
      "()\n",
      "Converting to list\n",
      "[835, 30, 9, 0]\n",
      "835\n",
      "()\n",
      "Converting to list\n",
      "[1027, 332, 10, 0]\n",
      "1027\n",
      "()\n",
      "Converting to list\n",
      "[354, 101, 11, 0]\n",
      "354\n",
      "()\n",
      "Converting to list\n",
      "[1708, 7, 12, 0]\n",
      "1708\n",
      "()\n",
      "Converting to list\n",
      "[1663, 356, 13, 0]\n",
      "1663\n",
      "()\n",
      "Converting to list\n",
      "[1591, 58, 14, 0]\n",
      "1591\n",
      "()\n",
      "Converting to list\n",
      "[222, 135, 15, 0]\n",
      "222\n",
      "()\n",
      "Converting to list\n",
      "[1560, 160, 16, 0]\n",
      "1560\n",
      "()\n",
      "Converting to list\n",
      "[1357, 23, 17, 0]\n",
      "1357\n",
      "()\n",
      "Converting to list\n",
      "[534, 242, 18, 0]\n",
      "534\n",
      "()\n",
      "Converting to list\n",
      "[1181, 374, 19, 0]\n",
      "1181\n",
      "()\n",
      "Converting to list\n",
      "[323, 535, 20, 0]\n",
      "323\n",
      "()\n",
      "Converting to list\n",
      "[854, 521, 21, 0]\n",
      "854\n",
      "()\n",
      "Converting to list\n",
      "[419, 70, 22, 0]\n",
      "419\n",
      "()\n",
      "Converting to list\n",
      "[1770, 172, 23, 0]\n",
      "1770\n",
      "()\n",
      "Converting to list\n",
      "[303, 470, 24, 0]\n",
      "303\n",
      "()\n",
      "Converting to list\n",
      "[1516, 76, 25, 0]\n",
      "1516\n",
      "()\n",
      "Converting to list\n",
      "[896, 148, 26, 0]\n",
      "896\n",
      "()\n",
      "Converting to list\n",
      "[885, 521, 27, 0]\n",
      "885\n",
      "()\n",
      "Converting to list\n",
      "[335, 218, 28, 0]\n",
      "335\n",
      "()\n",
      "Converting to list\n",
      "[1178, 225, 29, 0]\n",
      "1178\n",
      "()\n",
      "Converting to list\n",
      "[1543, 64, 30, 0]\n",
      "1543\n",
      "()\n",
      "Converting to list\n",
      "[1669, 513, 31, 0]\n",
      "1669\n",
      "()\n",
      "Converting to list\n",
      "[586, 274, 32, 0]\n",
      "586\n",
      "()\n",
      "Converting to list\n",
      "[379, 461, 33, 0]\n",
      "379\n",
      "()\n",
      "Converting to list\n",
      "[1628, 372, 34, 0]\n",
      "1628\n",
      "()\n",
      "Converting to list\n",
      "[992, 211, 35, 0]\n",
      "992\n",
      "()\n",
      "Converting to list\n",
      "[271, 551, 36, 0]\n",
      "271\n",
      "()\n",
      "Converting to list\n",
      "[161, 11, 37, 0]\n",
      "161\n",
      "()\n",
      "Converting to list\n",
      "[1602, 499, 38, 0]\n",
      "1602\n",
      "()\n",
      "Converting to list\n",
      "[1609, 188, 39, 0]\n",
      "1609\n",
      "()\n",
      "Converting to list\n",
      "[343, 74, 40, 0]\n",
      "343\n",
      "()\n",
      "Converting to list\n",
      "[309, 436, 41, 0]\n",
      "309\n",
      "()\n",
      "Converting to list\n",
      "[284, 366, 42, 0]\n",
      "284\n",
      "()\n",
      "Converting to list\n",
      "[813, 437, 43, 0]\n",
      "813\n",
      "()\n",
      "Converting to list\n",
      "[64, 375, 44, 0]\n",
      "64\n",
      "()\n",
      "Converting to list\n",
      "[1707, 137, 45, 0]\n",
      "1707\n",
      "()\n",
      "Converting to list\n",
      "[1592, 482, 46, 0]\n",
      "1592\n",
      "()\n",
      "Converting to list\n",
      "[338, 95, 47, 0]\n",
      "338\n",
      "()\n",
      "Converting to list\n",
      "[1051, 262, 48, 0]\n",
      "1051\n",
      "()\n",
      "Converting to list\n",
      "[1726, 371, 49, 0]\n",
      "1726\n",
      "()\n",
      "Converting to list\n",
      "[1112, 266, 50, 0]\n",
      "1112\n",
      "()\n",
      "Converting to list\n",
      "[92, 148, 51, 0]\n",
      "92\n",
      "()\n",
      "Converting to list\n",
      "[1528, 241, 52, 0]\n",
      "1528\n",
      "()\n",
      "Converting to list\n",
      "[1741, 274, 53, 0]\n",
      "1741\n",
      "()\n",
      "Converting to list\n",
      "[781, 532, 54, 0]\n",
      "781\n",
      "()\n",
      "Converting to list\n",
      "[1241, 24, 55, 0]\n",
      "1241\n",
      "()\n",
      "Converting to list\n",
      "[1730, 572, 56, 0]\n",
      "1730\n",
      "()\n",
      "Converting to list\n",
