oddt.docking package¶
Submodules¶
oddt.docking.AutodockVina module¶
-
class
oddt.docking.AutodockVina.
autodock_vina
(protein=None, auto_ligand=None, size=(10, 10, 10), center=(0, 0, 0), exhaustivness=8, num_modes=9, energy_range=3, seed=None, prefix_dir='/tmp', n_cpu=1, executable=None, autocleanup=True)[source]¶ Bases:
object
Autodock Vina docking engine, which extends it’s capabilities: automatic box (autocentering 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=(10,10,10))
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
- 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 (default=/tmp)
Temporary directory for Autodock Vina files
- 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?
Attributes
tmp_dir
Methods
clean
()dock
(ligands[, protein, single])Automated docking procedure. score
(ligands[, protein, single])Automated scoring procedure. set_protein
(protein)Change protein to dock to. -
dock
(ligands, protein=None, single=False)[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.
- single: bool (default=False)
A flag to indicate single ligand docking (performance reasons (eg. there is no need for subdirectory for one ligand)
Returns: ligands : array of oddt.toolkit.Molecule objects
Array of ligands (scores are stored in mol.data method)
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score
(ligands, protein=None, single=False)[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.
- single: bool (default=False)
A flag to indicate single ligand scoring (performance reasons (eg. there is no need for subdirectory for one ligand)
Returns: ligands : array of oddt.toolkit.Molecule objects
Array of ligands (scores are stored in mol.data method)
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set_protein
(protein)[source]¶ Change protein to dock to.
Parameters: protein: oddt.toolkit.Molecule object
Protein object to be used.
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tmp_dir
¶
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oddt.docking.AutodockVina.
parse_vina_docking_output
(output)[source]¶ Function parsing Autodock Vina docking output to a dictionary
Parameters: output : string
Autodock Vina standard ouptud (STDOUT).
Returns: out : dict
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: output : string
Autodock Vina standard ouptud (STDOUT).
Returns: out : dict
dicitionary containing scores computed by Autodock Vina
-
oddt.docking.AutodockVina.
random
() → x in the interval [0, 1).¶
Module contents¶
-
class
oddt.docking.
autodock_vina
(protein=None, auto_ligand=None, size=(10, 10, 10), center=(0, 0, 0), exhaustivness=8, num_modes=9, energy_range=3, seed=None, prefix_dir='/tmp', n_cpu=1, executable=None, autocleanup=True)[source]¶ Bases:
object
Autodock Vina docking engine, which extends it’s capabilities: automatic box (autocentering 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=(10,10,10))
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
- 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 (default=/tmp)
Temporary directory for Autodock Vina files
- 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?
Attributes
tmp_dir
Methods
-
dock
(ligands, protein=None, single=False)[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.
- single: bool (default=False)
A flag to indicate single ligand docking (performance reasons (eg. there is no need for subdirectory for one ligand)
Returns: ligands : array of oddt.toolkit.Molecule objects
Array of ligands (scores are stored in mol.data method)
-
score
(ligands, protein=None, single=False)[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.
- single: bool (default=False)
A flag to indicate single ligand scoring (performance reasons (eg. there is no need for subdirectory for one ligand)
Returns: ligands : array 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.
-
tmp_dir
¶