Official government website icon

bit	Xplor-NIH	VMD-XPLOR

Pydoc: module planeDistTools

planeDistTools

index

Tools to help create, manipulate and analyze distance restraints measured between an atom and a plane.

Functions

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 one of A, B, C, or D is not specified, it is taken to be zero.

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.

if list is not specified, then pseudoatoms associated with
all registered PlaneDistPot objects are configured.

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

if list is not specified, then pseudoatoms associated with
all registered PlaneDistPot objects are configured.

Data
		default_resid = 1100 default_segid = 'PLAN' psfTemplate = '\nstructure\nPSF\n\n 1 !NTITLE\n REMARKS plan... 0 !NGRP\n 0 0 0\nend \n'