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
Descriptor build from binana script (as used in NNScore 2.0
Parameters: protein: oddt.toolkit.Molecule object (default=None)
Protein object to be used while generating descriptors.
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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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
Close contacts descriptor which tallies atoms of type X in certain cutoff from atoms of type Y.
Parameters: protein: oddt.toolkit.Molecule or None (default=None)
Default protein to use as reference
- cutoff: int or list, shape=[n,] or shape=[n,2] (default=4)
Cutoff for atoms in Angstroms given as an integer or a list of ranges, eg. [0, 4, 8, 12] or [[0,4],[4,8],[8,12]]. Upper bound is always inclusive, lower exclusive.
- mode: string (default=’atomic_nums’)
Method of atoms selection, as used in atoms_by_type
- ligand_types: array
List of ligand atom types to use
- protein_types: array
List of protein atom types to use
- aligned_pairs: bool (default=False)
Flag indicating should permutation of types should be done, otherwise the atoms are treated as aligned pairs.
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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class
oddt.scoring.descriptors.
fingerprints
(fp='fp2', toolkit='ob')[source]¶ Bases:
object
Methods
build
(mols[, single])
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class
oddt.scoring.descriptors.
autodock_vina_descriptor
(protein=None, vina_scores=None)[source]¶ Bases:
object
Methods
build
(ligands[, protein, single])set_protein
(protein)