  simtk | |
 openmm | |
 app | |
  amberinpcrdfile | |
  AmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it |
| amberprmtopfile | |
 HCT | |
| OBC1 | |
| OBC2 | |
| GBn | |
| GBn2 | |
| AmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it |
| charmmcrdfiles | |
| CharmmCrdFile | Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc |
| CharmmRstFile | Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes |
| charmmparameterset | |
| CharmmParameterSet | Stores a parameter set defined by CHARMM files |
| charmmpsffile | |
| CharmmPsfFile | A chemical structure instantiated from CHARMM files |
| checkpointreporter | |
| CheckpointReporter | CheckpointReporter saves periodic checkpoints of a simulation |
| dcdfile | |
| DCDFile | DCDFile provides methods for creating DCD files |
| dcdreporter | |
| DCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file |
| desmonddmsfile | |
| DesmondDMSFile | DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it |
| element | |
| Element | An Element represents a chemical element |
| forcefield | |
| NoCutoff | |
| CutoffNonPeriodic | |
| CutoffPeriodic | |
| Ewald | |
| PME | |
| HBonds | |
| AllBonds | |
| HAngles | |
| ForceField | A ForceField constructs OpenMM System objects based on a Topology |
| gromacsgrofile | |
| GromacsGroFile | GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it |
| gromacstopfile | |
| GromacsTopFile | GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it |
| modeller | |
| Modeller | Modeller provides tools for editing molecular models, such as adding water or missing hydrogens |
| pdbfile | |
| PDBFile | PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it |
| pdbreporter | |
| PDBReporter | PDBReporter outputs a series of frames from a Simulation to a PDB file |
| simulation | |
| Simulation | Simulation provides a simplified API for running simulations with OpenMM and reporting results |
| statedatareporter | |
| StateDataReporter | StateDataReporter outputs information about a simulation, such as energy and temperature, to a file |
 topology | |
| Topology | Topology stores the topological information about a system |
| Chain | A Chain object represents a chain within a Topology |
| Residue | A Residue object represents a residue within a Topology |
| Atom | An Atom object represents a residue within a Topology |
| openmm | |
| State | A State object records a snapshot of the current state of a simulation at a point in time |
| Force | Force objects apply forces to the particles in a System, or alter their behavior in other ways |
| AmoebaAngleForce | This class implements an interaction between triplets of particles that varies with the angle between them |
| AmoebaBondForce | This class implements an interaction between pairs of particles that varies with the distance between them |
| AmoebaGeneralizedKirkwoodForce | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model |
| AmoebaInPlaneAngleForce | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles |
| AmoebaMultipoleForce | This class implements the Amoeba multipole interaction |
| AmoebaOutOfPlaneBendForce | This class implements the Amoeba out-of-plane bend interaction |
| AmoebaPiTorsionForce | This class implements the Amoeba pi-torsion interaction |
| AmoebaStretchBendForce | This class implements the Amoeba stretch-bend interaction |
| AmoebaTorsionTorsionForce | This class implements the Amoeba torsion-torsion interaction |
| AmoebaVdwForce | This class implements a buffered 14-7 potential used to model van der Waals forces |
| AmoebaWcaDispersionForce | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model |
| AndersenThermostat | This class uses the Andersen method to maintain constant temperature |
| Integrator | An Integrator defines a method for simulating a System by integrating the equations of motion |
| BrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics |
| CMAPTorsionForce | This class implements an interaction between pairs of dihedral angles |
| CMMotionRemover | This class prevents the center of mass of a System from drifting |
| Context | A Context stores the complete state of a simulation |
| TabulatedFunction | A TabulatedFunction uses a set of tabulated values to define a mathematical function |
| Continuous1DFunction | This is a TabulatedFunction that computes a continuous one dimensional function |
| Continuous2DFunction | This is a TabulatedFunction that computes a continuous two dimensional function |
| Continuous3DFunction | This is a TabulatedFunction that computes a continuous three dimensional function |
| CustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them |
| CustomBondForce | This class implements bonded interactions between pairs of particles |
| CustomCompoundBondForce | This class supports a wide variety of bonded interactions |
| CustomExternalForce | This class implements an "external" force on particles |
| CustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles |
| CustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding |
| CustomIntegrator | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms |
| CustomNonbondedForce | This class implements nonbonded interactions between particles |
| CustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them |
| Discrete1DFunction | This is a TabulatedFunction that computes a discrete one dimensional function f(x) |
| Discrete2DFunction | This is a TabulatedFunction that computes a discrete two dimensional function f(x,y) |
| Discrete3DFunction | This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z) |
| DrudeForce | This class implements forces that are specific to Drude oscillators |
| DrudeLangevinIntegrator | This Integrator simulates systems that include Drude particles |
| DrudeSCFIntegrator | This is a leap-frog Verlet Integrator that simulates systems with Drude particles |
| GBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model |
| GBVIForce | This class implements an implicit solvation force using the GB/VI model |
| HarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them |
| HarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them |
| LangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics |
| VirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles |
| LocalCoordinatesSite | This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system |
| LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
| MonteCarloAnisotropicBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| MonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| NonbondedForce | This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions |
| OpenMMException | This class is used for all exceptions thrown by OpenMM |
| OutOfPlaneSite | This is a VirtualSite that computes the particle location based on three other particles' locations |
| PeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them |
| Platform | A Platform defines an implementation of all the kernels needed to perform some calculation |
| RBTorsionForce | This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential |
| RPMDIntegrator | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD) |
| System | This class represents a molecular system |
| ThreeParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations |
| TwoParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations |
| VariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics |
| VariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm |
| VerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm |
| XmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again |
| vec3 | |
| Vec3 | Vec3 is a 3-element tuple that supports many math operations |
| version | |
1.8.5 
