Removed references to free energy plugin

wrappers/python/CMakeLists.txt

@@ -177,7 +177,7 @@ set (STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES}
 ### Make a list of all folders containing include files the wrappers must be compiled against. ###
 ##################################################################################################
 
-SET(WRAPPER_BASE_SUBDIRS . openmmapi olla serialization plugins/amoeba/openmmapi plugins/freeEnergy/openmmapi plugins/rpmd/openmmapi)
+SET(WRAPPER_BASE_SUBDIRS . openmmapi olla serialization plugins/amoeba/openmmapi plugins/rpmd/openmmapi)
 SET(WRAPPER_INCLUDE_DIRS) # start empty
 FOREACH(subdir ${WRAPPER_BASE_SUBDIRS})
     # append

wrappers/python/setup.py

@@ -111,7 +111,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
 
     libraries=['OpenMM',
                'OpenMMSerialization', 
-               'OpenMMFreeEnergy',
                'OpenMMAmoeba',
                'OpenMMRPMD',
               ]

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -41,7 +41,6 @@ namespace std {
 
 #include <exception>
 #include "OpenMM.h"
-#include "OpenMMFreeEnergy.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/serialization/SerializationNode.h"

wrappers/python/src/swig_doxygen/doxygen/Doxyfile

@@ -565,7 +565,6 @@ WARN_LOGFILE           =
 # with spaces.
 
 INPUT                  = "$(OPENMM_INCLUDE_PATH)/OpenMM.h" \
-                         "$(OPENMM_INCLUDE_PATH)/OpenMMFreeEnergy.h" \
                          "$(OPENMM_INCLUDE_PATH)/openmm"
 
 # This tag can be used to specify the character encoding of the source files 

wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in

@@ -570,8 +570,7 @@ INPUT                  = "@CMAKE_SOURCE_DIR@/openmmapi" \
                          "@CMAKE_SOURCE_DIR@/serialization/include/openmm/serialization/SerializationProxy.h" \
                          "@CMAKE_SOURCE_DIR@/serialization/include/openmm/serialization/XmlSerializer.h" \
                          "@CMAKE_SOURCE_DIR@/plugins/amoeba/openmmapi" \
-                         "@CMAKE_SOURCE_DIR@/plugins/rpmd/openmmapi" \
-                         "@CMAKE_SOURCE_DIR@/plugins/freeEnergy/openmmapi"
+                         "@CMAKE_SOURCE_DIR@/plugins/rpmd/openmmapi"
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -56,14 +56,11 @@ SKIP_METHODS = [('State',),
                 ('CalcCustomTorsionForceKernel',),
                 ('CalcForcesAndEnergyKernel',),
                 ('CalcGBSAOBCForceKernel',),
-                ('CalcGBSAOBCSoftcoreForceKernel',),
                 ('CalcGBVIForceKernel',),
-                ('CalcGBVISoftcoreForceKernel',),
                 ('CalcHarmonicAngleForceKernel',),
                 ('CalcHarmonicBondForceKernel',),
                 ('CalcKineticEnergyKernel',),
                 ('CalcNonbondedForceKernel',),
-                ('CalcNonbondedSoftcoreForceKernel',),
                 ('CalcPeriodicTorsionForceKernel',),
                 ('CalcRBTorsionForceKernel',),
                 ('CMAPTorsionForceImpl',),
@@ -86,11 +83,7 @@ SKIP_METHODS = [('State',),
                 ('ForceImpl',),
                 ('FunctionInfo',),
                 ('GBSAOBCForceImpl',),
-                ('GBSAOBCSoftcoreForce', 'getParticleParameters', 4),
-                ('GBSAOBCSoftcoreForceImpl',),
                 ('GBVIForceImpl',),
-                ('GBVISoftcoreForce', 'getParticleParameters', 4),
-                ('GBVISoftcoreForceImpl',),
                 ('GlobalParameterInfo',),
                 ('HarmonicAngleForceImpl',),
                 ('HarmonicBondForceImpl',),
@@ -107,9 +100,6 @@ SKIP_METHODS = [('State',),
                 ('MonteCarloBarostatImpl',),
                 ('MultipoleInfo',),
                 ('NonbondedForceImpl',),
-                ('NonbondedSoftcoreForce', 'getParticleParameters', 4),
-                ('NonbondedSoftcoreForce', 'getExceptionParameters', 6),
-                ('NonbondedSoftcoreForceImpl',),
                 ('OutOfPlaneBendInfo',),
                 ('ParameterInfo',),
                 ('ParticleInfo',),
@@ -416,21 +406,6 @@ UNITS = {
 ("GBVIForce", "getParticleParameters")
  : (None, ('unit.elementary_charge',
            'unit.nanometer', 'unit.kilojoule_per_mole')),
-("GBSAOBCSoftcoreForce", "getNonbondedMethod") : (None, ()),
-("GBSAOBCSoftcoreForce", "getParticleParameters")
- : (None, ('unit.elementary_charge', 'unit.nanometer',
-           None, None)),
-("GBSAOBCSoftcoreForce", "getNonPolarPrefactor")
- : ('unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)', ()),
-("GBVISoftcoreForce", "getParticleParameters")
- : (None, ('unit.elementary_charge', 'unit.nanometer',
-           'unit.kilojoule_per_mole', None)),
-("GBVISoftcoreForce", "getBondParameters")
- : (None, (None, None, 'unit.nanometer')),
-("GBVISoftcoreForce", "getNonbondedMethod") : (None, ()),
-("GBVISoftcoreForce", "getBornRadiusScalingMethod") : (None, ()),
-("GBVISoftcoreForce", "getQuinticLowerLimitFactor") : (None, ()),
-("GBVISoftcoreForce", "getQuinticUpperBornRadiusLimit") : ('unit.nanometer',()),
 ("HarmonicAngleForce", "getAngleParameters")
  : (None, (None, None, None, 'unit.radian',
            'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
@@ -446,15 +421,6 @@ UNITS = {
 ("NonbondedForce", "getParticleParameters")
  : (None, ('unit.elementary_charge',
            'unit.nanometer', 'unit.kilojoule_per_mole')),
-("NonbondedSoftcoreForce", "getNonbondedMethod") : (None, ()),
-("NonbondedSoftcoreForce", "getParticleParameters")
- : (None, ('unit.elementary_charge', 'unit.nanometer',
-           'unit.kilojoule_per_mole', None)),
-("NonbondedSoftcoreForce", "getExceptionParameters")
- : (None, (None, None,
-           'unit.elementary_charge*unit.elementary_charge',
-           'unit.nanometer', 'unit.kilojoule_per_mole',
-           None)),
 ("PeriodicTorsionForce", "getTorsionParameters")
  : (None, (None, None, None, None,
            None, 'unit.radian', 'unit.kilojoule_per_mole')),