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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


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,
Load a DMS file


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

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

def __del__ (   self)

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


- 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)

Member Data Documentation


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