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Pydoc: module posDiffPotTools

posDiffPotTools

index

Tools to help create/analyze potential terms based on atomic coordinate difference

Functions

analyze(potList): perform analysis of PosDiffPot terms and return nicely formatted
summary

cmpRMSD(self): Report the positional RMSD cooresponding to cmpSel, specified in
create_PosDiffPot.

create_PosDiffPot(name, selection, selection2=None, pdbFile=None, psf=None, absoluteFit=False, removeMissing=False, cmpSel=None, **kwargs): Create a PosDiffPot term based on the specified atom selection.

The name of the PosDiffPot term is given by the name argument (string).
If selection2 is not specified, it is taken to be the same as selection.
If pdbFile is specified, the comparison is made with the coordinates in that
file (using selection2).  It is an error to omit both the selection2 and
pdbFile arguments.  For this potential term, the order of atom indices in
selection2 must match that in selection. If selection is an ordered
atomSel.AtomSel object, then selection2 will also be ordered if omitted
or specified by string. If selection2 is the string "initial", the
selection string is taken from selection, while the comparison coordinates
are those loaded when create_PosDiffPot is called.

This potential term is based on the posSymmPot.PosSymmPot potential.
In this case each atom is placed in its own equivalent set (as in the
NCS potential).

If absoluteFit=True, selection and selection2 will be physically overlaid,
as rigid body translation and rotation will not be performed before the
fit.

cmpSel is a selection or pair of selections (the later is required if
selection2 is supplied) to use for an additional rmsd computation.  It is
not used in an energy calculation. The corresponding RMSD value can be
obtained using the cmpRMSD() method.

If removeMissing=True, remove from a selection atoms not present in
the other, for cases where the selections (selection, selection2),
(cmpSel, cmpSel2) do not have the same number of atoms. This will
fail if more than one segid (chain) is selected.

A non-standard topology for the input PDB file can be accomodated by
specifying a value for the psf argument: the value None (default) will
cause the pdbFile (a string with a PDB filename) to be loaded using
protocol.loadPDB (with deleteUnknownAtoms=True); this assumes a
standard topology. Alternatively, psf can be a string with the contents
of a PSF file, a string with a PSF filename, or a sequence with one of
more PSF filenames which are loaded by protocol.initStruct, and then
the  coordinates are loaded with protocol.initCoords, with
deleteUnknownAtoms=True. Finally, a psf value of "none" (a string), will
cause atom information to be loaded without a PSF- no connectivity
information will be present. With this choice, processing of ATOM records
will stop when a ENDMDL record is encountered.

The additional keyword argument can be specified:
   includeHETATM, which is passed to protocol.initCoords

The returned potential term has four members beyond those in a
posSymmPot.PosSymmPot term:

    pdbFile     - the value of the pdbFile argument.
    selection   - an atomSel.AtomSel corresponding to the selection
                  argument.
    selection2  - an atomSel.AtomSel corresponding to the selection2
                  argument.
    xsim        - a xplorSimulation.XplorSimulation generated for
                  containing atomic information if pdbFile is
                  specified.

findMatchingSubSel(sel1, sel2, name1, name2): Return selections corresponding to the inputs which
have the same length and matching segid, resid, atom name.

As a special case, if both selections contain atoms with a single
segment name each, then segid mismatch will be ignored.