schrodinger.application.scaffold_enumeration.linknode module

Implements “link node”/”repearing unit” enumeration (see ENUM-253).

class schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup(atoms, repeats, connect)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

atoms

Alias for field number 0

connect

Alias for field number 2

count(value, /)

Return number of occurrences of value.

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

Return first index of value.

Raises ValueError if the value is not present.

repeats

Alias for field number 1

class schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable(mol, linknodes=None)[source]

Bases: schrodinger.application.scaffold_enumeration.common.EnumerableMixin

__init__(mol, linknodes=None)[source]
Parameters

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

  • linknodes (list(LinknodeSgroup)) – List of link nodes.

getExtents()[source]
getRealization(idx)[source]
Parameters

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

Returns

RDKit molecule without “link nodes”.

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.