Code

Automated Solvation Shell Analysis#227

Code

Open

cadeduckworth wants to merge 115 commits intodevelopBecksteinlab/MDPOW:developfrom automated-solvation-shellBecksteinlab/MDPOW:automated-solvation-shellCopy head branch name to clipboard

+204-16

Commits

Commits on Sep 15, 2022

• developing back end run methods

  Show description for e71456d
  cadeduckworth

  committed
  e71456d

  Copy full SHA for e71456d

• condensed backend run methods

  Show description for 6c67ec1
  cadeduckworth

  committed
  6c67ec1

  Copy full SHA for 6c67ec1

Commits on Oct 20, 2022

• Initial adding of automation functionality to dihedral.py

  Show description for 9914675
  cadeduckworth

  committed
  9914675

  Copy full SHA for 9914675

• moved directory_paths function to reside within the DihedralAnalysis class to test possible ways to call automation-related functions

  cadeduckworth

  committed
  f9b6646

  Copy full SHA for f9b6646

Commits on Oct 22, 2022

• Addressed change requests by Oliver

  Show description for 7bcdf49
  cadeduckworth

  committed
  7bcdf49

  Copy full SHA for 7bcdf49

• fixed indentation error for _single_frame() block

  cadeduckworth

  committed
  a87cb11

  Copy full SHA for a87cb11

• reverting previous tab issue, necessary for normal function

  cadeduckworth

  committed
  7edde0d

  Copy full SHA for 7edde0d

Commits on Oct 23, 2022

• fixed errors previously reverted for testing

  Show description for 48016c5
  cadeduckworth

  committed
  48016c5

  Copy full SHA for 48016c5

• Merge branch 'develop' into ensemble_run_update

  cadeduckworth

  authored
  59c819c

  Copy full SHA for 59c819c

Commits on Oct 28, 2022

• restored original dihedral.py file

  cadeduckworth

  committed
  6b1be1b

  Copy full SHA for 6b1be1b

• created automation/dihedral subdirectory under mdpow/analysis/ to house automation for DihedralAnalysis

  Show description for 2ddea0e
  cadeduckworth

  committed
  2ddea0e

  Copy full SHA for 2ddea0e

• updated docstrings and added examples for directory_paths.py

  cadeduckworth

  committed
  ad6db6e

  Copy full SHA for ad6db6e

• added docstrings and examples for directory_iteration.py

  cadeduckworth

  committed
  848dd87

  Copy full SHA for 848dd87

• added initial draft of docstrings and examples for all functions contained within automated_dihedral_analysis.py

  cadeduckworth

  committed
  6394d7a

  Copy full SHA for 6394d7a

Commits on Nov 12, 2022

• added the option to save the DihedralAnalysis results DataFrame as csv files in provided parent directory

  cadeduckworth

  committed
  d8f3ca3

  Copy full SHA for d8f3ca3

Commits on Nov 17, 2022

• removed redundant DataFrame saving pattern from automated_dihedral_analysis

  cadeduckworth

  committed
  d8137cb

  Copy full SHA for d8137cb

• Merge remote-tracking branch 'origin/ensemble_run_update' into automated-dihedral-analysis

