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Add OpenMM module #482

Merged
merged 80 commits into from
Oct 4, 2024
Merged

Add OpenMM module #482

merged 80 commits into from
Oct 4, 2024

Commits on Jun 20, 2022

  1. Add OpenMM module 

    The code presented in this commit was enterily done by Ivar de Leeuw
during his Master course: Major Research Project (GSLS), academic year 2021-2022.

I am pushing the code after Ivar's request and in its exact original form.

In the next commits, the team will work on Ivar's code to accommodate it fully
to the HADDOCK3 project.

Thanks Ivar for all your great work and best luck on your future studies!
    @joaomcteixeira
    joaomcteixeira committed Jun 20, 2022
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  2. lint openmm init file

    @joaomcteixeira
    joaomcteixeira committed Jun 20, 2022
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  3. general lint openmm functions

    @joaomcteixeira
    joaomcteixeira committed Jun 20, 2022
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Commits on Jun 21, 2022

  1. added installation procedure for openmm

    @mgiulini
    mgiulini committed Jun 21, 2022
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  2. modified openmm installation instructions

    @mgiulini
    mgiulini committed Jun 21, 2022
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  3. corrects linting and compatibility with Paths

    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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  4. solve the globals

    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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  5. correct extra paths and list to string parameters

    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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  6. adds dots and bars to string in config reader

    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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  7. additional changes

    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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  8. Revert original files to their original version 

    Undo linting from all previous commits. After linting, some deep bug
appeared and I found no way to reproduce the original results. So, we need to
lint block by block very carefully.

I left the other files: install.md and config_read untouched because
those changes will surely go through.
    @joaomcteixeira
    joaomcteixeira committed Jun 21, 2022
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Commits on Jun 28, 2022

  1. Merge branch 'main' into openmm

    @mgiulini
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  2. changed run folders and parameters

    @mgiulini
    mgiulini committed Jun 28, 2022
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Commits on Jul 7, 2022

  1. updated openmm cfg file

    @mgiulini
    mgiulini committed Jul 7, 2022
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  2. rewritten openmm functions

    @mgiulini
    mgiulini committed Jul 7, 2022
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  3. deleted old openmm functions

    @mgiulini
    mgiulini committed Jul 7, 2022
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  4. fixed lint

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    mgiulini committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. added refinement feature to openmm

    @mgiulini
    mgiulini committed Jul 8, 2022
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  2. fixed lint

    @mgiulini
    mgiulini committed Jul 8, 2022
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  3. added log on solvent type

    @mgiulini
    mgiulini committed Jul 8, 2022
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  4. removed unnecessary comments

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    mgiulini committed Jul 8, 2022
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  5. completed example of topoaa after openmm

    @mgiulini
    mgiulini committed Jul 8, 2022
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Commits on Jul 12, 2022

  1. address issues

    @joaomcteixeira
    joaomcteixeira committed Jul 12, 2022
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  2. revert config_reader

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  3. correct params in examples cfg

    @joaomcteixeira
    joaomcteixeira committed Jul 12, 2022
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  4. revert to string parameters

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  5. and the cfg test files

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Commits on Jul 13, 2022

  1. correct variables in example

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    joaomcteixeira committed Jul 13, 2022
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  2. added documentation pages

    @joaomcteixeira
    joaomcteixeira committed Jul 13, 2022
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Commits on Jul 15, 2022

  1. changed parameter names and descriptions

    @mgiulini
    mgiulini committed Jul 15, 2022
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Commits on Jul 28, 2022

  1. modifications to parameter intermediates

    @mgiulini
    mgiulini committed Jul 28, 2022
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  2. Merge branch 'main' into openmm

    @mgiulini
    mgiulini committed Jul 28, 2022
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  3. modified example

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Commits on Aug 9, 2022

  1. Merge branch 'main' into openmm

    @mgiulini
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  2. Merge branch 'main' into openmm

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Commits on Aug 31, 2022

  1. merged main

    @mgiulini
    mgiulini committed Aug 31, 2022
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  2. added updated examples

    @mgiulini
    mgiulini committed Aug 31, 2022
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  3. fixed lint

    @mgiulini
    mgiulini committed Aug 31, 2022
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  4. Update src/haddock/modules/refinement/openmm/openmm.py 

    Co-authored-by: João M.C. Teixeira <joaomcteixeira@gmail.com>
    @mgiulini @joaomcteixeira
    mgiulini and joaomcteixeira authored Aug 31, 2022
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  5. Update src/haddock/modules/refinement/openmm/openmm.py 

