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Python: module xplorSimulation

xplorSimulation

simulation based on an XPLOR backend. constructor: XplorSimulation(clone=False): create a new xplor process and associated XplorSimulation object. If the optional clone argument is True, the atomic coordinates and PSF information of the XplorSimulation associated with the simulation.currentSimulation() are mirrored in the new object. Otherwise, the object will have no atoms or PSF information. Methods: This objects contains all of the methods of the simulation.Simulation class. In addition, it contains the following: type() - returns the string "XplorSimulation" potList() - return the potList.PotList of potential terms which are evaluated when the SCRIpting XPLOR energy term is active. scriptingIndex() - index into XPLOR renr array corresponding to SCRIpting term. wrap() - return the associated xplorWrap.XplorWrap object. This member is not usually needed. deleteAtoms(selection, noSync=False) - delete atoms specified by the given (string) atom selection. Specify noSync=True for a performance improvement, but it requires the caller to call the syncFrom() method before manipulating any atom information on the C++ side. addAtom(atomName,residueNum,residueName, chemicalType="", segmentName="", mass=10., pos=None, isPseudo=False) - add a single atom to this XplorSimulation with the specified atomName, residueNum, residueName, segmentName and mass. If pos is specified it is also set. The isPeudo flag specifies whether or not the atom will be selected with the PSEUdo atom selection keyword. Do note that currently pseudo atoms are identified by residue name, so that if isPseudo=True is specified in this call, all atoms with the given residueName will be identified as PSEUDO. The created atom is returned as an atom.Atom. data() - return a XplorSimData object (described below) containing per-XplorSimulation information. The following method with this name from the underlying xplorWrap.XplorWrap object. command(cmd, names) fastCommand(cmd, names) shell() disableOutput() enableOutpu() The following routines synchronize simulation values to/from xplor. They are not usually needed. initFrom() - initialize quantities from XPLOR syncFrom() - copy all information from XPLOR to C++ data structures syncAtomIDFrom() syncPosFrom() syncVelFrom() syncFricFrom() syncChargeFrom() syncMassFrom() syncTo() - copy modified coordinates, etc. variables to xplor The following static function is also defined: getXplorSimulation(sim=None) - given a simulation, determine the associated XplorSimulation. If simulation is None, use simulation.currentSimulation. The XplorSimData class Methods: residueTypeSystems() - return list of type systems (strings) residueTypes(system) - given a system (string), return a list of defined residues types. residueTypeIsVariant(system, resType) - given a system and residue type, return bool describing whether or not the residue type is a variant. residueTypeAdd(system, type, isVariant=false) - add a residue type of given system, optionally specifying if it is a variant residue type. residueTypesClear() - clear the residue types database. # This file was automatically generated by SWIG (http://www.swig.org). # Version 4.0.2 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead.

Classes



builtins.object

Modified
ModifiedBase
XplorSimData

simulation.Simulation(builtins.object)

XplorSimulation

class Modified(builtins.object)

    Modified(*args, **kwargs)

Methods defined here:

__call__(self, *args, **kwargs) -> 'int'
Call self as a function.

__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

asString(self, *args, **kwargs) -> 'String'

assertClear(self, *args, **kwargs) -> 'void'

clear(self, *args, **kwargs) -> 'void'

set(self, *args, **kwargs) -> 'void'

update(self, *args, **kwargs) -> 'void'

value(self, *args, **kwargs) -> 'int'

Static methods defined here:

__swig_destroy__ = delete_Modified(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

thisown

The membership flag

Data and other attributes defined here:

MOD_SELF = 1

MOD_SIMULATION = 2

class ModifiedBase(builtins.object)

    ModifiedBase(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

registerTo(self, *args, **kwargs) -> 'void'

unRegister(self, *args, **kwargs) -> 'void'

updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

modified

registeredSimulations

thisown

The membership flag

class XplorSimData(builtins.object)

    XplorSimData(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

residueTypeAdd(self, *args, **kwargs) -> 'void'

residueTypeIsVariant(self, *args, **kwargs) -> 'bool'

residueTypeSystems(self, *args, **kwargs) -> 'CDSList< String >'

residueTypes(self, *args, **kwargs) -> 'CDSList< String >'

residueTypesClear(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_XplorSimData(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

thisown

The membership flag

class XplorSimulation(simulation.Simulation)

    XplorSimulation(clone=False)

Method resolution order:

XplorSimulation

simulation.Simulation

builtins.object

Methods defined here:

__init__(self, clone=False)
Initialize self.  See help(type(self)) for accurate signature.

__oldinit__ = __init__(self, *args, **kwargs)

__repr__ = _swig_repr(self)

addAtom(self, atomName, residueNum, residueName, chemicalType='', segmentName='', mass=10.0, pos=None, isPseudo=False)

calcNonXplorEnergyAndDeriv(self, *args, **kwargs) -> 'float_type'

command(self, c, r=())

data(self, *args, **kwargs) -> 'XplorSimData *'

deleteAtoms(self, arg, noSync=False, force=False)

deleteAtoms_byIndex(self, *args, **kwargs) -> 'void'

disableOutput(self)

enableOutput(self, state)

fastCommand(self, c, r=())
call xplorWrap.XplorWrap.fastCommand

initFrom(self, *args, **kwargs) -> 'void'

potList(self, *args, **kwargs) -> 'PotList &'

pyXplorHelp(self, *args, **kwargs) -> 'String'

rcWrap(self, *args, **kwargs) -> 'rc_XplorWrap'

scriptingIndex(self, *args, **kwargs) -> 'int'

select(self, selString)

setAtomCharge(self, *args, **kwargs) -> 'void'

setAtomFric(self, *args, **kwargs) -> 'void'

setAtomMass(self, *args, **kwargs) -> 'void'

setAtomMassArr(self, *args, **kwargs) -> 'void'

setAtomName(self, *args, **kwargs) -> 'void'

setAtomPos(self, *args, **kwargs) -> 'void'

setAtomPosArr(self, *args, **kwargs) -> 'void'

setAtomVel(self, *args, **kwargs) -> 'void'

setAtomVelArr(self, *args, **kwargs) -> 'void'

setChemType(self, *args, **kwargs) -> 'void'

setModifiedProp(self, *args, **kwargs) -> 'void'

setResidueName(self, *args, **kwargs) -> 'void'

setResidueNum(self, *args, **kwargs) -> 'void'

setSegmentName(self, *args, **kwargs) -> 'void'

shell(self)

syncAtomIDFrom(self, *args, **kwargs) -> 'void'

syncChargeFrom(self, *args, **kwargs) -> 'void'

syncFricFrom(self, *args, **kwargs) -> 'void'

syncFrom(self, *args, **kwargs) -> 'void'

syncMassFrom(self, *args, **kwargs) -> 'void'

syncPosFrom(self, *args, **kwargs) -> 'void'

syncTo(self, *args, **kwargs) -> 'void'

syncVelFrom(self, *args, **kwargs) -> 'void'

type(self, *args, **kwargs) -> 'String const'

wrap(self, *args, **kwargs) -> 'XplorWrap *'

xplorVars(self, *args, **kwargs) -> 'XplorVars *'

Static methods defined here:

__swig_destroy__ = delete_XplorSimulation(...)

defaultSimulation(*args, **kwargs) -> 'XplorSimulation *'

deleteDefaultSimulation(*args, **kwargs) -> 'void'

initSimulation(*args, **kwargs) -> 'void'

resetDefaultSimulation(*args, **kwargs) -> 'void'

Data descriptors defined here:

thisown

The membership flag

Methods inherited from simulation.Simulation:

__eq__(self, other)
Return self==value.

__ne__(self, other)
Return self!=value.

addDependent(self, *args, **kwargs) -> 'void'

atomByID(self, *args, **kwargs) -> 'Atom'

atomCharge(self, *args, **kwargs) -> 'float_type const &'

atomFric(self, *args, **kwargs) -> 'float_type const &'

atomID(self, *args, **kwargs) -> 'int'

atomMass(self, *args, **kwargs) -> 'float_type const &'

atomMassArr(self, *args, **kwargs) -> 'CDSVector< float_type >'

atomName(self, *args, **kwargs) -> 'String'

atomNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'

atomPos(self, *args, **kwargs) -> 'Vec3 const &'

atomPosArr(self, *args, **kwargs) -> 'CDSVector< Vec3 >'

atomString(self, *args, **kwargs) -> 'String'

atomVel(self, *args, **kwargs) -> 'Vec3 const &'

atomVelArr(self, *args, **kwargs) -> 'CDSVector< Vec3 >'

bondPairByID(self, *args, **kwargs) -> 'BondIDPair const &'

chemType(self, *args, **kwargs) -> 'String'

chemTypeArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'

forceUpdate(self, *args, **kwargs) -> 'int const'

kineticEnergy(self, *args, **kwargs) -> 'float_type'

lookupID(self, *args, **kwargs) -> 'int'

markAsModified(self, *args, **kwargs) -> 'void'

modifiedID(self, *args, **kwargs) -> 'Simulation const *'

name(self, *args, **kwargs) -> 'String const'

noFit(self, *args, **kwargs) -> 'bool const'

numAtoms(self, *args, **kwargs) -> 'int'

numBonds(self, *args, **kwargs) -> 'int'

numDependents(self, *args, **kwargs) -> 'int'

rawID(self, *args, **kwargs) -> 'int'

registerCallbacks(self, *args, **kwargs) -> 'void'

removeDependent(self, *args, **kwargs) -> 'void'

residueName(self, *args, **kwargs) -> 'String'

residueNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'

residueNum(self, *args, **kwargs) -> 'int'

residueNumArr(self, *args, **kwargs) -> 'CDSVector< int >'

segmentName(self, *args, **kwargs) -> 'String'

segmentNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'

setForceUpdate(self, *args, **kwargs) -> 'void'

setNoFit(self, *args, **kwargs) -> 'void'

sync(self, *args, **kwargs) -> 'void'

syncDerivs(self, *args, **kwargs) -> 'void'

Static methods inherited from simulation.Simulation:

currentSimulation(*args, **kwargs) -> 'Simulation *'

deleteSimulation(*args, **kwargs) -> 'void'

getReference(*args, **kwargs) -> 'rc_Simulation &'

makeCurrent(*args, **kwargs) -> 'void'

numSimulations(*args, **kwargs) -> 'int'

simulationByID(*args, **kwargs) -> 'Simulation *'

syncAllSimulations(*args, **kwargs) -> 'void'

validSimulation(*args, **kwargs) -> 'bool'

Data descriptors inherited from simulation.Simulation:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

Data and other attributes inherited from simulation.Simulation:

__hash__ = None

Functions

XplorSimulation_defaultSimulation(*args) -> 'XplorSimulation *'

XplorSimulation_deleteDefaultSimulation(*args) -> 'void'

XplorSimulation_initSimulation(*args) -> 'void'

XplorSimulation_resetDefaultSimulation(*args) -> 'void'

currentSimulation(*args) -> 'Simulation *'

fromSimulation(*args, **kwargs) -> 'XplorSimulation *'

getXplorSimulation(simulation=0)
given a simulation, determine the associated XplorSimulation
if simulation is None, use simulation.currentSimulation.

makeCurrent(*args, **kwargs) -> 'void'

pyXplorHelp(*args) -> 'String'

Data

orig_LD_LIBRARY_PATH = '/home/schwitrs/lib/Linux_x86_64:/home/schwitrs/lib/Linux_x86_64::/usr/local/lib:/usr/local/lib'
psfTemplate = '\nstructure\nPSF\n\n 1 !NTITLE\n REMARKS addD... 0 !NGRP\n 0 0 0\nend \n'

Data
		orig_LD_LIBRARY_PATH = '/home/schwitrs/lib/Linux_x86_64:/home/schwitrs/lib/Linux_x86_64::/usr/local/lib:/usr/local/lib' psfTemplate = '\nstructure\nPSF\n\n 1 !NTITLE\n REMARKS addD... 0 !NGRP\n 0 0 0\nend \n'