Changed formatting and order alchemical region parameters
@@ -566,13 +566,16 @@ class AlchemicalState(object):
# ALCHEMICAL REGION
# =============================================================================
-_ALCHEMICAL_REGION_ARGS = collections.OrderedDict(
- [('alchemical_atoms', None), ('alchemical_bonds', None),
- ('alchemical_angles', None), ('alchemical_torsions', None),
- ('annihilate_electrostatics', True), ('annihilate_sterics', False),
- ('softcore_alpha', 0.5), ('softcore_beta', 0.0), ('softcore_a', 1), ('softcore_b', 1),
- ('softcore_c', 6), ('softcore_d', 1), ('softcore_e', 1), ('softcore_f', 2)]
-)
+_ALCHEMICAL_REGION_ARGS = collections.OrderedDict([
+ ('alchemical_atoms', None),
+ ('alchemical_bonds', None),
+ ('alchemical_angles', None),
+ ('alchemical_torsions', None),
+ ('annihilate_electrostatics', True),
+ ('annihilate_sterics', False),
+ ('softcore_alpha', 0.5), ('softcore_a', 1), ('softcore_b', 1), ('softcore_c', 6),
+ ('softcore_beta', 0.0), ('softcore_d', 1), ('softcore_e', 1), ('softcore_f', 2)
+])
# The class is just a way to document the namedtuple.
@@ -603,19 +606,20 @@ class AlchemicalRegion(collections.namedtuple('AlchemicalRegion', _ALCHEMICAL_RE
entries are softened with 'lambda_torsions'. If set to True, this list
is auto-generated to include al proper torsions involving any alchemical
atoms. Improper torsions are not softened (default is None).
- annihilate_electrostatics : bool
- If True, electrostatics should be annihilated, rather than decoupled.
- annihilate_sterics : bool
+ annihilate_electrostatics : bool, optional
+ If True, electrostatics should be annihilated, rather than decoupled
+ (default is True).
+ annihilate_sterics : bool, optional
If True, sterics (Lennard-Jones or Halgren potential) will be annihilated,
- rather than decoupled.
+ rather than decoupled (default is False).
softcore_alpha : float, optional
Alchemical softcore parameter for Lennard-Jones (default is 0.5).
- softcore_beta : float, optional
- Alchemical softcore parameter for electrostatics. Set this to zero
- to recover standard electrostatic scaling (default is 0.0).
softcore_a, softcore_b, softcore_c : float, optional
Parameters modifying softcore Lennard-Jones form. Introduced in
Eq. 13 of Ref. [1] (default is 1).
+ softcore_beta : float, optional
+ Alchemical softcore parameter for electrostatics. Set this to zero
+ to recover standard electrostatic scaling (default is 0.0).
softcore_d, softcore_e, softcore_f : float, optional
Parameters modifying softcore electrostatics form (default is 1).