  Show description for 29477ab
  cadeduckworth

  committed
  29477ab

  Copy full SHA for 29477ab

• merged updates from PR #216 and PR #218

  cadeduckworth

  committed
  642e87e

  Copy full SHA for 642e87e

• Merge branch 'develop' into automated-dihedral-analysis

  orbeckst

  authored
  4814376

  Copy full SHA for 4814376

Commits on Nov 18, 2022

• Merge branch 'develop' into automated-dihedral-analysis

  orbeckst

  authored
  f333ee8

  Copy full SHA for f333ee8

Commits on Dec 14, 2022

• resolved conflicts to merge updates in from develop from PR#216

  cadeduckworth

  committed
  6f16b84

  Copy full SHA for 6f16b84

• adding data for testing automated dihedral analysis

  cadeduckworth

  committed
  ddffbdf

  Copy full SHA for ddffbdf

Commits on Dec 15, 2022

• added starting framework for testing automated dihedral analysis

  cadeduckworth

  committed
  c850448

  Copy full SHA for c850448

• reorganized automation directory into workflows directory

  cadeduckworth

  committed
  69b0351

  Copy full SHA for 69b0351

• added preliminary simple core tests for automated dihedral analysis

  cadeduckworth

  committed
  4cf176d

  Copy full SHA for 4cf176d

• initial reformatting of existing docs for sphinx markup compatibility

  Show description for 97c4a73
  cadeduckworth

  committed
  97c4a73

  Copy full SHA for 97c4a73

• fix errors in docs for workflows

  cadeduckworth

  committed
  930d54e

  Copy full SHA for 930d54e

• added imports for automated dihedral analysis tests

  cadeduckworth

  committed
  84536ff

  Copy full SHA for 84536ff

• added init file for workflows module

  cadeduckworth

  committed
  f01b2a4

  Copy full SHA for f01b2a4

• added logging functionality for workflows modules

  cadeduckworth

  committed
  61ff494

  Copy full SHA for 61ff494

• sphinx markup corrections for workflow modules

  cadeduckworth

  committed
  f7b3f53

  Copy full SHA for f7b3f53

Commits on Dec 16, 2022

• redo of reduced testing data for GAFF SM25 from original full dataset, reduced original by factor of 100 this time, timestep is now 50ps, amount of frames and total length of simulation preserved

  cadeduckworth

  committed
  d16dc7d

  Copy full SHA for d16dc7d

• sphinx docs automodule test

  cadeduckworth

  committed
  bcfa10f

  Copy full SHA for bcfa10f

• sphinx docs test base.txt

  cadeduckworth

  committed
  b8c309d

  Copy full SHA for b8c309d

• docs

  cadeduckworth

  committed
  837f53e

  Copy full SHA for 837f53e

• docs

  cadeduckworth

  committed
  44db567

  Copy full SHA for 44db567

• docs

  cadeduckworth

  committed
  e53dfb6

  Copy full SHA for e53dfb6

Commits on Dec 17, 2022

• edit docs

  cadeduckworth

  committed
  5f28b46

  Copy full SHA for 5f28b46

• edit docs

  cadeduckworth

  committed
  e58703a

  Copy full SHA for e58703a

• edit docs

  cadeduckworth

  committed
  bbcb5de

  Copy full SHA for bbcb5de

• edit docs

  cadeduckworth

  committed
  45892b6

  Copy full SHA for 45892b6

• edit docs

  cadeduckworth

  committed
  eaf767a

  Copy full SHA for eaf767a

• update py.path to pathlib in test_automated_dihedral_analysis

  cadeduckworth

  committed
  f19f32e

  Copy full SHA for f19f32e

• update reference testing values for new reduced dataset, test_automated_dihedral_analysis

  cadeduckworth

  committed
  41166a4

  Copy full SHA for 41166a4

• change syntax in test_automated_dihedral_analysis to compare objects instead of strings

  cadeduckworth

  committed
  1de662e

  Copy full SHA for 1de662e

• update assert_almost_equal to pytest.approx

  cadeduckworth

  committed
  4eafa23

  Copy full SHA for 4eafa23

• bounce redundant function calls to a pytest.fixture for use with multiple tests

  cadeduckworth

  committed
  4833a45

  Copy full SHA for 4833a45

• add bz2 compression for dataframe storage of automated dihedral analysis data

  cadeduckworth

  committed
  5be6684

  Copy full SHA for 5be6684

• Update ci.yaml

  cadeduckworth

  authored
  ef750f1

  Copy full SHA for ef750f1

Commits on Jan 5, 2023

• added functionality for user input of alternative SMARTS string selection for automated dihedral analysis, including docs and tests

