Update for super

Docking/ProgressiveDocking/activation_script.sh

@@ -1,3 +1,3 @@
 echo Activating virtual environment
 source ~/.bashrc
-conda activate DeepDockingRemote
+conda activate app-deepdocking-gui-remote

Docking/ProgressiveDocking/phase_2.sh

@@ -32,7 +32,7 @@ python $script_path/jobid_writer.py -file_path $project_path -n_it $iteration -j
 # For some reason, running this with the conda environment activated causes an error.
 # We must deactivate it before running!
 source ~/.bashrc
-source $local_path/deactivation_script.sh
+source $script_path/deactivation_script.sh
 
 # Move into the project
 cd $project_path/iteration_$iteration

Docking/ProgressiveDocking/phase_3.sh

@@ -42,7 +42,7 @@ python jobid_writer.py -file_path $project_path -n_it $iteration -jid $SLURM_JOB
 cd $project_path/iteration_$iteration
 echo Running Phase 3
 mkdir res
-for i in $(ls -d chunks_smi/*); do fld=$(echo $i | rev | cut -d'/' -f 1 | rev); mkdir res/$fld; cd res/$fld; sbatch $slurm_args_g $scripts/autodock_gpu_ad.sh 64 sw $PATH_FLD ../../$i'/'$fld'_'pdbqt list.txt $num_energy_evaluations $num_runs $path_to_auto_dock_gpu $scripts; cd ../../;done
+for i in $(ls -d chunks_smi/*); do fld=$(echo $i | rev | cut -d'/' -f 1 | rev); mkdir res/$fld; cd res/$fld; sbatch $slurm_args_g $scripts/autodock_gpu_ad.sh 128 sw $PATH_FLD ../../$i'/'$fld'_'pdbqt list.txt $num_energy_evaluations $num_runs $path_to_auto_dock_gpu $scripts; cd ../../;done
 
 cd $scripts
 python phase_changer.py -pf phase_3.sh -itr $project_path/iteration_$iteration

Docking/ProgressiveDocking/phase_a.sh

@@ -46,6 +46,10 @@ echo - Chunk Size: $chunk_size
 echo - Percent First Mol: $percent_fist_mol
 echo - Percent Last Mol: $percent_last_mol
 
+# This should activate the conda environment
+source ~/.bashrc
+source $local_path/activation_script.sh
+
 # Grab everything from the logs file
 file_path=$(sed -n '1p' $2/$3/logs.txt)
 protein=$(sed -n '2p' $2/$3/logs.txt)

Docking/ProgressiveDocking/sampling.py

@@ -131,7 +131,7 @@ def train_valid_test(file_name):
 
     f_names = []
     # Getting all the morgan_1024_predictions/smile_all_##.txt files
-    for f in glob.glob(data_directory+'/smile*_all_*.txt'):
+    for f in glob.glob(data_directory+'/*.txt'):
         f_names.append(f)
 
     print("num_f_names: ", len(f_names))

GUI/package.json

@@ -38,8 +38,9 @@
   "scripts": {
     "test": "mocha",
     "start-lin": "export FLASK_APP=server.py && export FLASK_ENV=local_host && flask run",
-    "start-win": "conda activate DeepDockingLocal && set FLASK_APP=server.py && set FLASK_ENV=local_host && flask run",
-    "start-dev": "conda activate DeepDockingLocal && set FLASK_APP=server.py && set FLASK_ENV=development && set FLASK_DEBUG=1 && flask run",
+    "start-lin-global": "export FLASK_APP=server.py && export FLASK_ENV=local_host && flask run --host=0.0.0.0",
+    "start-win": "conda activate app-deepdocking-gui && set FLASK_APP=server.py && set FLASK_ENV=local_host && flask run",
+    "start-dev": "conda activate app-deepdocking-gui && set FLASK_APP=server.py && set FLASK_ENV=development && set FLASK_DEBUG=1 && flask run",
     "build": "webpack --progress --config webpack.config.js",
     "dev-build": "webpack -d --progress --config webpack.config.js"
   },

GUI/server.py

@@ -29,16 +29,16 @@
 MODE_SCAFFOLD = None
 PROJECTS_PATH = './src/backend/projects/'
 
-# Launching the app automatically if prompted
-if not app.debug:
-    # Ask user if they want to open the DD website automatically
-    prompt = "\nOpen Website On Default Browser? \nEnter y to launch or any other key to open manually: "
-    open_site = True if input(prompt).rstrip() == "y" else False
-    if open_site:
-        import webbrowser
-        webbrowser.open("http://127.0.0.1:5000/")
-    else:
-        print("Enter the provided link into your browser.")
+# # Launching the app automatically if prompted
+# if not app.debug:
+#     # Ask user if they want to open the DD website automatically
+#     prompt = "\nOpen Website On Default Browser? \nEnter y to launch or any other key to open manually: "
+#     open_site = True if input(prompt).rstrip() == "y" else False
+#     if open_site:
+#         import webbrowser
+#         webbrowser.open("http://127.0.0.1:5000/")
+#     else:
+#         print("Enter the provided link into your browser.")
 
 def serve_pil_image(pil_img):
     img_io = BytesIO()

