gistfile1.txt

$ doccheck simtk.openmm.openmm
simtk.openmm.openmm.AmoebaAngleForce.addAngle ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'quadratic'}

simtk.openmm.openmm.AmoebaAngleForce.getAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle3', 'length', 'quadratic', 'particle2'}

simtk.openmm.openmm.AmoebaAngleForce.setAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'quadratic'}

simtk.openmm.openmm.AmoebaBondForce.addBond ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'k'}

simtk.openmm.openmm.AmoebaBondForce.getBondParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'length', 'quadratic', 'particle2'}

simtk.openmm.openmm.AmoebaBondForce.setBondParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'k'}

simtk.openmm.openmm.AmoebaGeneralizedKirkwoodForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'radius', 'scalingFactor', 'charge'}

simtk.openmm.openmm.AmoebaInPlaneAngleForce.addAngle ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'quadratic'}

simtk.openmm.openmm.AmoebaInPlaneAngleForce.getAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'quadratic', 'particle2', 'particle1', 'length', 'particle3', 'particle4'}

simtk.openmm.openmm.AmoebaInPlaneAngleForce.setAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'quadraticK'}
  Documented non-arguments:  {'quadratic'}

simtk.openmm.openmm.AmoebaMultipoleForce.getCovalentMap ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'covalentAtoms'}

simtk.openmm.openmm.AmoebaMultipoleForce.getCovalentMaps ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'covalentLists'}

simtk.openmm.openmm.AmoebaMultipoleForce.getElectrostaticPotential ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'outputElectrostaticPotential'}

simtk.openmm.openmm.AmoebaMultipoleForce.getInducedDipoles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'dipoles'}

simtk.openmm.openmm.AmoebaMultipoleForce.getMultipoleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'multipoleAtomX', 'molecularDipole', 'charge', 'polarity', 'multipoleAtomZ', 'axisType', 'dampingFactor', 'molecularQuadrupole', 'multipoleAtomY', 'thole'}

simtk.openmm.openmm.AmoebaMultipoleForce.getPMEParametersInContext ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'alpha', 'nx', 'ny', 'nz'}

simtk.openmm.openmm.AmoebaMultipoleForce.getSystemMultipoleMoments ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'outputMultipoleMoments'}

simtk.openmm.openmm.AmoebaMultipoleForce.setAEwald ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'aewald'}
  Documented non-arguments:  {'Ewald'}

simtk.openmm.openmm.AmoebaMultipoleForce.setMutualInducedMaxIterations ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'inputMutualInducedMaxIterations'}
  Documented non-arguments:  {'max'}

simtk.openmm.openmm.AmoebaMultipoleForce.setMutualInducedTargetEpsilon ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'inputMutualInducedTargetEpsilon'}
  Documented non-arguments:  {'target'}

simtk.openmm.openmm.AmoebaMultipoleForce.setPmeGridDimensions ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'gridDimension'}
  Documented non-arguments:  {'the'}

simtk.openmm.openmm.AmoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle3', 'k', 'particle4', 'particle2'}

simtk.openmm.openmm.AmoebaPiTorsionForce.getPiTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle2', 'particle1', 'particle5', 'particle6', 'particle3', 'k', 'particle4'}

simtk.openmm.openmm.AmoebaStretchBendForce.getStretchBendParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'k2', 'particle2', 'particle1', 'lengthCB', 'lengthAB', 'particle3', 'k1', 'angle'}

simtk.openmm.openmm.AmoebaTorsionTorsionForce.getTorsionTorsionGrid ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'index'}
  Documented non-arguments:  {'gridIndex'}

simtk.openmm.openmm.AmoebaTorsionTorsionForce.getTorsionTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'chiralCheckAtomIndex', 'gridIndex', 'particle2', 'particle1', 'particle5', 'particle3', 'particle4'}

simtk.openmm.openmm.AmoebaVdwForce.getParticleExclusions ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'exclusions'}

simtk.openmm.openmm.AmoebaVdwForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'epsilon', 'parentIndex', 'sigma', 'reductionFactor'}

simtk.openmm.openmm.AmoebaWcaDispersionForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'epsilon', 'radius'}

simtk.openmm.openmm.CMAPTorsionForce.getMapParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'size', 'energy'}

simtk.openmm.openmm.CMAPTorsionForce.getTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'a1', 'b2', 'a4', 'a2', 'map', 'b4', 'a3', 'b1', 'b3'}

