Python: module symSimulation

symSimulation

A simulation.Simulation which contains copies of a subsimulation related by strict symmetry operations. A SymSimulation should not be manipulated directly by an IVM. Rather, energies can be evaluated for atoms in the SymSimulation, but the underlying Simulation should instead by manipulated by the IVM. Constructor: SymSimulation(name, subSel, cloneFirst=True) A SymSimulation with given name is created based on the specified subSel, which is an atomSel.AtomSel object. By default the atoms in subSel are inserted into the newly created SymSimulation as a first copy with an identity transformation. If cloneFirst is set to False, all copies must be added with addCopy(). For SymSimulations, the simulation.Simulation noFit property of the subSel Simulation is set to True, as the absolute position of the protomer is significant. Methods: This objects contains all of the methods of the simulation.Simulation class, but some write operations may be disallowed. In addition, it contains the following: type() - returns the string "SymSimulation" subSel() - returns the atomSel.AtomSel subSel specified during object construction. addCopy(rot, - add a copy of the specified subSel atoms trans, with the specified transformation parameters, centroidMult, and one or more characters to use as a prefix, or centroidProj, suffix for the segment name (one of these must be translateSel, specified). Within a copy, the coordinates q_copy translateMult, are generated from those of subSel q via the rotateSel, transformation: rotateAmount, segidPrefix, segidSuffix) q_copy = rotMat * q + trans + centroidMult * centroidProj * q_centroid + translateMult * translatePos where q_centroid is the geometric center, centroidMult and translateMult are floating point numbers, centroidProj can be used to specify that only a subset of the centroid position is used for the translation calculation, and translateSel is an atomSel.AtomSel which specifies two atoms whose difference defines a translation vector. rotMat is specified by the rot argument if it is fixed in space, or by the rotateSel and rotateAmount arguments for a rotation matrix whose orientation is allowed to vary. In the later case, rotateSel should specify two atoms defining a rotation axis, and rotationAmount will specify the amount of rotation (in radians). numCopies() - return the number of subSel copies are present. This will be the number of times addCopy was called if cloneFirst=False in the ctor, else it will be one less than this number. symOp(copyID) - return a SymSimulationOp object corresponding to the specified copy. copyID 0 corresponds to the initial identity copy. The SymSimulationOp object has the following members: Mat3 rot Vec3 trans float_type centroidMult Mat3 centroidProj AtomSel transAtoms float_type transMult String segidPrefix String segidSuffix Functions: fromSimulation(sim) - given a simulation.Simulation object, return (cast to) a SymSimulation. Will throw an exception if sim is does not have SymSimulation type. # 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

SymSimulation(simulation.Simulation, ModifiedBase)

SymSimulationOp

simulation.Simulation(builtins.object)

SymSimulation(simulation.Simulation, ModifiedBase)

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'

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 SymSimulation(simulation.Simulation, ModifiedBase)

SymSimulation(*args, **kwargs)

Method resolution order:: SymSimulation; simulation.Simulation; ModifiedBase; builtins.object

Methods defined here:

__del__(self): #somewhat fragile...

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

__repr__ = _swig_repr(self)

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

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 >'

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

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

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

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

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

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

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

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

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

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

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 >'

select(self, *args, **kwargs) -> 'CDSList< int >'

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'

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

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

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

subSel(self, *args) -> 'AtomSel const'

symOp(self, *args, **kwargs) -> 'SymSimulation::SymOp &'

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_SymSimulation(...)

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'

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

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

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

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'

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

setNoFit(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

Methods inherited from ModifiedBase:

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

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

Data descriptors inherited from ModifiedBase:

modified

registeredSimulations

class SymSimulationOp(builtins.object)

SymSimulationOp(*args, **kwargs)

Methods defined here:

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

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_SymSimulationOp(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

centroidMult

centroidProj

rot

rotAmount

rotAtoms

segidPrefix

segidSuffix

thisown: The membership flag

trans

transAtoms

transMult

Functions

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

pyXplorHelp(*args) -> 'String'