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__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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atom
¶ Alias for field number 0
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count
(value, /)¶ Return number of occurrences of value.
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elements
¶ Alias for field number 1
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index
(value, start=0, stop=9223372036854775807, /)¶ 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)[source]¶ 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)[source]¶ Makes
atom
into an atom list (in ENUM-246 sense).- Parameters
atom (
rdkit.Chem.Atom
) – RDKit atom.elements (iterable over str) – Iterable over elements.
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class
schrodinger.application.scaffold_enumeration.atomlist.
AtomListEnumerable
(mol)[source]¶ Bases:
schrodinger.application.scaffold_enumeration.common.EnumerableMixin
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getRealization
(idx)[source]¶ - 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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