diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py index b4c749ee9..0cad12a09 100644 --- a/prody/proteins/interactions.py +++ b/prody/proteins/interactions.py @@ -471,11 +471,11 @@ def plot_barh(result, bond_type, **kwargs): """Plot horizontal bar plots of percentages of interactions, splitting the data into fixed-sized plots. :arg n_per_plot: The number of results per one plot - by default is 20 if set to None + Default is 20 if set to None :type n_per_plot: int :arg min_height: Size of the bar plot - by default is 8 + Default is 8 :type min_height: int """ @@ -614,15 +614,15 @@ def calcSASA(atoms, **kwargs): :type atoms: :class:`.Atomic` :arg selection: selection string - by default all the protein structure is used + Default all the protein structure is used :type selection: str :arg sasa_cutoff: cutoff for SASA values - default is 0.0 + Default is 0.0 :type sasa_cutoff: float, int :arg resnames: residues name included - default is False + Default is False :type resnames: bool """ @@ -672,19 +672,19 @@ def calcVolume(atoms, **kwargs): :type atoms: :class:`.Atomic` :arg selection: selection string - by default all the protein structure is used + Default all the protein structure is used :type selection: str :arg volume_cutoff: cutoff for volume - default is 0.0 to include all the results + Default is 0.0 to include all the results :type sasa_volume: float, int :arg split_residues: it will provide values for each residue - default is False + Default is False :type split_residues: bool :arg resnames: residues name included - default is False + Default is False True - will give residue names and values for each residue False - will give only the values for each residues :type resnames: bool @@ -2114,35 +2114,35 @@ def showInteractionsGraph(statistics, **kwargs): :type statistics: list :arg cutoff: Minimal number of counts per residue in the trajectory - by default 0.1. + Default is 0.1. :type cutoff: int, float :arg code: representation of the residues, 3-letter or 1-letter - by default 3-letter + Default is 3-letter :type code: str :arg multiple_chains: display chain name for structure with many chains - by default False + Default is False :type multiple_chains: bool :arg edge_cmap: color of the residue connection - by default plt.cm.Blues (blue color) + Default is plt.cm.Blues (blue color) :type edge_cmap: str :arg node_size: size of the nodes which describes residues - by default 300 + Default is 300 :type node_size: int :arg node_distance: value which will scale residue-residue interactions - by default 5 + Default is 5 :type node_distance: int :arg font_size: size of the font - by default 14 + Default is 14 :type font_size: int :arg seed: random number which affect the distribution of residues - by default 42 + Default is 42 :type seed: int """ @@ -2278,11 +2278,11 @@ def showInteractionsHist(statistics, **kwargs): :type statistics: list :arg clip: maxmimal number of residue pairs on the bar plot - by default 20 + Default is 20 :type clip: int :arg font_size: size of the font - by default 18 + Default is 18 :type font_size: int """ @@ -2584,7 +2584,7 @@ def listLigandInteractions(PLIP_output, **kwargs): :arg output: parameter to print the interactions on the screen while analyzing the structure (True | False) - by default is False + Default is False :type output: bool Note that five types of interactions are considered: hydrogen bonds, salt bridges, @@ -2966,23 +2966,23 @@ def calcSminaBindingAffinity(atoms, trajectory=None, **kwargs): :arg protein_selection: selection string for the protein and other compoment of the system that should be included, e.g. "protein and chain A", - by default "protein" + Default is "protein" :type protein_selection: str :arg ligand_selection: selection string for ligand, e.g. "resname ADP", - by default "all not protein" + Default is "all not protein" :type ligand_selection: str :arg ligand_selection: scoring function (vina or vinardo) - by default is "vina" + Default is "vina" :type ligand_selection: str :arg atom_terms: write per-atom interaction term values. It will provide more information as dictionary for each frame/model, and details for atom terms will be saved in terms_*frame_number*.txt, - by default is False + Default is False :type