Major cleanup of the AMOEBA API

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -24,9 +24,7 @@ SKIP_METHODS = [('State',),
                 ('AmoebaOutOfPlaneBendForceImpl',),
                 ('AmoebaPiTorsionForceImpl',),
                 ('AmoebaStretchBendForceImpl',),
-                ('AmoebaTorsionForceImpl',),
                 ('AmoebaTorsionTorsionForceImpl',),
-                ('AmoebaUreyBradleyForceImpl',),
                 ('AmoebaVdwForceImpl',),
                 ('AmoebaWcaDispersionForceImpl',),
                 ('AndersenThermostatImpl',),
@@ -44,9 +42,7 @@ SKIP_METHODS = [('State',),
                 ('CalcAmoebaOutOfPlaneBendForceKernel',),
                 ('CalcAmoebaPiTorsionForceKernel',),
                 ('CalcAmoebaStretchBendForceKernel',),
-                ('CalcAmoebaTorsionForceKernel',),
                 ('CalcAmoebaTorsionTorsionForceKernel',),
-                ('CalcAmoebaUreyBradleyForceKernel',),
                 ('CalcAmoebaVdwForceKernel',),
                 ('CalcAmoebaWcaDispersionForceKernel',),
                 ('CalcCMAPTorsionForceKernel',),
@@ -134,7 +130,6 @@ SKIP_METHODS = [('State',),
                 ('TorsionTorsionInfo',),
                 ('UpdateStateDataKernel',),
                 ('UpdateTimeKernel',),
-                ('UreyBradleyInfo',),
                 ('VdwInfo',),
                 ('WcaDispersionInfo',),
                 ('Context',  'getState'),
@@ -161,9 +156,6 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
                   ('System', 'getDefaultPeriodicBoxVectors', 'b'),
                   ('System', 'getDefaultPeriodicBoxVectors', 'c'),
                   ('Platform', 'setPropertyValue', 'context'),
-                  ('AmoebaTorsionForce', 'addTorsion', 'torsion1'),
-                  ('AmoebaTorsionForce', 'addTorsion', 'torsion2'),
-                  ('AmoebaTorsionForce', 'addTorsion', 'torsion3'),
                   ('AmoebaTorsionTorsionForce', 'setTorsionTorsionGrid', 'grid'),
                   ('AmoebaVdwForce', 'setParticleExclusions', 'exclusions'),
                   ('AmoebaMultipoleForce', 'addParticle', 'molecularDipole'),
@@ -264,7 +256,6 @@ UNITS = {
 ("AmoebaMultipoleForce",                 "getCutoffDistance")                             :  (  'unit.nanometer',()),
 ("AmoebaMultipoleForce",                 "getAEwald")                                     :  (  '1/unit.nanometer',()),
 ("AmoebaMultipoleForce",                 "getPmeBSplineOrder")                            :  ( None,()),
-("AmoebaMultipoleForce",                 "getMutualInducedIterationMethod")               :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getMutualInducedMaxIterations")                 :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getMutualInducedTargetEpsilon")                 :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getEwaldErrorTolerance")                        :  ( None, ()),
@@ -305,26 +296,17 @@ UNITS = {
 ("AmoebaStretchBendForce",                "getNumStretchBends")                            :  ( None, ()),
 ("AmoebaStretchBendForce",                "getStretchBendParameters")                      :  ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer')),
 
-("AmoebaTorsionForce",                    "getNumTorsions")                                :  ( None, ()),
-("AmoebaTorsionForce",                    "getTorsionParameters")                          :  ( None, ()),
-
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsions")                         :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsionGrids")                     :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionParameters")                   :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionGrid")                         :  ( None, ()),
 
-("AmoebaUreyBradleyForce",                "getNumInteractions")                            :  ( None, ()),
-("AmoebaUreyBradleyForce",                "getAmoebaGlobalUreyBradleyCubic")               :  ( None, ()),
-("AmoebaUreyBradleyForce",                "getAmoebaGlobalUreyBradleyQuartic")             :  ( None, ()),
-("AmoebaUreyBradleyForce",                "getUreyBradleyParameters")                      :  ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')),
-
 ("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
 ("AmoebaVdwForce",                        "getSigmaCombiningRule")                         :  ( None, ()),
 ("AmoebaVdwForce",                        "getEpsilonCombiningRule")                       :  ( None, ()),
 ("AmoebaVdwForce",                        "getParticleExclusions")                         :  ( None, ()),
 ("AmoebaVdwForce",                        "getCutoff")                                     :  ( 'unit.nanometer', ()),
-("AmoebaVdwForce",                        "getUseNeighborList")                            :  ( None, ()),
-("AmoebaVdwForce",                        "getPBC")                                        :  ( None, ()),
+("AmoebaVdwForce",                        "getNonbondedMethod")                            :  ( None, ()),
 ("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
 
 ("AmoebaWcaDispersionForce",              "getParticleParameters")                         :  ( None, ('unit.nanometer', 'unit.kilojoule_per_mole')),