simtk.openmm.openmm.CustomAngleForce.getAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle2', 'particle1', 'particle3', 'parameters'}

simtk.openmm.openmm.CustomAngleForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomBondForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomCentroidBondForce.getGroupParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particles', 'weights'}

simtk.openmm.openmm.CustomCentroidBondForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomCompoundBondForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomExternalForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle', 'parameters'}

simtk.openmm.openmm.CustomExternalForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomGBForce.getComputedValueParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'expression', 'name', 'type'}

simtk.openmm.openmm.CustomGBForce.getEnergyTermParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'expression', 'type'}

simtk.openmm.openmm.CustomGBForce.getExclusionParticles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle2'}

simtk.openmm.openmm.CustomGBForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'parameters'}

simtk.openmm.openmm.CustomGBForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomHbondForce.getAcceptorParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'a3', 'a1', 'a2', 'parameters'}

simtk.openmm.openmm.CustomHbondForce.getDonorParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'d1', 'd2', 'd3', 'parameters'}

simtk.openmm.openmm.CustomHbondForce.getExclusionParticles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle2'}

simtk.openmm.openmm.CustomHbondForce.setExclusionParticles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'acceptor', 'donor'}
  Documented non-arguments:  {'particle1', 'particle2'}

simtk.openmm.openmm.CustomHbondForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomIntegrator.beginIfBlock ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'condition'}
  Documented non-arguments:  {'expression'}

simtk.openmm.openmm.CustomIntegrator.beginWhileBlock ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'condition'}
  Documented non-arguments:  {'expression'}

simtk.openmm.openmm.CustomIntegrator.getPerDofVariableByName ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'values'}

simtk.openmm.openmm.CustomManyParticleForce.getExclusionParticles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle2'}

simtk.openmm.openmm.CustomManyParticleForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'type', 'parameters'}

simtk.openmm.openmm.CustomManyParticleForce.getTypeFilter ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'types'}

simtk.openmm.openmm.CustomManyParticleForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomNonbondedForce.getExclusionParticles ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'particle2'}

simtk.openmm.openmm.CustomNonbondedForce.getInteractionGroupParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'set1', 'set2'}

simtk.openmm.openmm.CustomNonbondedForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'parameters'}

simtk.openmm.openmm.CustomNonbondedForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.CustomTorsionForce.getTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'parameters', 'particle1', 'particle3', 'particle4', 'particle2'}

simtk.openmm.openmm.CustomTorsionForce.setGlobalParameterDefaultValue ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'defaultValue'}
  Documented non-arguments:  {'name'}

simtk.openmm.openmm.DrudeForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'aniso34', 'particle', 'particle2', 'charge', 'particle1', 'particle3', 'polarizability', 'particle4', 'aniso12'}

simtk.openmm.openmm.DrudeForce.getScreenedPairParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'thole', 'particle2'}

simtk.openmm.openmm.GBSAOBCForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'radius', 'scalingFactor', 'charge'}

simtk.openmm.openmm.GBVIForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'gamma', 'radius', 'charge'}

simtk.openmm.openmm.HarmonicAngleForce.getAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'angle', 'particle1', 'particle3', 'k', 'particle2'}

simtk.openmm.openmm.NonbondedForce.getExceptionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle1', 'epsilon', 'chargeProd', 'sigma', 'particle2'}

simtk.openmm.openmm.NonbondedForce.getPMEParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'alpha', 'nx', 'ny', 'nz'}

simtk.openmm.openmm.NonbondedForce.getPMEParametersInContext ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'alpha', 'nx', 'ny', 'nz'}

simtk.openmm.openmm.NonbondedForce.getParticleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'epsilon', 'sigma', 'charge'}

simtk.openmm.openmm.PeriodicTorsionForce.getTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'particle2', 'particle1', 'particle3', 'phase', 'periodicity', 'particle4', 'k'}

simtk.openmm.openmm.RBTorsionForce.getTorsionParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'c2', 'c1', 'particle2', 'particle1', 'c3', 'c0', 'particle3', 'c4', 'c5', 'particle4'}

simtk.openmm.openmm.SerializationNode.createChildNode ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Documented non-arguments:  {'object'}

simtk.openmm.openmm.SerializationNode.hasProperty ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
  Undocumented arguments:    {'name'}
  Documented non-arguments:  {'the'}