schrodinger.application.scaffold_enumeration.posvarbond module

Implements “position variant bond” enumeration (see ENUM-252).

class schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup(atoms, center)

Bases: tuple

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

atoms

Alias for field number 0

center

Alias for field number 1

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

class schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable(mol, pvbonds=None)

Bases: schrodinger.application.scaffold_enumeration.common.EnumerableMixin

__init__(mol, pvbonds=None)
Parameters:
  • mol (rdkit.Chem.Mol) – RDKit molecule.
  • pvbonds (list(MulticenterSgroup)) – List of position variant bonds.
getExtents()
getRealization(idx)
Parameters:idx (iterable over int) – “Index” of a realization.
Returns:RDKit molecule without “position variant bonds”.
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.