GUI/src/backend/auto_ssh.py

@@ -7,7 +7,7 @@ class SSH:
 
     """ This class will automatically ssh into the host cluster. """
 
-    def __init__(self, host=None):
+    def __init__(self, host=None, port=None):
         if host is None:
             try:
                 json_str = open('src/backend/db.json').read() # TODO: Sibling files not recognizing each other when called from another file path.
@@ -16,9 +16,19 @@ def __init__(self, host=None):
             except FileNotFoundError as e:
                 print(e.__traceback__, "'db.json' not found! Please run the installation first before running GUI.")
                 raise e
+
+        if port is None:
+            try:
+                json_str = open('src/backend/db.json').read() # TODO: Sibling files not recognizing each other when called from another file path.
+                db_dict = json.loads(json_str)
+                port = db_dict['port']
+            except FileNotFoundError as e:
+                print(e.__traceback__, "'db.json' not found! Please run the installation first before running GUI.")
+                raise e
 
         # The information that will allow for ssh
         self.host = host
+        self.port = port
         self.user = ""
         self.pwrd = ""
         self.ssh = None
@@ -40,7 +50,7 @@ def connect(self, username, password):
         # Connect to ssh and set out ssh object
         ssh = paramiko.SSHClient()
         ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
-        ssh.connect(self.host, username=self.user, password=self.pwrd)
+        ssh.connect(self.host, port=self.port, username=self.user, password=self.pwrd)
         self.ssh = ssh
 
     def download(self, remote_path, local_path):

GUI/src/backend/backend_sanity_check.py

@@ -8,10 +8,11 @@ def check_backend():
     json_str = open('src/backend/db.json').read()  # TODO: Sibling files not recognizing each other when called from another file path.
     db_dict = json.loads(json_str)
     ip = db_dict['ip']
+    port = db_dict.get['port']
 
     user = input("cluster username: ")
     password = input("cluster password: ")
-    ssh_connection = SSH(host=ip)
+    ssh_connection = SSH(host=ip, port=port)
     ssh_connection.connect(username=user, password=password)
     backend = Backend(ssh=ssh_connection)
     return backend

README.md

@@ -70,7 +70,7 @@ bash prepare_receptor.py receptor.pdb 'x_size,y_size,z_size' 'x_center,y_center,
 - path_adt_scripts: path to folder with AutodockTools python scripts (prepare_receptor4.py, etc etc..)
 
 ## 1. Starting up the GUI
-After installation, a new Conda environment on your local device called *DeepDockingLocal* should now be available. To start up the GUI, activate the *DeepDockingLocal* environment then navigate to `Deep-Docking/GUI` and run the appropriate command to start up the server.
+After installation, a new Conda environment on your local device called *app-deepdocking-gui* should now be available. To start up the GUI, activate the *app-deepdocking-gui* environment then navigate to `Deep-Docking/GUI` and run the appropriate command to start up the server.
 
 For mac and linux:
 ```bash 
@@ -84,7 +84,7 @@ npm run start-win
 After running the above, you should see something similar to the following: 
 ```bash 
 > [email protected] start-win
-> conda activate DeepDockingLocal && set FLASK_APP=server.py && set FLASK_ENV=local_host && flask run
+> conda activate app-deepdocking-gui && set FLASK_APP=server.py && set FLASK_ENV=local_host && flask run
 
  * Serving Flask app "server.py "
  * Environment: local_host 
@@ -178,7 +178,7 @@ From the top scoring tab (figure 7) we can download a list of the top 1000 molec
     model_config = json.loads(model_config.decode('utf-8'))
 AttributeError: 'str' Object has no attribute 'decode'
 ```
-  >This error is followed by an `IndexError` on line 264 of `get_model_image` and is most likely a dependancy issue with keras, make sure you have version 2.10.0 of `h5py` (versions 3.0+ cause issues) installed on the cluster side in the `DeepDockingRemote` conda environment. You can check the version by first activating the conda environment and then typing `pip show h5py`.<br>
+  >This error is followed by an `IndexError` on line 264 of `get_model_image` and is most likely a dependancy issue with keras, make sure you have version 2.10.0 of `h5py` (versions 3.0+ cause issues) installed on the cluster side in the `app-deepdocking-gui-remote` conda environment. You can check the version by first activating the conda environment and then typing `pip show h5py`.<br>
   >You can install/downgrade it using pip: `pip install h5py==2.10.0` 
 
 

installation/DeepDockingLocal.yml → installation/app-deepdocking-gui.yml

@@ -1,4 +1,4 @@
-name: DeepDockingLocal
+name: app-deepdocking-gui
 channels:
   - conda-forge
   - bioconda

installation/install-linux.sh

@@ -1,8 +1,8 @@
-#!/bin/bash
+#!/bin/bash -l
 
 # Create the local env
 python3 install.py --phase install_local
 # Activate the env
-conda activate DeepDockingLocal 2> conda.out
+conda activate app-deepdocking-gui 2> conda.out
 # Install remote files and create remote env
 python3 install.py --phase install_remote

installation/install-windows.bat

@@ -1,3 +1,3 @@
 python install.py --phase install_local
-call conda activate DeepDockingLocal > conda.out
+call conda activate app-deepdocking-gui > conda.out
 python install.py --phase install_remote