Application Layer¶
Loaders and Setup¶
AmberInpcrdFile (file[, loadVelocities, …]) |
AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it. |
AmberPrmtopFile (file) |
AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it. |
CharmmCrdFile (fname) |
Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc. |
CharmmParameterSet (*args, **kwargs) |
Stores a parameter set defined by CHARMM files. |
CharmmPsfFile (psf_name) |
A chemical structure instantiated from CHARMM files. |
CharmmRstFile (fname) |
Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name ‘fname’ into class attributes |
DCDFile (file, topology, dt[, firstStep, …]) |
DCDFile provides methods for creating DCD files. |
DesmondDMSFile (file) |
DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it |
GromacsGroFile (file) |
GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it. |
GromacsTopFile (file[, periodicBoxVectors, …]) |
GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it. |
PDBFile (file[, extraParticleIdentifier]) |
PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it. |
PDBxFile (file) |
PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it. |
Representation and Manipulation¶
Topology () |
Topology stores the topological information about a system. |
Chain (index, topology, id) |
A Chain object represents a chain within a Topology. |
Residue (name, index, chain, id, insertionCode) |
A Residue object represents a residue within a Topology. |
Atom (name, element, index, residue, id) |
An Atom object represents an atom within a Topology. |
Modeller (topology, positions) |
Modeller provides tools for editing molecular models, such as adding water or missing hydrogens. |
Simulation¶
ForceField (*files) |
A ForceField constructs OpenMM System objects based on a Topology. |
Simulation (topology, system, integrator[, …]) |
Simulation provides a simplified API for running simulations with OpenMM and reporting results. |
Reporting Output¶
CheckpointReporter (file, reportInterval) |
CheckpointReporter saves periodic checkpoints of a simulation. |
DCDReporter (file, reportInterval[, append, …]) |
DCDReporter outputs a series of frames from a Simulation to a DCD file. |
PDBReporter (file, reportInterval[, …]) |
PDBReporter outputs a series of frames from a Simulation to a PDB file. |
PDBxReporter (file, reportInterval[, …]) |
PDBxReporter outputs a series of frames from a Simulation to a PDBx/mmCIF file. |
StateDataReporter (file, reportInterval[, …]) |
StateDataReporter outputs information about a simulation, such as energy and temperature, to a file. |
Extras¶
CharmmPSFWarning |
For non-fatal PSF parsing issues |
Element (number, name, symbol, mass) |
An Element represents a chemical element. |
Units¶
BaseDimension |
A physical dimension such as length, mass, or temperature. |
BaseUnit |
Physical unit expressed in exactly one BaseDimension. |
Quantity |
Physical quantity, such as 1.3 meters per second. |
ScaledUnit |
ScaledUnit is like a BaseUnit, but it is based on another Unit. |
SiPrefix |
Unit prefix that can be multiplied by a unit to yield a new unit. |
Unit |
Physical unit such as meter or ampere. |
UnitSystem |
A complete system of units defining the base unit in each dimension |