simulation |
index |
structure information for a simulation
Simulations provide structure information, including atom information
and connectivity. It is generally easier to get and set this
information using the higher level atom.Atom interface accessed
through the atomSel.AtomSel class.
The following functions are provided:
currentSimulation()
return the current Simulation
makeCurrent(sim)
make the specified Simulation current.
numSimulations()
return the current number of Simulations.
simulationByID(simID)
return the specified Simulation. simIDs take values between 0 and
numSimulation()-1. Valid return values are non-None.
validSimulation(sim)
check that the specified Simulation is registered.
The following methods for the Simulation class are available
currentSimulation() - static method returning the current active Simulation
name() - Simulation name
type() - returns the string "Simulation"
numAtoms() - number of atoms in Simulation
numBonds() - number of bonds in Simulation
atomByID(index) - return an atom.Atom object by its index
bondPairByID(index) - return a pair of atom indices for bond indexed by index
select(sel,ordered=False) - low level selector returns list of atom indices
given string sel. Use atomSel.AtomSel
object instead. See the atomSelLang
documentation for the meaning of the optional
ordered argument.
kineticEnergy() - calculate kinetic energy associated with the current
masses, velocities.
atomString(index) - a 19 character string unique identifier of an atom,
given an atom index.
deleteAtoms(string,
noSync=False,
force=False) - delete the atoms corresponding selected by
the atom selection string, whose syntax is
described in atomSelLang. If this method is
called after potential terms are created
(associated with this simulation) then an
exception will be raised, unless the force
argument is set to True. Setting the noSync
argument to True will prevent synchronization
with associated sub-processes, and requires that
the sync() method be called before using
energy terms which depend on these subprocesses.
sync(testResize=true) - barrier and synchronize subprocess data. If the
argument is true, allow for changes in numAtoms,
numBonds.
modifiedID() - Return current Simulation, except for
EnsembleMemberSimulations.
There are three integer id values:
rawID() - always unique.
lookupID() - used to find Simulation using simulationByID()- for
EnsembleSimulations of size 1, returns the underlying
Simulation's rawID()
atomID() - used to compare atoms which might be in mirrored/overlay
Simulations.
The quantities below may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value)
atomPosArr - a CDSVector of all atom positions
atomVelArr - a CDSVector of all atom velocities
atomMassArr - a CDSVector of all atom masses
noFit - used by simulationTools.StructureLoop to set a
default value for which atoms to use in fitting.
The quantities below may be retrieved using the member function form
quantity(index), while they are set using the form setQuantity(index,value),
where index is an atom index.
atomPos
atomVel
atomMass
atomFric
atomCharge
segmentName
residueName
residueNum
atomName
fullName
# 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.
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