Code

Converter for OpenMM#2917

Code

Merged

jbarnoud merged 70 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom ahy3nz:issue-2863-openmmtopahy3nz/mdanalysis:issue-2863-openmmtopCopy head branch name to clipboardMay 5, 2021

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Commits

Commits on Aug 22, 2020

• Topology from omm topology and simulation objects. Coordinates from omm simulation

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  b3a43c6

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• Remove debug lines

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  f103d91

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• Move omm topology parsing code outside class for re-use in multiple omm reader objects

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• Change openmm trajectory reader into single frame reader

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Commits on Aug 23, 2020

• Add coordinates conversions for openmm modeller and pdbfile classes

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  4665de1

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• Add topology parsing for openmm pdbfile and modeller objects

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• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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• Tests for openmmtopology parser

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• Revert init

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• Test openmm topology parsing on pdb file with connections, add atomtypes

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• Use guesser for guessing atomtypes from atomnames

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Commits on Aug 24, 2020

• Off by one errors for 1-indexed resids

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• Set frame to 0 for first timestep

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Commits on Aug 25, 2020

• Unwrap simtk quantity for time

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• Coordinates tests for openmm pdbfile, modeller, simulation objects

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  6feb097

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• update error messsage

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  1725d18

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• Update documentation

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• Try updating some yaml files

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  1bb0fd0

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• Include datafiles and tests for pdbx files

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• More documentation for pdbx

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• Typo in format

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  4c11d06

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• Blacken code

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• Refactor so generic application objects share the same readers and functions

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Commits on Aug 26, 2020

• Adjust line length

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Commits on Aug 27, 2020

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Aug 31, 2020

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Sep 2, 2020

• Revert datafiles without black formatting

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  23a8c84

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• Add pdbx file to datafiles, update changelog

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  906da5e

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• Update docstring with proper versionadded tag

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  1bbf543

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• Missing comma in list

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  6c7756f

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• Add pytest importorskip for testing openmm topology c onversion

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  170304d

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Commits on Sep 19, 2020

• Update changelog

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  36e652e

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• Merge conflict

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Commits on Sep 30, 2020

• Merge branch 'develop' into issue-2863-openmmtop

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Commits on Oct 7, 2020

• Merge conflicts

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  d65a641

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• Remove unnecessary imports, more documentation for openmm application layer objects, additional openmm test from a basic openmm simulation made from scratch

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  6a4229c

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• Update changelog

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  b7347d9

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• Example usage in documentation

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  1b4d0c2

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• Convert simtk quanitties into default internal units

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Commits on Oct 29, 2020

• Merge conflict with develop

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Commits on Nov 4, 2020

• Update travis with extra variables for openmm, installing only on py37 tests

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• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

  ahy3nz

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  b189f2f

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• Revert back to atomtype guessing

  ahy3nz

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  eec5d9d

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• Use proper openmm atom naming conventions for unit test

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  76c9053

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Commits on Nov 5, 2020

• Modify appveyor config to specify openmm on py36 vs py38

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• Correct syntax for appveyor env vars

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  cd637db

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• Change appveyor var syntax

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  292a52e

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• Empty string for conda openmm var

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  3c2322d

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Commits on Nov 9, 2020

• Fix merge conflicts

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Commits on Nov 16, 2020

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Dec 11, 2020

• Merge conflict

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• Merge conflict

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• Update GHA conda min dependencies for openmm on conda-forge

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Commits on Dec 12, 2020

• Remove inplace flag for converting energies, not used anywhere in openmm conversions

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• Update appveyor to pull openmm from conda-forge

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Commits on Dec 26, 2020

• Merge conflict

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Commits on Dec 31, 2020

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Jan 7, 2021

• Merge conflict

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Commits on Feb 2, 2021

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Feb 20, 2021

• Merge conflict

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Commits on Mar 11, 2021

• Update gh ci from merge conflict

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Commits on Mar 14, 2021

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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Commits on Apr 24, 2021

• Merge conflict with develop

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  f64e18d

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• Use simtk syntax for unit conversions

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Commits on Apr 27, 2021

• - Sanitize box angles when converting from OpenMM unitcell to MDA unitcell

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Commits on Apr 29, 2021

• Merge with upstream

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Commits on May 5, 2021

• Merge remote-tracking branch 'upstream/develop' into issue-2863-openmmtop

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• Make sure OpenMM appears in the documentation

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• PEP8 fixes for OpenMM reader and parser

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• Merge pull request #1 from jbarnoud/openmm

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