      "[127, 293, 57, 0]\n",
      "127\n",
      "()\n",
      "Converting to list\n",
      "[210, 165, 58, 0]\n",
      "210\n",
      "()\n",
      "Converting to list\n",
      "[1476, 10, 59, 0]\n",
      "1476\n",
      "()\n",
      "Converting to list\n",
      "[971, 19, 60, 0]\n",
      "971\n",
      "()\n",
      "Converting to list\n",
      "[805, 429, 61, 0]\n",
      "805\n",
      "()\n",
      "Converting to list\n",
      "[1761, 383, 62, 0]\n",
      "1761\n",
      "()\n",
      "Converting to list\n",
      "[274, 543, 63, 0]\n",
      "274\n",
      "()\n",
      "Converting to list\n",
      "[210, 220, 64, 0]\n",
      "210\n",
      "()\n",
      "Converting to list\n",
      "[809, 200, 65, 0]\n",
      "809\n",
      "()\n",
      "Converting to list\n",
      "[66, 367, 66, 0]\n",
      "66\n",
      "()\n",
      "Converting to list\n",
      "[400, 221, 67, 0]\n",
      "400\n",
      "()\n",
      "Converting to list\n",
      "[316, 102, 68, 0]\n",
      "316\n",
      "()\n",
      "Converting to list\n",
      "[255, 304, 69, 0]\n",
      "255\n",
      "()\n",
      "Converting to list\n",
      "[1241, 332, 70, 0]\n",
      "1241\n",
      "()\n",
      "Converting to list\n",
      "[1631, 0, 71, 0]\n",
      "1631\n",
      "()\n",
      "Converting to list\n",
      "[714, 32, 72, 0]\n",
      "714\n",
      "()\n",
      "Converting to list\n",
      "[10, 231, 73, 0]\n",
      "10\n",
      "()\n",
      "Converting to list\n",
      "[1647, 270, 74, 0]\n",
      "1647\n",
      "()\n",
      "Converting to list\n",
      "[1556, 263, 75, 0]\n",
      "1556\n",
      "()\n",
      "Converting to list\n",
      "[26, 460, 76, 0]\n",
      "26\n",
      "()\n",
      "Converting to list\n",
      "[873, 328, 77, 0]\n",
      "873\n",
      "()\n",
      "Converting to list\n",
      "[1006, 231, 78, 0]\n",
      "1006\n",
      "()\n",
      "Converting to list\n",
      "[1089, 3, 79, 0]\n",
      "1089\n",
      "()\n",
      "Converting to list\n",
      "[321, 171, 80, 0]\n",
      "321\n",
      "()\n",
      "Converting to list\n",
      "[1549, 270, 81, 0]\n",
      "1549\n",
      "()\n",
      "Converting to list\n",
      "[372, 220, 82, 0]\n",
      "372\n",
      "()\n",
      "Converting to list\n",
      "[1677, 19, 83, 0]\n",
      "1677\n",
      "()\n",
      "Converting to list\n",
      "[980, 426, 84, 0]\n",
      "980\n",
      "()\n",
      "Converting to list\n",
      "[1078, 179, 85, 0]\n",
      "1078\n",
      "()\n",
      "Converting to list\n",
      "[1084, 404, 86, 0]\n",
      "1084\n",
      "()\n",
      "Converting to list\n",
      "[1184, 30, 87, 0]\n",
      "1184\n",
      "()\n",
      "Converting to list\n",
      "[1519, 15, 88, 0]\n",
      "1519\n",
      "()\n",
      "Converting to list\n",
      "[1747, 249, 89, 0]\n",
      "1747\n",
      "()\n",
      "Converting to list\n",
      "[1368, 66, 90, 0]\n",
      "1368\n",
      "()\n",
      "Converting to list\n",
      "[1610, 223, 91, 0]\n",
      "1610\n",
      "()\n",
      "Converting to list\n",
      "[1015, 58, 92, 0]\n",
      "1015\n",
      "()\n",
      "Converting to list\n",
      "[453, 11, 93, 0]\n",
      "453\n",
      "()\n",
      "Converting to list\n",
      "[1691, 408, 94, 0]\n",
      "1691\n",
      "()\n",
      "Converting to list\n",
      "[1709, 213, 95, 0]\n",
      "1709\n",
      "()\n",
      "Converting to list\n",
      "[292, 14, 96, 0]\n",
      "292\n",
      "()\n",
      "Converting to list\n",
      "[1637, 473, 97, 0]\n",
      "1637\n",
      "()\n",
      "Converting to list\n",
      "[1708, 526, 98, 0]\n",
      "1708\n",
      "()\n",
      "Converting to list\n",
      "[1248, 8, 99, 0]\n",
      "1248\n",
      "Saving \"/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/all_clusterer_100clusters_1samples_samples_kdtree_indices.h5\"... (<class 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters= 100\n",
