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- 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: use pseudoatoms to rotate and center the molecular
system on 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: use pseudoatoms to rotate and center the molecular
system on 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.
- 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 language contains the following keywords:
- 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.
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