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Pydoc: module probDistPotTools

probDistPotTools

index

tool for creating a probDistPot

Functions

Rfactor(term): overall real-space R factor
using densityGrid.CompareData for the target and calculated maps
normalized by their respective maximum values.

addAxisAtoms(resid=-1, segid='', sim=None): add atoms to the current structure. If the resid argument
is omitted, a new number is automatically generated. If the
segment name is omitted, the default is used. Initial coords
for the various atoms are also generated.

Returns a tuple of (oAtom, xAtom, yAtom, zAtom, tAtom)

analyze(potList): Perform analysis of ProbDistPot terms and return nicely formatted
summary.

centerOnMap(term, moveAtoms=False, verbose=False): Given the ProbDistPot instance term, set its translation member (tAtom)
to center on its selection. This routine also resets the axis atoms such
that the OO atom is at the origin.

Alternatively, if moveAtoms=True, translate all atoms such that the
term.atomProb().selection() is centered on term.targetMap().centroid().
This approach should be used only if there is a single ProbDistPot term
(fitting to a single map).

correlation(term)

create_ProbDistPot(name, targetMap, selection='not PSEUDO', potType='diff', rotateCenterMap=False, ensembleRotateCenter=False, scale=1, mapType='density'): creates a probDistPot.ProbDistPot with given name

targetMap contains the target Map which is an DenstiyGrid object

potType: switches the energy type.
   "diff" which is the default energy function, is based on the squared
          distance between the target density & current density calculated
   "cross_correlation" is based on a cross correlation
   "correlation" is the correct correlation function

rotateCenterMap: if True, use pseudoatoms to rotate and center the
                 map on the molecular system. If False, the molecular
                 system is rotated to fit the map. This facility can be
                 used in circumstances in which the absolute position or
                 orientation in space should be independent of the map,
                 for instance when fitting multiple maps simultaneously.
                 When this argument is False, the noFit property of the
                 associated simulation.Simulation is set so that the
                 resulting structures are not fit in
                 simulationTools.StructureLoop.

ensembleRotateCenter: for EnsembleSimulation calculations, a True value
                      causes a separate rotation and translation to be
                      used for each ensemble member, while a False value
                      causes ensemble member 0's values to be used in
                      all ensemble members.

scale: set the energy scale (force constant) for the term.

create_probDistPot = create_ProbDistPot(name, targetMap, selection='not PSEUDO', potType='diff', rotateCenterMap=False, ensembleRotateCenter=False, scale=1, mapType='density'): creates a probDistPot.ProbDistPot with given name

targetMap contains the target Map which is an DenstiyGrid object

potType: switches the energy type.
   "diff" which is the default energy function, is based on the squared
          distance between the target density & current density calculated
   "cross_correlation" is based on a cross correlation
   "correlation" is the correct correlation function

rotateCenterMap: if True, use pseudoatoms to rotate and center the
                 map on the molecular system. If False, the molecular
                 system is rotated to fit the map. This facility can be
                 used in circumstances in which the absolute position or
                 orientation in space should be independent of the map,
                 for instance when fitting multiple maps simultaneously.
                 When this argument is False, the noFit property of the
                 associated simulation.Simulation is set so that the
                 resulting structures are not fit in
                 simulationTools.StructureLoop.

ensembleRotateCenter: for EnsembleSimulation calculations, a True value
                      causes a separate rotation and translation to be
                      used for each ensemble member, while a False value
                      causes ensemble member 0's values to be used in
                      all ensemble members.

scale: set the energy scale (force constant) for the term.

fitMapToStruct(term, numOrientTries=10, verbose=False): Given a ProbDistPot, update the associated pseudoatoms to rotate
and translate the map to an optimized position. Use gradient minimization
from numOrientTries orientations, with translation chosed to center the
maps on the selection in term.

maskedCorrelation(term, tol=0.1): Return a correlation for which zero pixels are not included. Zero
pixels are those whose values are less than tol. Thus, regions where both
the computed and target map are masked do not contribute to the returned
value.

massSetup(list=[], axisMass=None): appropriately setup pseudo-atom masses to axisMass.

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

If axisMass is omitted, it is set to the sum of masses in the
associated term's atomProb.selection().

setVdWRadii(term, radiusScale=1.0): Given a probDistPot.ProbDistPot term, set atomic radii to
Van der Waal values in the module-local dictionary radiusMap.

topologySetup(ivm, list=[], options=[]): configure the given IVM object's topology setup to allow projection
rotation and translation for each ProbDistPot in list. This function
should be called prior to ivm.IVM.autoTorsion() or
protocol.torsionTopology().

The freedom specification allows the following keywords:
  fix     - allow no rotation or translation
  default - full rotation of rotation pseudoatoms and translation of t
            pseudoatom.
  translate - allow translation only.
  rotateAbout <spec>
          - specify that rotation is allowed about a single axis
            given by spec. Allowed values of spec are currently X and Z.
  ignore  - perform no IVM setup

weightByAtomElectrons(term): Set the per-atom weights in ProbDistPot as the number of electrons in
each atom.

weightByResidueElectrons(term): Set the per-atom weights in ProbDistPot as the number of electrons in
the respective containg residue.

Data
		current_axisResid = 5000 current_axisSegid = 'AXIS' psfTemplate = '\nstructure\nPSF\n\n 3 !NTITLE\n REMARKS auto... 0 !NGRP\n 0 0 0\nend \n'