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Dihedral Plots: RDKit Mol Object #243

Merged
merged 90 commits into from
Jul 4, 2023
Merged

Dihedral Plots: RDKit Mol Object #243

merged 90 commits into from
Jul 4, 2023

Commits on Feb 21, 2023

  1. new PR

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  2. update mol object methods, change dihedral_indices naming convention … 

    …to atom_indices/get_atom_indices
    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  3. add get_bond_indices

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  4. reflect name change in tests from dihedrals automated workflow

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  5. missed name change in test

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  6. fix bond highlighting and add low resolution plotting function for di… 

    …hedrals
    @cadeduckworth
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  7. add atom_indices to titles of plot columns

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  8. add atom_indices to label Mol object on plots

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  9. cleaner plot titles

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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  10. current best plot resolution/proportion

    @cadeduckworth
    cadeduckworth committed Feb 21, 2023
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Commits on Mar 4, 2023

  1. add svgutils and cairosvg methods to plot svg mol object

    @cadeduckworth
    cadeduckworth committed Mar 4, 2023
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  2. reimplement DF input option and fix most tests to reflect name change… 

    …s and altered function definitions
    @cadeduckworth
    cadeduckworth committed Mar 4, 2023
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  3. add svgutils and cairosvg to dependencies, install, requirements list… 

    …s, remove broken test, add reminder to update func list in docs
    @cadeduckworth
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  4. remove unneccessary import

    @cadeduckworth
    cadeduckworth committed Mar 4, 2023
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  5. remove import

    @cadeduckworth
    cadeduckworth committed Mar 4, 2023
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Commits on Mar 21, 2023

  1. remove temp svg files and build, convert, and save as pdf through mem

    @cadeduckworth
    cadeduckworth committed Mar 21, 2023
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  2. fix legend issue when plotting one solvent

    @cadeduckworth
    cadeduckworth committed Mar 21, 2023
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Commits on Mar 25, 2023

  1. Merge branch 'develop' into plot-Mol

    @cadeduckworth
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Commits on Mar 28, 2023

  1. Merge branch 'develop' into plot-Mol

    @orbeckst
    orbeckst authored Mar 28, 2023
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  2. cleanup

    @cadeduckworth
    cadeduckworth committed Mar 28, 2023
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  3. move title setting and cleanup

    @cadeduckworth
    cadeduckworth committed Mar 28, 2023
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  4. split plot_violins into new build_svg function

    @cadeduckworth
    cadeduckworth committed Mar 28, 2023
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  5. merge updates from develop

    @cadeduckworth
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Commits on Apr 2, 2023

  1. change, better function names for dihedrals workflow module

    @cadeduckworth
    cadeduckworth committed Apr 2, 2023
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  2. cleanup

    @cadeduckworth
    cadeduckworth committed Apr 2, 2023
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Commits on Apr 3, 2023

  1. docs and cleanup, plot width docs, dict comprehension for ab_pairs

    @cadeduckworth
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  2. cleanup and add list and dict comprehension methods for get_paired_in… 

    …dices function
    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  3. intersphinx mapping

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  4. remove assert method for notebook test

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  5. tests: new fixtures and tests for bond_indices and ab_pairs

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  6. tests: new fixtures and tests for bond_indices and ab_pairs, skip 3.7

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  7. test_build_universe method

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  8. confirm build universe test

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  9. fix df input test

    @cadeduckworth
    cadeduckworth committed Apr 3, 2023
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  10. Update dihedrals.py 

    cleanup '#' inline comments
    @cadeduckworth
    cadeduckworth authored Apr 3, 2023
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Commits on Apr 4, 2023

  1. Merge branch 'develop' into plot-Mol

    @orbeckst
    orbeckst authored Apr 4, 2023
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Commits on Apr 15, 2023

  1. remove unused kwargs and update docs for new functions

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  2. rewrite docs to cover new functions and kwarg changes

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  3. fix tests to accommodate kwarg updates in dihedrals module

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  4. explanation of why figdir is a kwarg at top level of dihedrals module… 

    … but a positional argument elsewhere - workflows base **kwargs, issue #244, see in-line comment in dihedrals.py
    @cadeduckworth
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  5. reorder positional and key word args

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  6. accommodation for figdir kwarg

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  7. docs typo

    @cadeduckworth
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  8. docs typos

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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  9. temporary fix for figdir issue which should currently be a positional… 

    … argument, but would require redundant rewrite of workflows base module, pending issue #244
    @cadeduckworth
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  10. upcoming CHANGES

    @cadeduckworth
    cadeduckworth committed Apr 15, 2023
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Commits on Jun 9, 2023

  1. update to specify where enhancements are occurring

    @cadeduckworth
    cadeduckworth committed Jun 9, 2023
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  2. remove dafault scope specification for defined functions

