schrodinger.application.scaffold_enumeration.atomlist module¶
Implements “atom list” enumeration (see ENUM-246).
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class
schrodinger.application.scaffold_enumeration.atomlist.
AtomListInfo
(atom, elements)¶ Bases:
tuple
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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atom
¶ Alias for field number 0
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count
(value) → integer -- return number of occurrences of value¶
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elements
¶ Alias for field number 1
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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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)
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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.
- atom (
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class
schrodinger.application.scaffold_enumeration.atomlist.
AtomListEnumerable
(mol)¶ Bases:
schrodinger.application.scaffold_enumeration.common.EnumerableMixin
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__init__
(mol)¶ Parameters: mol (ROMol) – RDKit molecule.
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getExtents
()¶
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getRealization
(idx)¶ Parameters: idx (iterable over int) – “Index” of a realization. Returns: RDKit molecule without enumerable “atom lists”. Return type: rdkit.Chem.Mol
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getIter
()¶ Returns iterator over realizations.
Returns: Iterator over getRealization()
returns.Return type: iterator
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getRandomRealization
(prng)¶ Returns random realization.
Parameters: prng ( numpy.random.RandomState
) – mt19937 pseudorandom number generator from numpy.
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