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__

Return key in self.

__init__

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

__len__

Return len(self).

atoms

Alias for field number 0

connect

Alias for field number 2

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.

repeats

Alias for field number 1

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

Bases: schrodinger.application.scaffold_enumeration.common.EnumerableMixin

__init__(mol, linknodes=None)

Parameters:

• mol (rdkit.Chem.Mol) – RDKit molecule.
• linknodes (list(LinknodeSgroup)) – List of link nodes.

getExtents()

getRealization(idx)

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.