schrodinger.application.scaffold_enumeration.common module¶
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schrodinger.application.scaffold_enumeration.common.
get_atom_id
(atom)¶ Returns atom ID obtained either from the CML ID property or derived from the atom index in case the ID property is not available.
Parameters: atom (rdkit.Chem.Atom) – Atom. Returns: Atom ID. Return type: str
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schrodinger.application.scaffold_enumeration.common.
get_atom_id_map
(mol)¶ Returns a dictionary that maps “atom IDs” (obtained via
get_atom_id()
) onto atom indices.Parameters: mol (rdkit.Chem.Mol) – Molecule. Returns: Map between atom IDs and their indices in mol
.Return type: dict(str, int)
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schrodinger.application.scaffold_enumeration.common.
get_bond_id
(bond)¶ Returns bond ID obtained either from the CML ID property or derived from the bond index in case the ID property is not available.
Parameters: bond (rdkit.Chem.Bond) – Bond. Returns: Bond ID. Return type: str
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schrodinger.application.scaffold_enumeration.common.
get_sgroups
(mol)¶ Returns list of dictionaries that represent “S-groups” from CML input. CML reader stores this data as a molecule-level property in JSON format.
Parameters: mol (rdkit.Chem.Mol) – Molecule. Returns: List of dictionaries that contain “S-groups” as captured from CML input (XML attributes stored as key/value pairs). Return type: list(dict(str, str))
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schrodinger.application.scaffold_enumeration.common.
set_sgroups
(mol, sgroups)¶ Serializes list of dictionaries
sgroups
as JSON and stores the outcome as a molecular-level property (CML_SGROUPS_PROP).Parameters: - mol (rdkit.Chem.Mol) – Molecule.
- sgroups (list(dict(str, str))) – List of dictionaries that meant to represent “S-groups”.
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schrodinger.application.scaffold_enumeration.common.
product_of_ranges
(extents)¶ Returns iterator over Cartesian product of ranges.
Parameters: extents (iterable over positive int) – Iterable over the range extents. For example, if extents is (3, 8), iterator domain is going to be [0, 3) x [0, 8). Returns: Iterator over tuples of integers.
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class
schrodinger.application.scaffold_enumeration.common.
EnumerableMixin
¶ Bases:
object
Methods common to several “enumerables”.
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getIter
()¶ Returns iterator over realizations.
Returns: Iterator over getRealization()
returns.Return type: iterator
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getRandomRealization
(prng)¶ Returns random realization.
Parameters: prng ( numpy.random.RandomState
) – mt19937 pseudorandom number generator from numpy.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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