    "samples_dir = \"%s/all_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/all_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(clusterer_dir, projected_features_dir, traj_files, \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=None, parallel=False, lig_name=\"NON\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/enf/md_simulations/MOR/h8_reimaged/sparse-tICA_t50_n_components10all_residues_4dkl_5c1m_under_cutoff6A-CA-py3-far_regularization_wolf_autoShrinkage0pt01-backup/all_clusterer_100clusters_1samples_samples_kdtree'"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "get_trajectory_files(traj_dir, traj_ext)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 5\n",
    "n_clusters=250\n",
    "samples_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "\n",
    "sample_from_clusterer(apo_clusterer_file, apo_tica_file, [traj_files[i] for i in apo_trajs],\n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=None, parallel=True, lig_name=\"LIG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "traj_files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "feature_name_residues_dict.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "\n",
    "np.shape(apo_pnas_resampled)\n",
    "msm_dir = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d_analysis\" %(lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(msm_dir): os.makedirs(msm_dir)\n",
    "\n",
    "#plot_columns(msm_dir, apo_pnas_resampled_file, titles = feature_name_residues_dict.keys(), main = \"Apo-mOR\", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pip\n",
    "\n",
    "def install(package):\n",
    "    pip.main(['install', package])\n",
    "    \n",
    "install(\"moviepy\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "\n",
    "for i, traj in enumerate(get_trajectory_files(traj_dir, traj_ext)):\n",
    "    if \"apo_rep_68.\" in traj:\n",
    "        index=i\n",
    "        break\n",
    "\n",
    "jointplot(apo_pnas_resampled[::10,[6,3]], \"%s/test.pdf\" %msm_dir, trajectory=apo_pnas[index][::1,[6,3]], \n",
    "          titles=[\"TM6 to TM3 distance\", \"RMSD of NPxxY to Inactive\"], main = \"mOR Activation Pathway\", \n",
    "          video_file = \"%s/apo_68.mp4\" %msm_dir, custom_xlim=[4.0, 16.0], custom_ylim= [0.0, 1.0])\n",
    "#test(\"%s/test2.mp4\" %msm_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "build_msm(bu72_clusterer_file, lag_time, msm_model_dir)\n",
    "build_msm(apo_clusterer_file, lag_time, msm_model_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tics_1_5_file = os.path.join(tica_dir, \"tICs_1_5.h5\")\n",
    "tics = load_file(projected_features_dir)\n",
    "tics_1_5 = [x[:,range(1,5)] for x in tics]\n",
    "verbosedump(tics_1_5, tics_1_5_file)\n",
    "\n",
    "clusterer300_clusters = os.path.join(tica_dir, \"clusterer300_clusters_tICs1_5.h5\")\n",
    "cluster_minikmeans(tica_dir, tics_1_5_file, traj_dir, n_clusters=300, clusterer_dir=clusterer300_clusters)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "len(dview)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "suf_traj_files = [t for t in featurized_trajectories if \"suf\" in t]\n",
    "reduced_clusterer = compat_verboseload(clusterer300_clusters)\n",
    "suf_reduced_clusterer_file = \"%s/suf_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "suf_reduced_tica_file = \"%s/suf_reduced_tica.h5\" %tica_dir\n",
    "suf_reduced_tica = [x[:,range(1,5)] for x in suf_tica]\n",
    "suf_reseeded_dir = \"%s/suf_reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(suf_reseeded_dir):\n",
    "    os.makedirs(suf_reseeded_dir)\n",
    "verbosedump(suf_reduced_tica, suf_reduced_tica_file)\n",
    "\n",
    "suf_reduced_clusters = [reduced_clusterer.labels_[i] for i in suf_trajs]\n",
    "suf_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "suf_reduced_clusterer.labels_ = suf_reduced_clusters\n",
    "verbosedump(suf_reduced_clusterer, suf_reduced_clusterer_file)\n",
    "#reseed_from_clusterer(suf_reduced_clusterer_file, \"suf\", suf_reseeded_dir, suf_reduced_tica_file, suf_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(suf_reduced_clusterer_file, suf_reduced_tica_file, [traj_files[i] for i in suf_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "bu72_traj_files = [t for t in featurized_trajectories if \"bu72\" in t]\n",
    "reduced_clusterer = compat_verboseload(clusterer300_clusters)\n",
    "bu72_reduced_clusterer_file = \"%s/bu72_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "bu72_reduced_tica_file = \"%s/bu72_reduced_tica.h5\" %tica_dir\n",
    "bu72_reduced_tica = [x[:,range(1,5)] for x in bu72_tica]\n",
