oddt.scoring.descriptors package

Submodules

oddt.scoring.descriptors.binana module

Internal implementation of binana software (http://nbcr.ucsd.edu/data/sw/hosted/binana/)

class oddt.scoring.descriptors.binana.binana_descriptor(protein=None)[source]

Bases: object

Descriptor build from binana script (as used in NNScore 2.0

Parameters:
protein: oddt.toolkit.Molecule object (default=None)

Protein object to be used while generating descriptors.

Methods

build(ligands[, protein]) Descriptor building method
set_protein(protein) One function to change all relevant proteins
build(ligands, protein=None)[source]

Descriptor building method

Parameters:
ligands: array-like

An array of generator of oddt.toolkit.Molecule objects for which the descriptor is computed

protein: oddt.toolkit.Molecule object (default=None)

Protein object to be used while generating descriptors. If none, then the default protein (from constructor) is used. Otherwise, protein becomes new global and default protein.

Returns:
descs: numpy array, shape=[n_samples, 351]

An array of binana descriptors, aligned with input ligands

set_protein(protein)[source]

One function to change all relevant proteins

Parameters:
protein: oddt.toolkit.Molecule object

Protein object to be used while generating descriptors. Protein becomes new global and default protein.

Module contents

class oddt.scoring.descriptors.close_contacts_descriptor(protein=None, cutoff=4, mode='atomic_nums', ligand_types=None, protein_types=None, aligned_pairs=False)[source]

Bases: object

Close contacts descriptor which tallies atoms of type X in certain cutoff from atoms of type Y.

Parameters:
protein: oddt.toolkit.Molecule or None (default=None)

Default protein to use as reference

cutoff: int or list, shape=[n,] or shape=[n,2] (default=4)

Cutoff for atoms in Angstroms given as an integer or a list of ranges, eg. [0, 4, 8, 12] or [[0,4],[4,8],[8,12]]. Upper bound is always inclusive, lower exclusive.

mode: string (default=’atomic_nums’)

Method of atoms selection, as used in atoms_by_type

ligand_types: array

List of ligand atom types to use

protein_types: array

List of protein atom types to use

aligned_pairs: bool (default=False)

Flag indicating should permutation of types should be done, otherwise the atoms are treated as aligned pairs.

Methods

build(ligands[, protein]) Builds descriptors for series of ligands
build(ligands, protein=None)[source]

Builds descriptors for series of ligands

Parameters:
ligands: iterable of oddt.toolkit.Molecules or oddt.toolkit.Molecule

A list or iterable of ligands to build the descriptor or a single molecule.

protein: oddt.toolkit.Molecule or None (default=None)

Default protein to use as reference

class oddt.scoring.descriptors.fingerprints(fp='fp2', toolkit='ob')[source]

Bases: object

Methods

build  
build(mols)[source]
class oddt.scoring.descriptors.autodock_vina_descriptor(protein=None, vina_scores=None)[source]

Bases: object

Methods

build  
set_protein  
build(ligands, protein=None)[source]
set_protein(protein)[source]
class oddt.scoring.descriptors.oddt_vina_descriptor(protein=None, vina_scores=None)[source]

Bases: object

Methods

build  
set_protein  
build(ligands, protein=None)[source]
set_protein(protein)[source]