* add RDKit Mol object to dihedral analysis plots * add tests, and close #238 * add svgutils and cairosvg methods to plot svg mol object * reimplement DF input option and fix most tests to reflect name changes and altered function definitions * add svgutils and cairosvg to dependencies, install, requirements lists, remove broken test, add reminder to update func list in docs * split plot_violins into new build_svg function * change, better function names for dihedrals workflow module * docs and cleanup, plot width docs, dict comprehension for ab_pairs * intersphinx mapping * tests: new fixtures and tests for bond_indices and ab_pairs * tests: new fixtures and tests for bond_indices and ab_pairs, skip 3.7 * test_build_universe method * confirm build universe test * rewrite docs to cover new functions and kwarg changes * fix tests to accommodate kwarg updates in dihedrals module * 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 * temporary fix for figdir issue which should currently be a positional argument, but would require redundant rewrite of workflows base module, pending issue #244 * upcoming CHANGES * remove dafault scope specification for defined functions * reimplement try/except method for rdkit conversion topology element guessing * generate combined plots pdf for automated dihedral analysis * updates for implementation of pypdf in workflows dihedrals module: CHANGES, testing environment, requirements, sphinx source configuration * documentation for dihedral_violins function in workflows dihedrals module * documentation for get_paired_indices function in workflows dihedrals module * documentation and kwarg definition for get_paired_indices function and ab_pairs dictionary object in workflows dihedrals module * kwarg definition for plot_title for dihedral_violins function in workflows dihedrals module * move in-line comments explaining figdir kward for workflows dihedrals module * reorganize kwargs for plot_dihedral_violins in top-level automated_dihedral_analysis function call in workflows dihedrals module * add assert method to make figdir kwarg required in workflows dihedrals module * change MDA guess_atom_element to MDA guess_types for RDKit conversion in workflows dihedrals module * fix registry import error for workflows base, close #245 * remove guess_atom_element import * reimplement assert figdir reuired for workflows dihedrals module * add pypdf to setup.py install_requires for dihedrals workflow * change imports to follow PEP 8 * modify dihedrals workflow docs to explain figdir kwarg requirement * use first solvent specified to build MDAnalysis Universe * modify single solvent plotting method, add solvent count assertion * comment expected fixture scope changes, reference issue #235 * remove solute.unwrap, not needed * reference issue #260 to fix jupyter notebook figure output * finalize single solvent figure modifications and add test --------- Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

Add test to verify that dihedral analysis plots are labeled with the correct molecule and dihedral atom group #238

Description

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions