DesmondDMSFile

class simtk.openmm.app.desmonddmsfile.DesmondDMSFile(file)

DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it

__init__(file)

Load a DMS file

Parameters:file (string) – the name of the file to load

Methods

__init__(file) Load a DMS file
close() Close the SQL connection
createSystem([nonbondedMethod, ...]) Construct an OpenMM System representing the topology described by this
getPositions() Get the positions of each atom in the system
getProvenance() Get the provenance string of this system
getTopology() Get the topology of the system
getPositions()

Get the positions of each atom in the system

getTopology()

Get the topology of the system

getProvenance()

Get the provenance string of this system

createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None)

Construct an OpenMM System representing the topology described by this DMS file

Parameters:
  • nonbondedMethod (object=NoCutoff) – The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
  • nonbondedCutoff (distance=1*nanometer) – The cutoff distance to use for nonbonded interactions
  • ewaldErrorTolerance (float=0.0005) – The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
  • removeCMMotion (boolean=True) – If true, a CMMotionRemover will be added to the System
  • hydrogenMass (mass=None) – The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
close()

Close the SQL connection