From bf1b05dd42a7581ce797f929c983eed2461a4b8d Mon Sep 17 00:00:00 2001 From: cadeduckworth Date: Fri, 14 Apr 2023 21:34:40 -0700 Subject: [PATCH] remove unused kwargs and update docs for new functions --- mdpow/workflows/dihedrals.py | 145 +++++++++++++++++++---------------- 1 file changed, 77 insertions(+), 68 deletions(-) diff --git a/mdpow/workflows/dihedrals.py b/mdpow/workflows/dihedrals.py index 805fd0f9..debacf8f 100644 --- a/mdpow/workflows/dihedrals.py +++ b/mdpow/workflows/dihedrals.py @@ -115,7 +115,7 @@ def build_universe(dirname): """Builds :class:`~MDAnalysis.core.universe.Universe` from ``water/Coulomb/0000`` topology and trajectory for the specified project. - Used by :func:`~mdpow.workflows.dihedrals.rdkit_conversion` + Output used by :func:`~mdpow.workflows.dihedrals.rdkit_conversion` and :func:`~mdpow.workflows.dihedrals.get_atom_indices` to obtain atom indices for each dihedral atom group. @@ -194,32 +194,18 @@ def rdkit_conversion(u, resname): return mol, solute -def get_atom_indices(dirname, mol, SMARTS=SMARTS_DEFAULT): - '''Uses a SMARTS selection string to identify indices for - relevant dihedral atom groups. +def get_atom_indices(mol, SMARTS=SMARTS_DEFAULT): + '''Uses a SMARTS selection string to identify atom indices + for relevant dihedral atom groups. - Requires an MDPOW project directory and `resname` - as input. With :func:`~mdpow.workflows.dihedrals.build_universe` and - :func:`~mdpow.workflows.dihedrals.rdkit_conversion`, uses the topology - and trajectory from ``water/Coulomb/0000`` and creates a - :class:`~MDAnalysis.core.universe.Universe` object. - Uses a SMARTS string to obtain all relevant dihedral atom groups. + Requires a :class:`rdkit.Chem.rdchem.Mol` object as input + for the :data:`SMARTS_DEFAULT` kwarg to match patterns to and + identify relevant dihedral atom groups. :keywords: - *dirname* - Molecule Simulation directory. Loads simulation files present in - lambda directories into the new instance. With this method for - generating an :class:`~mdpow.analysis.ensemble.Ensemble` the - lambda directories are explored and - :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` - searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, - and .xtc files for trajectory. It will default to using the tpr file - available. - - *resname* - `resname` for the molecule as defined in - the topology and trajectory + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` *SMARTS* The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. @@ -237,6 +223,24 @@ def get_atom_indices(dirname, mol, SMARTS=SMARTS_DEFAULT): return atom_indices def get_bond_indices(mol, atom_indices): + '''From the :class:`rdkit.Chem.rdchem.Mol` object, uses + `atom_indices` to determine the indices of the bonds + between those atoms for each dihedral atom group. + + :keywords: + + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + + *atom_indices* + tuple of tuples of indices for each dihedral atom group + + :returns: + + *bond_indices* + tuple of tuples of indices for the bonds in each dihedral atom group + + ''' bonds = [] @@ -254,38 +258,24 @@ def get_bond_indices(mol, atom_indices): return bond_indices def get_dihedral_groups(solute, atom_indices): - '''Uses the indices of the relevant dihedral atom groups determined - by :func:`~mdpow.workflows.dihedral.get_atom_indices` - and returns the names for each atom in each group. - - Requires an MDPOW project directory and `resname` - as input. Expands upon usage of - :func:`~mdpow.workflows.dihedral.get_atom_indices` - to return an array of the names of each atom within - its respective dihedral atom group as identified by - the SMARTS selection string. Not necessary - for automation, useful for verifying all atom groups of interest - are properly identified before analysis. + '''Uses the 0-based `atom_indices` of the relevant dihedral atom groups + determined by :func:`~mdpow.workflows.dihedral.get_atom_indices` + and returns the 1-based index names for each atom in each group. + + Requires the `atom_indices` from :func:`~mdpow.workflows.dihedral.get_atom_indices` + to index the `solute` specified by :func:`~MDAnalysis.core.groups.select_atoms` + and return an array of the names of each atom within its respective + dihedral atom group as identified by the SMARTS selection string. :keywords: - *dirname* - Molecule Simulation directory. Loads simulation files present in - lambda directories into the new instance. With this method for - generating an :class:`~mdpow.analysis.ensemble.Ensemble` the - lambda