schrodinger.application.scaffold_enumeration.atomlist module

Implements “atom list” enumeration (see ENUM-246).

class schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo(atom, elements)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

atom

Alias for field number 0

count(value, /)

Return number of occurrences of value.

elements

Alias for field number 1

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

schrodinger.application.scaffold_enumeration.atomlist.get_atom_elements(atom)

Returns atom list associated with the atom.

Parameters

atom (rdkit.Chem.Atom) – RDKit atom.

Returns

List of elements.

Return type

list(str)

schrodinger.application.scaffold_enumeration.atomlist.set_atom_elements(atom, elements)

Makes atom into an atom list (in ENUM-246 sense).

Parameters

• atom (rdkit.Chem.Atom) – RDKit atom.

• elements (iterable over str) – Iterable over elements.

class schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable(mol)

Bases: schrodinger.application.scaffold_enumeration.common.EnumerableMixin

__init__(mol)

Parameters

mol (ROMol) – RDKit molecule.

getExtents()

getRealization(idx)

Parameters

idx (iterable over int) – “Index” of a realization.

Returns

RDKit molecule without enumerable “atom lists”.

Return type

rdkit.Chem.Mol

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.