    "bu72_reseeded_dir = \"%s/bu72_reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(bu72_reseeded_dir):\n",
    "    os.makedirs(bu72_reseeded_dir)\n",
    "verbosedump(bu72_reduced_tica, bu72_reduced_tica_file)\n",
    "\n",
    "bu72_reduced_clusters = [reduced_clusterer.labels_[i] for i in bu72_trajs]\n",
    "bu72_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "bu72_reduced_clusterer.labels_ = bu72_reduced_clusters\n",
    "verbosedump(bu72_reduced_clusterer, bu72_reduced_clusterer_file)\n",
    "#reseed_from_clusterer(bu72_reduced_clusterer_file, \"bu72\", bu72_reseeded_dir, bu72_reduced_tica_file, bu72_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/bu72_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/bu72_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/bu72_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(bu72_reduced_clusterer_file, bu72_reduced_tica_file, [traj_files[i] for i in bu72_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "apo_traj_files = [t for t in featurized_trajectories if \"apo\" in t]\n",
    "reduced_clusterer = compat_verboseload(clusterer300_clusters)\n",
    "apo_reduced_clusterer_file = \"%s/apo_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "apo_reduced_tica_file = \"%s/apo_reduced_tica.h5\" %tica_dir\n",
    "apo_reduced_tica = [x[:,range(1,5)] for x in apo_tica]\n",
    "apo_reseeded_dir = \"%s/apo_reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(apo_reseeded_dir):\n",
    "    os.makedirs(apo_reseeded_dir)\n",
    "verbosedump(apo_reduced_tica, apo_reduced_tica_file)\n",
    "\n",
    "apo_reduced_clusters = [reduced_clusterer.labels_[i] for i in apo_trajs]\n",
    "apo_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "apo_reduced_clusterer.labels_ = apo_reduced_clusters\n",
    "verbosedump(apo_reduced_clusterer, apo_reduced_clusterer_file)\n",
    "#reseed_from_clusterer(apo_reduced_clusterer_file, \"apo\", apo_reseeded_dir, apo_reduced_tica_file, apo_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(apo_reduced_clusterer_file, apo_reduced_tica_file, [traj_files[i] for i in apo_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "oxy_traj_files = [t for t in featurized_trajectories if \"oxy\" in t]\n",
    "reduced_clusterer = compat_verboseload(clusterer300_clusters)\n",
    "oxy_reduced_clusterer_file = \"%s/oxy_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "oxy_reduced_tica_file = \"%s/oxy_reduced_tica.h5\" %tica_dir\n",
    "oxy_reduced_tica = [x[:,range(1,10)] for x in oxy_tica]\n",
    "verbosedump(oxy_reduced_tica, oxy_reduced_tica_file)\n",
    "\n",
    "oxy_reduced_clusters = [reduced_clusterer.labels_[i] for i in oxy_trajs]\n",
    "oxy_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "oxy_reduced_clusterer.labels_ = oxy_reduced_clusters\n",
    "verbosedump(oxy_reduced_clusterer, oxy_reduced_clusterer_file)\n",
    "reseed_from_clusterer(oxy_reduced_clusterer_file, \"oxy\", tica_dir, oxy_reduced_tica_file, oxy_traj_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "closest_indices = find_closest_indices_to_cluster_center(tics_1_3_file, clusterer16_clusters)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "closest_indices"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from scipy.stats import gamma \n",
    "x = np.linspace(0.,16.0, 100)\n",
    "y = gamma.pdf(x, 5.0, loc=8.0, scale=1)\n",
    "plt.plot(x,y)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from scipy.stats import gamma \n",
    "x = np.linspace(0.,16.0, 100)\n",
    "y = gamma.pdf(x, 3.0, loc=8.0, scale=0.4)\n",
    "plt.plot(x,y)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "reseed_from_clusterer(oxy_clusterer_file, \"oxy\", tica_dir, oxy_tica_file, [trajs[i] for i in oxy_trajs])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "min_pop = [3, 4, 6, 8, 9, 26, 29, 30, 31, 32, 33, 39, 41, 43, 52, 55]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_all_tics_and_clusters(tica_dir, oxy_tica_file, oxy_clusterer_file, lag_time, tic_range=range(0,5), main = \"Oxy_Reseeds\", label = \"cluster_id\", active_cluster_ids = min_pop, intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=True, axes=tica_axes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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