  cadeduckworth

  committed
  4c9251b

  Copy full SHA for 4c9251b

• Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab/MDPOW into automated-dihedral-analysis

  cadeduckworth

  committed
  187632b

  Copy full SHA for 187632b

• add tests for automated directory iteration of dihedral analysis, workflows/base.py

  cadeduckworth

  committed
  7abb0bc

  Copy full SHA for 7abb0bc

• add tests for saving dataframes and saving figures, which covers the full automation of automated dihedral analysis

  cadeduckworth

  committed
  372a205

  Copy full SHA for 372a205

• add test for directory iteration of fully automated dihedral analysis

  Show description for 39518c2
  cadeduckworth

  committed
  39518c2

  Copy full SHA for 39518c2

Commits on Jan 7, 2023

• moved location of rdkit install used for testing/pytest

  cadeduckworth

  committed
  37eb085

  Copy full SHA for 37eb085

• remove misplaced hbonds documentation

  cadeduckworth

  committed
  85b54f3

  Copy full SHA for 85b54f3

• relocate test data for workflows and change test scripts accordingly

  cadeduckworth

  committed
  1e5aadc

  Copy full SHA for 1e5aadc

• removed unnecessary .ipynb, .lock, and .npz files

  cadeduckworth

  committed
  edc0a9a

  Copy full SHA for edc0a9a

• simplified keyword specification for default and user input of SMARTS string selection

  cadeduckworth

  committed
  eb41100

  Copy full SHA for eb41100

• fixed plotting issue for solvents (name and order)

  cadeduckworth

  committed
  b91240e

  Copy full SHA for b91240e

• variable name issue in testing module, user_SMARTS -> SMARTS

  cadeduckworth

  committed
  fbca70d

  Copy full SHA for fbca70d

Commits on Jan 8, 2023

• Delete dir.csv

  cadeduckworth

  authored
  b0081ef

  Copy full SHA for b0081ef

• import syntax

  cadeduckworth

  committed
  0520ffa

  Copy full SHA for 0520ffa

• sphinx docs

  cadeduckworth

  committed
  77df0ee

  Copy full SHA for 77df0ee

• Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab/MDPOW into automated-dihedral-analysis

