Fix doctest AlchemicalState
@@ -123,13 +123,14 @@ class AlchemicalState(object):
Examples
--------
- Create an alchemically modified system
+ Create an alchemically modified system.
>>> from openmmtools import testsystems
+ >>> factory = AlchemicalFactory(consistent_exceptions=False)
>>> alanine_vacuum = testsystems.AlanineDipeptideVacuum().system
- >>> alchemical_factory = AlchemicalFactory(reference_system=alanine_vacuum,
- ... ligand_atoms=range(0, 22))
- >>> alanine_alchemical_system = alchemical_factory.alchemically_modified_system
+ >>> alchemical_region = AlchemicalRegion(alchemical_atoms=range(22))
+ >>> alanine_alchemical_system = factory.create_alchemical_system(reference_system=alanine_vacuum,
+ ... alchemical_regions=alchemical_region)
Create a completely undefined alchemical state.
@@ -1809,3 +1810,4 @@ class AlchemicalFactory(object):
if __name__ == '__main__':
import doctest
doctest.testmod()
+ # doctest.run_docstring_examples(AlchemicalFunction, globals())
