oddt.docking package¶

Submodules¶

oddt.docking.AutodockVina module¶

class oddt.docking.AutodockVina.autodock_vina(protein=None, auto_ligand=None, size=(20, 20, 20), center=(0, 0, 0), exhaustiveness=8, num_modes=9, energy_range=3, seed=None, prefix_dir=None, n_cpu=1, executable=None, autocleanup=True, skip_bad_mols=True)[source]¶

Bases: object

Autodock Vina docking engine, which extends it’s capabilities: automatic box (auto-centering on ligand).

Parameters

protein: oddt.toolkit.Molecule object (default=None): Protein object to be used while generating descriptors.
auto_ligand: oddt.toolkit.Molecule object or string (default=None): Ligand use to center the docking box. Either ODDT molecule or a file (opened based on extesion and read to ODDT molecule). Box is centered on geometric center of molecule.
size: tuple, shape=[3] (default=(20, 20, 20)): Dimentions of docking box (in Angstroms)
center: tuple, shape=[3] (default=(0,0,0)): The center of docking box in cartesian space.
exhaustiveness: int (default=8): Exhaustiveness parameter of Autodock Vina
num_modes: int (default=9): Number of conformations generated by Autodock Vina. The maximum number of docked poses is 9 (due to Autodock Vina limitation).
energy_range: int (default=3): Energy range cutoff for Autodock Vina
seed: int or None (default=None): Random seed for Autodock Vina
prefix_dir: string or None (default=None): Temporary directory for Autodock Vina files. By default (None) system temporary directory is used, for reference see tempfile.gettempdir.
executable: string or None (default=None): Autodock Vina executable location in the system. It’s realy necessary if autodetection fails.
autocleanup: bool (default=True): Should the docking engine clean up after execution?
skip_bad_mols: bool (default=True): Should molecules that crash Autodock Vina be skipped.

Attributes

tmp_dir

Methods

`dock`(ligands[, protein])	Automated docking procedure.
`predict_ligand`(ligand)	Local method to score one ligand and update it’s scores.
`predict_ligands`(ligands)	Method to score ligands lazily
`score`(ligands[, protein])	Automated scoring procedure.
`set_protein`(protein)	Change protein to dock to.

clean

clean()[source]¶

dock(ligands, protein=None)[source]¶

Automated docking procedure.

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to dock
protein: oddt.toolkit.Molecule object or None: Protein object to be used. If None, then the default one is used, else the protein is new default.

Returns

ligandsarray of oddt.toolkit.Molecule objects: Array of ligands (scores are stored in mol.data method)

predict_ligand(ligand)[source]¶

Local method to score one ligand and update it’s scores.

Parameters

ligand: oddt.toolkit.Molecule object: Ligand to be scored

Returns

ligand: oddt.toolkit.Molecule object: Scored ligand with updated scores

predict_ligands(ligands)[source]¶

Method to score ligands lazily

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to be scored

Returns

ligand: iterator of oddt.toolkit.Molecule objects: Scored ligands with updated scores

score(ligands, protein=None)[source]¶

Automated scoring procedure.

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to score
protein: oddt.toolkit.Molecule object or None: Protein object to be used. If None, then the default one is used, else the protein is new default.

Returns

ligandsarray of oddt.toolkit.Molecule objects: Array of ligands (scores are stored in mol.data method)

set_protein(protein)[source]¶

Change protein to dock to.

Parameters

protein: oddt.toolkit.Molecule object: Protein object to be used.

property tmp_dir¶

oddt.docking.AutodockVina.parse_vina_docking_output(output)[source]¶

Function parsing Autodock Vina docking output to a dictionary

Parameters

outputstring: Autodock Vina standard ouptud (STDOUT).

Returns

outdict: dicitionary containing scores computed by Autodock Vina

oddt.docking.AutodockVina.parse_vina_scoring_output(output)[source]¶

Function parsing Autodock Vina scoring output to a dictionary

Parameters

outputstring: Autodock Vina standard ouptud (STDOUT).

