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- addPlaneAtoms(oAtom=None, xAtom=None, yAtom=None, A=None, B=None, C=None, D=None, resid=None, segid=None)
create the atoms defining the restraint plane.
Either (oAtom, xAtom, yAtom ) or (A,B,C,D) should be specified.
- analyze(potList)
- perform analysis of PlaneDistPot terms and return nicely formatted
summary
- create_PlaneDistPot(name, restraintsFile='', oAtom=None, xAtom=None, yAtom=None, replicatePlaneAtoms=True, A=None, B=None, C=None, D=None, restraints='')
- create a planeDistPot.PlaneDistPot using a plane defined by the
equation
A x + B y + C z + D = 0
or
by three atoms.
If the atom-type definition is used, replicatePlaneAtoms is consulted
as to whether the plane remains fixed to the plane-defining atoms or
the plane is decoupled from those atoms.
restraintsFile is a file name of a restraints assignment table, while
restraints is a string containing these restraints.
- massSetup(list, axisMass=300)
appropriately setup plane-atom masses to axisMass,
- topologySetup(ivm, list)
configure the given ivm.IVM object's topology setup using the
freedom string for each PlaneDistPot in list.
This function should be called prior to
ivm.IVM.autoTorsion() or protocol.torsionTopology()
The freedom specifier should be one of the following keywords:
fix
group
translate
rotate
free
ignore
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