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

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

oddt.scoring.descriptors.atoms_by_type(atom_dict, types, mode='atomic_nums')

Returns atom dictionaries based on given criteria. Currently we have 3 types of atom selection criteria:

• atomic numbers [‘atomic_nums’]
• Sybyl Atom Types [‘atom_types_sybyl’]
• AutoDock4 atom types [‘atom_types_ad4’] (http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters)

Parameters:

atom_dict: oddt.toolkit.Molecule.atom_dict

Atom dictionary as implemeted in oddt.toolkit.Molecule class

types: array-like

List of atom types/numbers wanted.

Returns:

out: dictionary of shape=[len(types)]

A dictionary of queried atom types (types are keys of the dictionary). Values are of oddt.toolkit.Molecule.atom_dict type.

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

Bases: object

Methods

build(ligands[, protein, single])

Builds descriptors for series of ligands

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

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

single: bool (default=False)

Flag indicating if the ligand is single.

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

Bases: object

Methods

build(mols[, single])

build(mols, single=False)