  Show description for 17a0b4a
  cadeduckworth

  committed
  17a0b4a

  Copy full SHA for 17a0b4a

• docs

  cadeduckworth

  committed
  7359319

  Copy full SHA for 7359319

• docs

  cadeduckworth

  committed
  8f8f26c

  Copy full SHA for 8f8f26c

• docs

  cadeduckworth

  committed
  c452475

  Copy full SHA for c452475

• docs

  cadeduckworth

  committed
  3dd1b31

  Copy full SHA for 3dd1b31

• docs

  cadeduckworth

  committed
  cecd928

  Copy full SHA for cecd928

• docs

  cadeduckworth

  committed
  5b87e83

  Copy full SHA for 5b87e83

• docs

  cadeduckworth

  committed
  86804d8

  Copy full SHA for 86804d8

• docs

  cadeduckworth

  committed
  0ab0299

  Copy full SHA for 0ab0299

• docs

  cadeduckworth

  committed
  3964a44

  Copy full SHA for 3964a44

• docs

  cadeduckworth

  committed
  dfb7e8e

  Copy full SHA for dfb7e8e

• docs

  cadeduckworth

  committed
  be86754

  Copy full SHA for be86754

• docs

  cadeduckworth

  committed
  f6330cb

  Copy full SHA for f6330cb

• docs

  cadeduckworth

  committed
  ab6800e

  Copy full SHA for ab6800e

• docs

  cadeduckworth

  committed
  6bdc521

  Copy full SHA for 6bdc521

• docs

  cadeduckworth

  committed
  0a7963d

  Copy full SHA for 0a7963d

• docs

  cadeduckworth

  committed
  1866d43

  Copy full SHA for 1866d43

• docs

  cadeduckworth

  committed
  495546c

  Copy full SHA for 495546c

• docs

  cadeduckworth

  committed
  956b359

  Copy full SHA for 956b359

• docs

  cadeduckworth

  committed
  0ad73db

  Copy full SHA for 0ad73db

• docs

  cadeduckworth

  committed
  f6beebb

  Copy full SHA for f6beebb

• docs

  cadeduckworth

  committed
  036d939

  Copy full SHA for 036d939

• docs

  cadeduckworth

  committed
  58f33c3

  Copy full SHA for 58f33c3

• moving workflows location, subsequent doc changes

  cadeduckworth

  committed
  d704f95

  Copy full SHA for d704f95

• import changed to reflect moving workflows module

  cadeduckworth

  committed
  02e10e5

  Copy full SHA for 02e10e5

• docs

  cadeduckworth

  committed
  891782e

  Copy full SHA for 891782e

• add requirements for sphinx build

  cadeduckworth

  committed
  148e56f

  Copy full SHA for 148e56f

• add requirements for sphinx build

  cadeduckworth

  committed
  a03951c

  Copy full SHA for a03951c

• add requirements for sphinx build

  cadeduckworth

  committed
  31291f1

  Copy full SHA for 31291f1

• add requirements for sphinx build

  cadeduckworth

  committed
  652e788

  Copy full SHA for 652e788

• add requirements for sphinx build

  cadeduckworth

  committed
  48c7e88

  Copy full SHA for 48c7e88

• docs

  cadeduckworth

  committed
  ba17ceb

  Copy full SHA for ba17ceb

• docs

  cadeduckworth

  committed
  68cbc9c

  Copy full SHA for 68cbc9c

• docs structure

  cadeduckworth

  committed
  8c5c2ec

  Copy full SHA for 8c5c2ec

• consistent keyword names in tests

  cadeduckworth

  committed
  8d29f91

  Copy full SHA for 8d29f91

• imports and docs

  cadeduckworth

  committed
  24f6c00

  Copy full SHA for 24f6c00

• imports

  cadeduckworth

  committed
  63e3de4

  Copy full SHA for 63e3de4

• imports

  cadeduckworth

  committed
  104bf93

  Copy full SHA for 104bf93

• generalizing automation base module for use with other analyses

  cadeduckworth

  committed
  1ad6b8c

  Copy full SHA for 1ad6b8c

• initialize PR for automated-solvation-shell module

  cadeduckworth

  committed
  3f65e28

  Copy full SHA for 3f65e28

Commits on Jan 9, 2023

• initial script for automated solvation shell analysis

  cadeduckworth

  committed
  80c641c

  Copy full SHA for 80c641c

• updated automated solvation module, incomplete, issue with compression

  cadeduckworth

  committed
  09721c7

  Copy full SHA for 09721c7

• fixed automated solvation shell analysis module

  Show description for 68c0b1e
  cadeduckworth

  committed
  68c0b1e

  Copy full SHA for 68c0b1e

• docs and func names

  cadeduckworth

  committed
  7181017

  Copy full SHA for 7181017

Commits on Jan 15, 2023

• cleanup and remove workflows base module/move to new PR

  cadeduckworth

  committed
  e3ef88f

  Copy full SHA for e3ef88f

Commits on Apr 5, 2023

• resolving conflicts

  cadeduckworth

  committed
  36be611

  Copy full SHA for 36be611

• add new version of testing resources

  cadeduckworth

  committed
  b876ad1

  Copy full SHA for b876ad1

• correct module name

  cadeduckworth

  committed
  1f62fa6

  Copy full SHA for 1f62fa6

• start test module for solvations

  cadeduckworth

  committed
  77f7054

  Copy full SHA for 77f7054

• change data obtained by SolvationAnalysis

  cadeduckworth

  committed
  041c6ed

  Copy full SHA for 041c6ed

Commits on Apr 6, 2023

• name top-level automated solvation function and complete addition to workflows registry/registry docs

  cadeduckworth

  committed
  61f53b9

  Copy full SHA for 61f53b9