schrodinger.application.scaffold_enumeration.common module

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

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)

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

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))

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”.

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.

class schrodinger.application.scaffold_enumeration.common.EnumerableMixin

Bases: object

Methods common to several “enumerables”.

getIter()

Returns iterator over realizations.

Returns

Iterator over getRealization() returns.

Return type

iterator

getRandomRealization(prng)

Returns random realization.

Parameters

prng (numpy.random.RandomState) – mt19937 pseudorandom number generator from numpy.