    @cadeduckworth
    cadeduckworth committed Jun 9, 2023
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  3. reimplement try/except method for rdkit conversion topology element g… 

    …uessing
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Commits on Jun 11, 2023

  1. generate combined plots pdf for automated dihedral analysis

    @cadeduckworth
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  2. updates for implementation of pypdf in workflows dihedrals module: CH… 

    …ANGES, testing environment, requirements, sphinx source configuration
    @cadeduckworth
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  3. intersphinx mapping, docs

    @cadeduckworth
    cadeduckworth committed Jun 11, 2023
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  4. fix solute kwarg description for workflows dihedrals module

    @cadeduckworth
    cadeduckworth committed Jun 11, 2023
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  5. fix ab_pairs kwarg description for workflows dihedrals module

    @cadeduckworth
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  6. documentation for dihedral_violins function in workflows dihedrals mo… 

    …dule
    @cadeduckworth
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  7. documentation for get_paired_indices function in workflows dihedrals … 

    …module
    @cadeduckworth
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  8. documentation and kwarg definition for get_paired_indices function an… 

    …d ab_pairs dictionary object in workflows dihedrals module
    @cadeduckworth
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  9. kwarg definition for plot_title for dihedral_violins function in work… 

    …flows dihedrals module
    @cadeduckworth
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  10. move in-line comments explaining figdir kward for workflows dihedrals… 

    … module
    @cadeduckworth
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  11. reorganize kwargs for plot_dihedral_violins in top-level automated_di… 

    …hedral_analysis function call in workflows dihedrals module
    @cadeduckworth
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  12. add assert method to make figdir kwarg required in workflows dihedral… 

    …s module
    @cadeduckworth
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Commits on Jun 22, 2023

  1. temporarily remove figdir required assertion

    @cadeduckworth
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  2. change MDA guess_atom_element to MDA guess_types for RDKit conversion… 

    … in workflows dihedrals module
    @cadeduckworth
    cadeduckworth committed Jun 22, 2023
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  3. fix registry import error for workflows base, close #245

    @cadeduckworth
    cadeduckworth committed Jun 22, 2023
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  4. remove guess_atom_element import

    @cadeduckworth
    cadeduckworth committed Jun 22, 2023
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  5. fix registry import for workflows base module

    @cadeduckworth
    cadeduckworth committed Jun 22, 2023
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  6. reimplement assert figdir reuired for workflows dihedrals module

    @cadeduckworth
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  7. require RDKit>=2023 for testing environment to investigate failed tes… 

    …ts for workflows dihedrals module
    @cadeduckworth
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  8. require RDKit<2023 for testing environment to investigate failed test… 

    …s for workflows dihedrals module
    @cadeduckworth
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  9. require RDKit<=2022.09.1 for testing environment to investigate faile… 

    …d tests for workflows dihedrals module
    @cadeduckworth
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Commits on Jun 27, 2023

  1. Merge branch 'develop' into plot-Mol

    @orbeckst
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Commits on Jun 30, 2023

  1. Merge branch 'develop' into plot-Mol

    @cadeduckworth
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  2. fix function name in dihedral workflows tests

    @cadeduckworth
    cadeduckworth committed Jun 30, 2023
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  3. fix variable reference in dihedral workflows test

    @cadeduckworth
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  4. fix fixture call and variable assignment in dihedral groups test for … 

    …workflows dihedrals
    @cadeduckworth
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  5. modify workflows base test for assertion of figure directory requirem… 

    …ent in dihedrals workflow
    @cadeduckworth
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  6. add name_index pairing tests for dihedral workflows atom indices cons… 

    …istency check
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Commits on Jul 1, 2023

  1. modify workflows base test for dihedral workflow figure directory req… 

    …uirement
    @cadeduckworth
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  2. add pypdf to setup.py install_requires for dihedrals workflow

    @cadeduckworth
    cadeduckworth committed Jul 1, 2023
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Commits on Jul 2, 2023

  1. Merge branch 'develop' into plot-Mol

    @cadeduckworth
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  2. change imports to follow PEP 8

    @cadeduckworth
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  3. modify dihedrals workflow docs to explain figdir kwarg requirement

    @cadeduckworth
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  4. use first solvent specified to build MDAnalysis Universe

    @cadeduckworth
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  5. Merge branch 'develop' into plot-Mol

    @cadeduckworth
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  6. Merge branch 'develop' into plot-Mol

    @orbeckst
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Commits on Jul 3, 2023

  1. modify single solvent plotting method, add solvent count assertion

    @cadeduckworth
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  2. comment expected fixture scope changes, reference issue #235

    @cadeduckworth
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  3. remove solute.unwrap, not needed

    @cadeduckworth
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  4. reference issue #260 to fix jupyter notebook figure output

    @cadeduckworth
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Commits on Jul 4, 2023

  1. finalize single solvent figure modifications and add test

    @cadeduckworth
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