DesmondDMSFile Class Reference

Inheritance diagram for DesmondDMSFile:

Public Member Functions
def	__init__
def	getPositions
def	getTopology
def	getProvenance
def	createSystem
def	close
def	__del__

Public Attributes
	provenance
	positions

Detailed Description

DesmondDMSFile parses a Desmond DMS (desmond molecular system) and

constructs a topology and (optionally) an OpenMM System from it

Constructor & Destructor Documentation

def __init__	(		self,
			file
	)

Load a DMS file



Parameters:

- file (string) the name of the file to load

References DesmondDMSFile._conn, DesmondDMSFile._open, DesmondDMSFile._readSchemas(), and DesmondDMSFile._tables.

def __del__

(

self

)

References DesmondDMSFile.close().

Member Function Documentation

def close

(

self

)

Close the SQL connection

References DesmondDMSFile._open.

Referenced by DesmondDMSFile.__del__().

def createSystem	(		self,
			nonbondedMethod = ff.NoCutoff,
			nonbondedCutoff = 1.0*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, or PME.

- 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 or PME.

- 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.

References DesmondDMSFile._addAnglesToSystem(), DesmondDMSFile._addBondsToSystem(), DesmondDMSFile._addCMAPToSystem(), DesmondDMSFile._addConstraintsToSystem(), DesmondDMSFile._addImproperHarmonicTorsionsToSystem(), DesmondDMSFile._addNonbondedForceToSystem(), DesmondDMSFile._addPeriodicTorsionsToSystem(), DesmondDMSFile._addVirtualSitesToSystem(), DesmondDMSFile._angleConstraints, DesmondDMSFile._atomBonds, DesmondDMSFile._checkForUnsupportedTerms(), DesmondDMSFile._hasTable(), and DesmondDMSFile._tables.

Referenced by DesmondDMSFile.getProvenance().

def getPositions

(

self

)

Get the positions of each atom in the system

References AmberInpcrdFile.positions, and DesmondDMSFile.positions.

def getProvenance

(

self

)

Get the provenance string of this system

References DesmondDMSFile.createSystem(), and DesmondDMSFile.provenance.

def getTopology

(

self

)

Get the topology of the system

References Simulation.topology, Modeller.topology, PDBFile.topology, AmberPrmtopFile.topology, Chain.topology, and GromacsTopFile.topology.

Member Data Documentation

positions

Referenced by Modeller.add(), Modeller.addExtraParticles(), Modeller.addHydrogens(), Modeller.addSolvent(), Modeller.convertWater(), Modeller.delete(), Modeller.getPositions(), and DesmondDMSFile.getPositions().

provenance

Referenced by DesmondDMSFile.getProvenance().

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The documentation for this class was generated from the following file:

• desmonddmsfile.py