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__

Return key in self.

__init__

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

__len__

Return len(self).

atom

Alias for field number 0

count(value) → integer -- return number of occurrences of value

elements

Alias for field number 1

index(value[, start[, stop]]) → integer -- 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.