schrodinger.application.scaffold_enumeration.layered module

schrodinger.application.scaffold_enumeration.layered.flat_enumerator(mol, prng=None, linknodes=None, pvbonds=None)

Returns iterator over realizations obtained via not nestable flavors of enumeration:

  • repeating units,

  • position variant bonds, and

  • atom lists

(in that order: “repeating units” must be expanded prior to “position variant bonds” because enumeration of the latter involves atom deletions).

Parameters

  • mol (rdkit.Chem.Mol) – Unadulterated molecule.

  • prng (Optional[numpy.random.RandomState]) – MT19937 pseudorandom number generator from numpy or None.

  • linknodes (list(linknode.LinknodeSgroup)) – Link nodes (repeating units).

  • pvbonds (list(posvarbond.MulticenterSgroup)) – Position variant bonds.

Returns

Iterator over molecules.

Return type

iterator over rdkit.Chem.Mol

schrodinger.application.scaffold_enumeration.layered.flat_list_enumerator(molecules, prng=None)

Returns iterator over structures obtained by applying “flat” enumeration to the molecules.

Parameters

  • molecules (list[rdkit.Chem.Mol]) – List of (kinky) molecules.

  • prng (Optional[numpy.random.RandomState]) – MT19937 pseudorandom number generator from numpy or None.

Returns

Iterator over molecules.

Return type

iterator over rdkit.Chem.Mol

schrodinger.application.scaffold_enumeration.layered.place_rgroups(mol, todo, rgroups, prng, homo)

Generator that yields realizations of mol with (some) atoms replaced by R-groups from todo (and, potentially, rgroups).

Parameters

  • mol (rdkit.Chem.Mol) – Scaffold molecule.

  • todo (list[tuple[int, rdkit.Chem.Mol]) – List of tuples of atom indices (in mol) paired with corresponding R-groups.

  • rgroups (dict[int, list[rdkit.Chem.Mol]]) – Dictionary that maps R-group numbers (positive integers) onto list of molecules. Assumed to contain “original” R-groups that may be necessary if some of the R-groups in todo include R-group references.

  • prng (Optional[numpy.random.RandomState]) – MT19937 pseudorandom number generator from numpy or None.

  • homo (Optional[set[int]]) – IDs (positive integers) of the homo R-groups.

schrodinger.application.scaffold_enumeration.layered.enumerate_rgroups(mol, rgroups, prng=None, homo=None)

Enumerates R-groups in mol using R-groups from rgroups.

Parameters

  • mol (rdkit.Chem.Mol) – Scaffold molecule.

  • rgroups (dict[int, list[rdkit.Chem.Mol]]) – Dictionary that maps R-group numbers (positive integers) onto list of molecules.

  • prng (Optional[numpy.random.RandomState]) – MT19937 pseudorandom number generator from numpy or None.

  • homo (Optional[set[int]]) – IDs (positive integers) of the homo R-groups.

schrodinger.application.scaffold_enumeration.layered.collection(mol, rgroups=None, prng=None, homo=None)

Top-level API: generator that yields molecules obtained from mol.

Parameters

  • mol (rdkit.Chem.Mol) – Scaffold molecule.

  • rgroups (dict[int, list[rdkit.Chem.Mol]]) – Dictionary that maps R-group numbers (positive integers) onto list of molecules.

  • prng (Optional[numpy.random.RandomState]) – MT19937 pseudorandom number generator from numpy or None.

  • homo (Optional[set[int]]) – IDs (positive integers) of the “homo” R-groups. Regular R-groups that share the same label get enumerated independently (e.g., four outcomes are expected for R1-CO-R1 with R1 = [*Cl, *F]). OTOH, homo R-groups with the same label end up with the same realization (within a nesting level), so that only two outcomes would be obtained in the example above.