    Co-authored-by: João M.C. Teixeira <joaomcteixeira@gmail.com>
    @mgiulini @joaomcteixeira
    mgiulini and joaomcteixeira authored Aug 31, 2022
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  6. Update src/haddock/modules/refinement/openmm/openmm.py 

    Co-authored-by: João M.C. Teixeira <joaomcteixeira@gmail.com>
    @mgiulini @joaomcteixeira
    mgiulini and joaomcteixeira authored Aug 31, 2022
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  7. moved run_subprocess function

    @mgiulini
    mgiulini committed Aug 31, 2022
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  8. corrected description format

    @mgiulini
    mgiulini committed Aug 31, 2022
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  9. fixed lint and docs

    @mgiulini
    mgiulini committed Aug 31, 2022
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  10. corrected formatting

    @mgiulini
    mgiulini committed Aug 31, 2022
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Commits on Sep 12, 2022

  1. added platform calls and restored scheduler execution

    @mgiulini
    mgiulini committed Sep 12, 2022
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  2. Update INSTALL.md

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    mgiulini authored Sep 12, 2022
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Commits on Sep 13, 2022

  1. ensembled output and renamed files

    @mgiulini
    mgiulini committed Sep 13, 2022
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  2. modified examples

    @mgiulini
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  3. Merge branch 'openmm' of https://github.com/haddocking/haddock3 into … 

    …openmm
    @mgiulini
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Commits on Feb 27, 2023

  1. Merge branch 'main' into openmm

    @mgiulini
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Commits on Feb 28, 2023

  1. refactored openmm

    @mgiulini
    mgiulini committed Feb 28, 2023
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Commits on Jun 1, 2023

  1. Solvent equilibration in openmm

    vreys committed Jun 1, 2023
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  2. Normalizing sampling factor to 20 in default config

    vreys committed Jun 1, 2023
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  3. Update openmm.py 

    Modified linting
Commenting the MonteCarloBarostat
    @VGPReys
    VGPReys authored Jun 1, 2023
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  4. Update __init__.py 

    Adding comments
    @VGPReys
    VGPReys authored Jun 1, 2023
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  5. Merge pull request #654 from VGPReys/openmm 

    Openmm
    @rvhonorato
    rvhonorato authored Jun 1, 2023
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  6. change default value to float

    @VGPReys
    VGPReys committed Jun 1, 2023
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  7. lint and tests fixes

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    VGPReys committed Jun 1, 2023
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Commits on Jun 5, 2023

  1. lint correction

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Commits on Jun 7, 2023

  1. Lint fix

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  2. Merge branch 'main' into openmm

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Commits on Jun 8, 2023

  1. lint fix

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Commits on Jun 12, 2023

  1. water box only

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Commits on Jun 13, 2023

  1. add @staticmethod

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Commits on Sep 19, 2024

  1. merge conflicts

    @VGPReys
    VGPReys committed Sep 19, 2024
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  2. types and lint fixes

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    VGPReys committed Sep 19, 2024
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  3. refix types ;)

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    VGPReys committed Sep 19, 2024
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  4. update install procedure

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    VGPReys committed Sep 19, 2024
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Commits on Sep 20, 2024

  1. check install

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    VGPReys committed Sep 20, 2024
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  2. fixture

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  3. add pH as parameter

    @VGPReys
    VGPReys committed Sep 20, 2024
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  4. fix parameters in examples

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    VGPReys committed Sep 20, 2024
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Commits on Sep 23, 2024

  1. Merge branch 'main' into openmm

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Commits on Sep 24, 2024

  1. Update examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg 

    Co-authored-by: Anna Engel <113177776+AljaLEngel@users.noreply.github.com>
    @VGPReys @AljaLEngel
    VGPReys and AljaLEngel authored Sep 24, 2024
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Commits on Oct 1, 2024

  1. Update src/haddock/core/exceptions.py 

    Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
    @VGPReys @mgiulini
    VGPReys and mgiulini authored Oct 1, 2024
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  2. Merge branch 'main' into openmm

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Commits on Oct 2, 2024

  1. fix ligand and implicit solvent

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  2. Merge branch 'main' into openmm

    @VGPReys
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Commits on Oct 4, 2024

  1. Merge branch 'main' into openmm

    @VGPReys
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