oddt.scoring.descriptors package¶
Submodules¶
oddt.scoring.descriptors.binana module¶
Internal implementation of binana software (http://nbcr.ucsd.edu/data/sw/hosted/binana/)
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class
oddt.scoring.descriptors.binana.
binana_descriptor
(protein=None)[source]¶ Bases:
object
Methods
build
(ligands[, protein])Descriptor building method set_protein
(protein)One function to change all relevant proteins -
build
(ligands, protein=None)[source]¶ 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
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Module contents¶
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oddt.scoring.descriptors.
atoms_by_type
(atom_dict, types, mode='atomic_nums')[source]¶ - 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.
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class
oddt.scoring.descriptors.
close_contacts
(protein=None, cutoff=4, mode='atomic_nums', ligand_types=None, protein_types=None, aligned_pairs=False)[source]¶ Bases:
object
Methods
build
(ligands[, protein, single])Builds descriptors for series of ligands -
build
(ligands, protein=None, single=False)[source]¶ 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.
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