Returns

outdict: dicitionary containing scores computed by Autodock Vina

oddt.docking.AutodockVina.write_vina_pdbqt(mol, directory, flexible=True, name_id=None)[source]¶: Write single PDBQT molecule to a given directory. For proteins use flexible=False to avoid encoding torsions. Additionally an name ID can be appended to a name to avoid conflicts.

oddt.docking.internal module¶

ODDT’s internal docking/scoring engines

oddt.docking.internal.change_dihedral(coords, a1, a2, a3, a4, target_angle, rot_mask)[source]¶

oddt.docking.internal.get_children(molecule, mother, restricted)[source]¶

oddt.docking.internal.get_close_neighbors(molecule, a_idx, num_bonds=1)[source]¶

oddt.docking.internal.num_rotors_pdbqt(lig)[source]¶

class oddt.docking.internal.vina_docking(rec, lig=None, box=None, box_size=1.0, weights=None)[source]¶

Bases: object

Methods

correct_radius
score
score_inter
score_intra
score_total
set_box
set_coords
set_ligand
set_protein
weighted_inter
weighted_intra
weighted_total

correct_radius(atom_dict)[source]¶

score(coords=None)[source]¶

score_inter(coords=None)[source]¶

score_intra(coords=None)[source]¶

score_total(coords=None)[source]¶

set_box(box)[source]¶

set_coords(coords)[source]¶

set_ligand(lig)[source]¶

set_protein(rec)[source]¶

weighted_inter(coords=None)[source]¶

weighted_intra(coords=None)[source]¶

weighted_total(coords=None)[source]¶

class oddt.docking.internal.vina_ligand(c0, num_rotors, engine, box_size=1)[source]¶

Bases: object

Methods

mutate

mutate(x2, force=False)[source]¶

Module contents¶

class oddt.docking.autodock_vina(protein=None, auto_ligand=None, size=(20, 20, 20), center=(0, 0, 0), exhaustiveness=8, num_modes=9, energy_range=3, seed=None, prefix_dir=None, n_cpu=1, executable=None, autocleanup=True, skip_bad_mols=True)[source]¶

Bases: object

Autodock Vina docking engine, which extends it’s capabilities: automatic box (auto-centering on ligand).

Parameters

protein: oddt.toolkit.Molecule object (default=None): Protein object to be used while generating descriptors.
auto_ligand: oddt.toolkit.Molecule object or string (default=None): Ligand use to center the docking box. Either ODDT molecule or a file (opened based on extesion and read to ODDT molecule). Box is centered on geometric center of molecule.
size: tuple, shape=[3] (default=(20, 20, 20)): Dimentions of docking box (in Angstroms)
center: tuple, shape=[3] (default=(0,0,0)): The center of docking box in cartesian space.
exhaustiveness: int (default=8): Exhaustiveness parameter of Autodock Vina
num_modes: int (default=9): Number of conformations generated by Autodock Vina. The maximum number of docked poses is 9 (due to Autodock Vina limitation).
energy_range: int (default=3): Energy range cutoff for Autodock Vina
seed: int or None (default=None): Random seed for Autodock Vina
prefix_dir: string or None (default=None): Temporary directory for Autodock Vina files. By default (None) system temporary directory is used, for reference see tempfile.gettempdir.
executable: string or None (default=None): Autodock Vina executable location in the system. It’s realy necessary if autodetection fails.
autocleanup: bool (default=True): Should the docking engine clean up after execution?
skip_bad_mols: bool (default=True): Should molecules that crash Autodock Vina be skipped.

Attributes

tmp_dir

Methods

`dock`(ligands[, protein])	Automated docking procedure.
`predict_ligand`(ligand)	Local method to score one ligand and update it’s scores.
`predict_ligands`(ligands)	Method to score ligands lazily
`score`(ligands[, protein])	Automated scoring procedure.
`set_protein`(protein)	Change protein to dock to.

clean

clean()[source]¶

dock(ligands, protein=None)[source]¶

Automated docking procedure.

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to dock
protein: oddt.toolkit.Molecule object or None: Protein object to be used. If None, then the default one is used, else the protein is new default.

Returns

ligandsarray of oddt.toolkit.Molecule objects: Array of ligands (scores are stored in mol.data method)

predict_ligand(ligand)[source]¶

Local method to score one ligand and update it’s scores.

Parameters

ligand: oddt.toolkit.Molecule object: Ligand to be scored

Returns

ligand: oddt.toolkit.Molecule object: Scored ligand with updated scores

predict_ligands(ligands)[source]¶

Method to score ligands lazily

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to be scored

Returns

ligand: iterator of oddt.toolkit.Molecule objects: Scored ligands with updated scores

score(ligands, protein=None)[source]¶

Automated scoring procedure.

Parameters

ligands: iterable of oddt.toolkit.Molecule objects: Ligands to score
protein: oddt.toolkit.Molecule object or None: Protein object to be used. If None, then the default one is used, else the protein is new default.

Returns

ligandsarray of oddt.toolkit.Molecule objects: Array of ligands (scores are stored in mol.data method)

set_protein(protein)[source]¶

Change protein to dock to.

Parameters

protein: oddt.toolkit.Molecule object: Protein object to be used.

property tmp_dir¶