oddt.docking package¶
Submodules¶
oddt.docking.autodock_vina module¶
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class
oddt.docking.autodock_vina.
autodock_vina
(protein=None, size=(10, 10, 10), center=(0, 0, 0), auto_ligand=None, exhaustivness=8, num_modes=9, energy_range=3, seed=None, prefix_dir='/tmp', n_cpu=1, executable=None, autocleanup=True)[source]¶ Bases:
object
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.autodock_vina.
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
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oddt.docking.autodock_vina.
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
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oddt.docking.autodock_vina.
random
() → x in the interval [0, 1).¶