diff --git a/mdpow/workflows/dihedrals.py b/mdpow/workflows/dihedrals.py index 05e678a9..050cbd10 100644 --- a/mdpow/workflows/dihedrals.py +++ b/mdpow/workflows/dihedrals.py @@ -511,10 +511,12 @@ def periodic_angle_padding(df, padding=45): def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None): """Plots kernel density estimates (KDE) of dihedral angle frequencies for one dihedral atom group as violin plots, using as input the augmented - :class:`pandas.DataFrame` from :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. + :class:`pandas.DataFrame` from + :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. Output is converted to SVG by :func:`~mdpow.workflows.dihedrals.build_svg` - and final output is saved as PDF by :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` + and final output is saved as PDF by + :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` :keywords: @@ -523,13 +525,13 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None): :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` *width* - width of the violin element (>1 overlaps) - default: 0.9 + width of the violin element (>1 overlaps); default: 0.9 *solvents* The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + Normally takes a two-tuple, but analysis is compatible with single + solvent selections. Single solvent analyses will result in a figure + with fully filled violins for the single solvent. *plot_title* generated by :func:`~mdpow.workflows.dihedrals.build_svg` using @@ -619,9 +621,8 @@ def build_svg( solvents=SOLVENTS_DEFAULT, width=0.9, ): - """Converts and combines figure components into an - SVG object to be converted and saved as a publication - quality PDF. + """Converts and combines figure components into an SVG object to be + converted and saved as a publication quality PDF. :keywords: @@ -629,14 +630,13 @@ def build_svg( :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` *molname* - molecule name to be used for labelling - plots, if different from `resname` - (in this case, carried over from an upstream - decision between the two) + molecule name to be used for labelling plots, if different from + `resname` (in this case, carried over from an upstream decision between + the two) *name_index_pairs* - dictionary with key-value pair for dihedral atom group, - atom indices, and bond indices + dictionary with key-value pair for dihedral atom group, atom indices, + and bond indices .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` @@ -647,12 +647,12 @@ def build_svg( *solvents* The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + Normally takes a two-tuple, but analysis is compatible with single + solvent selections. Single solvent analyses will result in a figure + with fully filled violins for the single solvent. *width* - width of the violin element (>1 overlaps) - default: 0.9 + width of the violin element (>1 overlaps); default: 0.9 :returns: