Table of Contents


Everything

Modules

_BBKIntegrator'
_CGMinimizerIntegrator'
_DMDLeapfrogIntegrator'
_DihedralForce'
_EigenvectorReader'
_EigenvectorTextReader'
_EwaldForce'
_ForceGroup'
_GromacsTopologyReader'
_HessianInt'
_ImproperForce'
_LeapfrogTruncatedShadow'
_MultiGridForce'
_NPTVerletIntegrator'
_NormalModeBrownian'
_NormalModeDiagonalize'
_NormalModeMinimizer'
_NormalModeUtilities'
_NoseNVTLeapfrogIntegrator'
_OutputCache'
_OutputDCDTrajectoryVel'
_OutputFinalPDBPos'
_OutputFinalXYZVel'
_OutputXYZTrajectoryForce'
_OutputXYZTrajectoryPos'
_PLeapfrogIntegrator'
_PyMTSIntegrator'
_ScalarStructure'
_XYZBinReader'
_XYZReader'
_XYZWriter'
interface
interface.ProtoMolApp
interface._ProtoMolApp
interface.base
interface.base.MathUtilities
interface.base._MathUtilities
interface.force
interface.force.ForceGroup
interface.force.bonded
interface.force.bonded.AngleForce
interface.force.bonded.BondForce
interface.force.bonded.DihedralForce
interface.force.bonded.HarmDihedralForce
interface.force.bonded.ImproperForce
interface.force.bonded._AngleForce
interface.force.bonded._BondForce
interface.force.bonded._HarmDihedralForce
interface.force.nonbonded
interface.force.nonbonded.CutoffForce
interface.force.nonbonded.EwaldForce
interface.force.nonbonded.MultiGridForce
interface.force.nonbonded.PMEForce
interface.force.nonbonded.SimpleFullForce
interface.force.nonbonded._CutoffForce
interface.force.nonbonded._PMEForce
interface.force.nonbonded._SimpleFullForce
interface.force.system
interface.force.system.PySystemForce
interface.force.system._PySystemForce
interface.integrator
interface.integrator.PyMTSIntegrator
interface.integrator.PySTSIntegrator
interface.integrator._PySTSIntegrator
interface.integrator.base
interface.integrator.base.CGMinimizerIntegrator
interface.integrator.base.ImpulseIntegrator
interface.integrator.base.LangevinImpulseIntegrator
interface.integrator.base.NumericalDifferentiation
interface.integrator.base._ImpulseIntegrator
interface.integrator.base._LangevinImpulseIntegrator
interface.integrator.base._NumericalDifferentiation
interface.integrator.hessian
interface.integrator.hessian.HessianInt
interface.integrator.leapfrog
interface.integrator.leapfrog.DMDLeapfrogIntegrator
interface.integrator.leapfrog.LeapfrogIntegrator
interface.integrator.leapfrog.LeapfrogTruncatedShadow
interface.integrator.leapfrog.NPTVerletIntegrator
interface.integrator.leapfrog.NoseNVTLeapfrogIntegrator
interface.integrator.leapfrog.PLeapfrogIntegrator
interface.integrator.leapfrog._LeapfrogIntegrator
interface.integrator.normal
interface.integrator.normal.BBKIntegrator
interface.integrator.normal.NormalModeBrownian
interface.integrator.normal.NormalModeDiagonalize
interface.integrator.normal.NormalModeLangevin
interface.integrator.normal.NormalModeMinimizer
interface.integrator.normal.NormalModeMori
interface.integrator.normal.NormalModeRelax
interface.integrator.normal.NormalModeUtilities
interface.integrator.normal._NormalModeLangevin
interface.integrator.normal._NormalModeMori
interface.integrator.normal._NormalModeRelax
interface.integrator.openMM
interface.integrator.openMM.OpenMMIntegrator
interface.integrator.openMM._OpenMMIntegrator
interface.io
interface.io.DCDTrajectoryReader
interface.io.EigenvectorReader
interface.io.EigenvectorTextReader
interface.io.PARReader
interface.io.PDBReader
interface.io.PDBWriter
interface.io.PSFReader
interface.io.XYZBinReader
interface.io.XYZReader
interface.io.XYZTrajectoryReader
interface.io.XYZTrajectoryWriter
interface.io.XYZWriter
interface.io._DCDTrajectoryReader
interface.io._PARReader
interface.io._PDBReader
interface.io._PDBWriter
interface.io._PSFReader
interface.io._XYZTrajectoryReader
interface.io._XYZTrajectoryWriter
interface.io.gromacs
interface.io.gromacs.GromacsParameterFileReader
interface.io.gromacs.GromacsTopologyReader
interface.io.gromacs.PortGromacsParameters
interface.io.gromacs._GromacsParameterFileReader
interface.io.gromacs._PortGromacsParameters
interface.output
interface.output.OutputCache
interface.output.OutputDCDTrajectory
interface.output.OutputDCDTrajectoryVel
interface.output.OutputEnergies
interface.output.OutputFAHGUI
interface.output.OutputFinalPDBPos
interface.output.OutputFinalXYZPos
interface.output.OutputFinalXYZVel
interface.output.OutputScreen
interface.output.OutputXYZTrajectoryForce
interface.output.OutputXYZTrajectoryPos
interface.output.OutputXYZTrajectoryVel
interface.output._OutputDCDTrajectory
interface.output._OutputEnergies
interface.output._OutputFAHGUI
interface.output._OutputFinalXYZPos
interface.output._OutputScreen
interface.output._OutputXYZTrajectoryVel
interface.pyWrap
interface.topology
interface.topology.GenericTopology
interface.topology.TopologyUtilities
interface.topology._GenericTopology
interface.topology._TopologyUtilities
interface.type
interface.type.ScalarStructure
interface.type.Vector3DBlock
interface.type._Vector3DBlock

[hide private]