directories are explored and - :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` - searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, - and .xtc files for trajectory. It will default to using the tpr file - available. + *solute* + molecule specified by :func:`~MDAnalysis.core.groups.select_atoms` + for :class:`~MDAnalysis.core.universe.Universe` object - *resname* - `resname` for the molecule as defined in - the topology and trajectory + *atom_indices* + tuple of tuples of indices for each dihedral atom group - *SMARTS* - The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. - :returns: *dihedral_groups* @@ -299,6 +289,33 @@ def get_dihedral_groups(solute, atom_indices): return dihedral_groups def get_paired_indices(atom_indices, bond_indices, dihedral_groups): + '''Combines `atom_indices` and `bond_indices` in tuples + to be paired with their respective `dihedral_groups` in + :func:`~MDAnalysis.core.groups.select_atoms` selection string format. + + A dictionary is created with key-value pairs as follows: + `atom_indices` and `bond_indices` are joined in a tuple + as the value, with the key being the respective member + of `dihedral_groups` to facilitate highlighting the + relevant dihedral atom group when generating violin plots. + + :keywords: + + *atom_indices* + tuple of tuples of indices for each dihedral atom group + + *bond_indices* + tuple of tuples of indices for the bonds in each dihedral atom group + + *dihedral_groups* + list of :func:`numpy.array` for atom names in each dihedral atom group + + :returns: + + *ab_pairs* + dictionary with key-value pair: '*#-*#-*#-*#': (atom_indices[i], bond_indices[i]) + + ''' all_dgs = [f'{dg[0]}-{dg[1]}-{dg[2]}-{dg[3]}' for dg in dihedral_groups] @@ -336,7 +353,7 @@ def dihedral_groups_ensemble(dirname, atom_indices, *atom_indices* tuples of atom indices for dihedral atom groups - .. seealso:: :func:`~mdpow.workflows.dihedrals.get_atom_indices` + .. seealso:: :func:`~mdpow.workflows.dihedrals.get_atom_indices`, :data:`SMARTS_DEFAULT` *solvents* The default solvents are documented under :data:`SOLVENTS_DEFAULT`. @@ -373,7 +390,7 @@ def dihedral_groups_ensemble(dirname, atom_indices, return df -def save_df(df, df_save_dir, resname=None, molname=None): +def save_df(df, df_save_dir, resname, molname=None): '''Takes a :class:`pandas.DataFrame` of results from :class:`~mdpow.analysis.dihedral.DihedralAnalysis` as input before padding the angles to optionaly save the raw @@ -429,13 +446,15 @@ def periodic_angle_padding(df, padding=45): Takes a :class:`pandas.DataFrame` of results from :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + or :func:`~mdpow.workflows.dihedrals.dihedral_groups_ensemble` as input and pads the angles to maintain periodicity for properly plotting dihedral angle frequencies as KDE violins - with :func:`~mdpow.workflows.dihedrals.dihedral_violins`. + with :func:`~mdpow.workflows.dihedrals.dihedral_violins` and + :func:`~mdpow.workflows.dihedrals.plot_violins`. Creates two new :class:`pandas.DataFrame` based on the - cutoff value specified, adds to the angle values, concatenates + `padding` value specified, pads the angle values, concatenates all three :class:`pandas.DataFrame`, maintaining original data and - adding padding, and returns new augmented :class:`pandas.DataFrame`. + adding padded values, and returns new augmented :class:`pandas.DataFrame`. :keywords: @@ -444,7 +463,7 @@ def periodic_angle_padding(df, padding=45): results, including all dihedral atom groups for molecule of current project *padding* - value in degrees + value in degrees to specify angle augmentation threshold default: 45 :returns: @@ -453,16 +472,6 @@ def periodic_angle_padding(df, padding=45): augmented results :class:`pandas.DataFrame` containing padded dihedral angles as specified by `padding` - .. rubric:: Example - - Typical Workflow:: - - da = DihedralAnalysis(all_dihedrals) - da.run(start=0, stop=100, step=10) - df = da.results - df_aug = periodic_angle_padding(df, padding=45) - plot = dihedral_violins(df_aug, width=0.9) - ''' df1 = df[df.dihedral > 180 - padding].copy(deep=True) @@ -746,9 +755,9 @@ def automated_dihedral_analysis(dirname=None, df_save_dir=None, figdir=None, Typical Workflow:: - import automated_dihedral_analysis as ada + import dihedrals - ada.automated_dihedral_analysis(dirname='/foo/bar/MDPOW_project_data', + dihedrals.automated_dihedral_analysis(dirname='/foo/bar/MDPOW_project_data', figdir='/foo/bar/MDPOW_figure_directory', resname='UNK', molname='benzene', padding=45, width=0.9,