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)

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)

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)

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.fingerprints(fp='fp2', toolkit='ob')

Bases: object

Methods

build(mols[, single])

build(mols, single=False)

class oddt.scoring.descriptors.autodock_vina_descriptor(protein=None, vina_scores=None)

Bases: object

Methods

build(ligands[, protein, single])
set_protein(protein)

build(ligands, protein=None, single=False)

set_protein(protein)

class oddt.scoring.descriptors.oddt_vina_descriptor(protein=None, vina_scores=None)

Bases: object

Methods

build(ligands[, protein, single])
set_protein(protein)

build(ligands, protein=None, single=False)

set_protein(protein)