atom_terms: bool @@ -3370,38 +3370,37 @@ def runFoldseek(pdb_file, chain, **kwargs): :type chain: str :arg coverage_threshold: Coverage threshold - by default 0.3 + Default is 0.3 :type coverage_threshold: float :arg tm_threshold: TM-score threshold - by default 0.5 + Default is 0.5 :type tm_threshold: float :arg database_folder: Folder with the database - by default '~/Downloads/foldseek/pdb' + Default is '~/Downloads/foldseek/pdb' To download the database use: 'foldseek databases PDB pdb tmp' in the console :type database_folder: str :arg fixer: The method for fixing lack of hydrogen bonds - by default is 'pdbfixer' + Default is 'pdbfixer' :type fixer: 'pdbfixer' or 'openbabel' :arg subset: subsets of atoms: 'ca', 'bb', 'heavy', 'noh', 'all' (see matchChains()) - by default is 'ca' + Default is 'ca' :type subset: str :arg seqid: Minimum value of the sequence identity (see matchChains()) - by default 5 + Default is 5 :type seqid: float :arg overlap: percent overlap (see matchChains()) - by default 50 + Default is 50 :type overlap: float :arg folder_name: Folder where the results will be collected - by default is 'struc_homologs' - :type folder_name: str - """ + Default is 'struc_homologs' + :type folder_name: str """ import os import subprocess @@ -3756,17 +3755,16 @@ def runDali(pdb, chain, **kwargs): :type subset: str :arg seqid: Minimum value of the sequence identity (see matchChains()) - Default 5 + Default is 5 :type seqid: float :arg overlap: percent overlap (see matchChains()) - Default 50 + Default is 50 :type overlap: float :arg folder_name: Folder where the results will be collected Default is 'struc_homologs' - :type folder_name: str - """ + :type folder_name: str """ import os import shutil @@ -3832,25 +3830,24 @@ def runBLAST(pdb, chain, **kwargs): :type chain: str :arg fixer: The method for fixing lack of hydrogen bonds - by default is 'pdbfixer' + Default is 'pdbfixer' :type fixer: 'pdbfixer' or 'openbabel' :arg subset: subsets of atoms: 'ca', 'bb', 'heavy', 'noh', 'all' (see matchChains()) - by default is 'bb' + Default is 'bb' :type subset: str :arg seqid: Minimum value of the sequence identity (see matchChains()) - by default 90 + Default is 90 :type seqid: float :arg overlap: percent overlap (see matchChains()) - by default 50 + Default is 50 :type overlap: float :arg folder_name: Folder where the results will be collected - by default is 'struc_homologs' - :type folder_name: str - """ + Default is 'struc_homologs' + :type folder_name: str """ import os import shutil @@ -3922,8 +3919,7 @@ def calcSignatureInteractions(PDB_folder, **kwargs): :arg mapping_file: Aligned residue indices, MSA file type required in Foldseek analyisis - :type mapping_file: str - """ + :type mapping_file: str """ import os mapping_file = kwargs.get('mapping_file') @@ -4415,7 +4411,7 @@ def buildInteractionMatrixEnergy(self, **kwargs): """Build matrix with interaction energy comming from energy of pairs of specific residues. :arg energy_list_type: name of the list with energies - default is 'IB_solv' + Default is 'IB_solv' :type energy_list_type: 'IB_nosolv', 'IB_solv', 'CS' """ @@ -4578,7 +4574,7 @@ def getFrequentInteractors(self, contacts_min=2): (7) Disulfide bonds (disb) :arg contacts_min: Minimal number of contacts which residue may form with other residues, - by default 2. + Default is 2. :type contacts_min: int """ atoms = self._atoms @@ -5611,7 +5607,7 @@ def getLigandInteractions(self, **kwargs): :arg include_frames: used with filters, it will leave selected keyword in orginal lists, if False it will collect selected interactions in one list, Use True to assign new selection using setLigandInteractions. - by default True + Default is True :type include_frames: bool """ @@ -5661,7 +5657,7 @@ def getLigandInteractionsNumber(self, **kwargs): be a total number of interactions or it can be divided into interaction types. :arg types: Interaction types can be included (True) or not (False). - by default is True. + Default is True. :type types: bool """ @@ -5803,7 +5799,7 @@ def saveInteractionsPDB(self, **kwargs): :type filename: str :arg ligand_sele: ligand selection, - by default is 'all not (protein or water or ion)'. + Default is 'all not (protein or water or ion)'. :type ligand_sele: str """