 simtk | |
  openmm | |
   app | |
    amberinpcrdfile | |
     AmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it |
    amberprmtopfile | |
     AmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it |
    dcdfile | |
     DCDFile | DCDFile provides methods for creating DCD files |
    dcdreporter | |
     DCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file |
    element | |
     Element | An Element represents a chemical element |
    forcefield | |
     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 |
    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 |
    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 |
    LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
    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 |
    VirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles |
    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 |