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- builtins.object
-
- TagDBInfo
-
- TagInfo
- TagTool
class TagDBInfo(builtins.object) |
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TagDBInfo(tagName, attachAtoms, topology=None, parameters=None, coords=None, coordsFilename=None, paraAtomname=None, rigidRegions=None, probWidth=None, distanceSigmoidWidth=None, paraAtomRadius=None, nonTagSelString=None, weights=None, otherNames=[], systemType='protein')
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Methods defined here:
- __init__(self, tagName, attachAtoms, topology=None, parameters=None, coords=None, coordsFilename=None, paraAtomname=None, rigidRegions=None, probWidth=None, distanceSigmoidWidth=None, paraAtomRadius=None, nonTagSelString=None, weights=None, otherNames=[], systemType='protein')
- where:
tagName - residueName of the tag
tagNames - list containing all residue names tag is known by
attachAtoms - name of 3 atoms used to attach tag to biomolecule-
order is significant
topology - filename of topoogy file
parameters - filename of parameters file
coords - after initialization, contains a dictionary
containing entries of
(segid,resid) -> "PDB ATOM RECORD"
coordFilename - filename of PDB containing tag coordinates with
optional rotamer weights.
paraAtomname - name of paramagnetic atom in tag.
rigidRegions - sequence of strings containing names of atoms to
grouped in rigid bodies.
probWidth - width of contribution to P(r)
distanceSigmoidWidth - cutoff distance for tag/nonTagSel
interactions
paraAtomRadius - tag radius
nonTagSelString- selection string specifying which atoms the tag
interacts with.
weights - rotamer weights
- readCoordsInfo(self, verbose)
- Populations tagInfo members:
coords,weights,probWidth,
distanceSigmoidWidth,paraAtomRadius,
coordsFilename
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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class TagInfo(TagDBInfo) |
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TagInfo(dbInfo, tool, simulation=None)
Inherits members from TagDBInfo.
Important members:
tool - the TagTool object which created this object.
simulation - Simulation containing the tag atoms. This may or may not
be the same as that of tool.taggedSim.
resid
segids
coords
weights
probWidth
distanceSigmoidWidth
paraAtomRadius
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- Method resolution order:
- TagInfo
- TagDBInfo
- builtins.object
Methods defined here:
- __init__(self, dbInfo, tool, simulation=None)
- where:
tagName - residueName of the tag
tagNames - list containing all residue names tag is known by
attachAtoms - name of 3 atoms used to attach tag to biomolecule-
order is significant
topology - filename of topoogy file
parameters - filename of parameters file
coords - after initialization, contains a dictionary
containing entries of
(segid,resid) -> "PDB ATOM RECORD"
coordFilename - filename of PDB containing tag coordinates with
optional rotamer weights.
paraAtomname - name of paramagnetic atom in tag.
rigidRegions - sequence of strings containing names of atoms to
grouped in rigid bodies.
probWidth - width of contribution to P(r)
distanceSigmoidWidth - cutoff distance for tag/nonTagSel
interactions
paraAtomRadius - tag radius
nonTagSelString- selection string specifying which atoms the tag
interacts with.
weights - rotamer weights
- attachTag(self, selection, fullSim=None, verbose=False)
- Attach all tag residues in this TagInfo instance to the residue
specified by the selection argument.
In the tagSimulation.TagSimulation specified by the fullSim
argument (self.tool.fullSim iffullSim is None), the
new tag will have the residueNum in the selection. The segmentName
will be that of the residue attachment point concatenated with that of
the tag, so is a requirement that the segment name of the atoms
specified in selection not be longer than one character.
- numCopies(self)
Methods inherited from TagDBInfo:
- readCoordsInfo(self, verbose)
- Populations tagInfo members:
coords,weights,probWidth,
distanceSigmoidWidth,paraAtomRadius,
coordsFilename
Data descriptors inherited from TagDBInfo:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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class TagTool(builtins.object) |
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TagTool(tagSimulation=None, nonTagSel='not PSEUDO', simName='TagSimulation')
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Methods defined here:
- __init__(self, tagSimulation=None, nonTagSel='not PSEUDO', simName='TagSimulation')
- Create a TagTool object given nonTagSel, a selection specifying
atoms to be used in computing tag occlusion, including positions to
anchor tags.
Members:
taggedSim: simulation.Simulation of the passed nonTagSel
argument.
tagSimulation: tagSimulation.TagSimulation created for
tags subsequently added using the addTags()
method.
tagEntries: list of TagInfo objects created/added.
- addAtoms(self, tagName, numCopies=None, useCoordLibrary=True, randomizeTorsions=False, resid=1, segid=None, tagSimulation='tagged', makePseudo=None, verbose=False)
- Add tag atoms to the TagSimulation fullSim. These are logically
separate from the copies attached to residues, and may be attached to
more than one residue using the attachTag method of the returned
TagInfo object.
The numCopies argument specifies the number of tag coordinate
sets to add. A numCopies value of None specifies that all
conformations in the rotamer library are read, if coordinates
are specified, otherwise a single rotamer is generated. If numCopies
is greater than the number of copies in the rotamer library,
conformations are cycled through in a round-robin fashion.
The resid parameter specifies residue number for all copies of the
generated tag residue.
Copies are distinguished by their segid. The segid (string)
argument specifies the start segid for the newly created tag
atoms. If specified, it should follow this rule: all but the
first character should be digit characters (0-9), else it
defaults to self.defaultSegid. The segid for subsequent copies are
generated by incrementing the numeric portion of this segid.
If randomizeTorsions==True, the tag torsion angles are randomized, so
that the coordinate library is no longer used.
The tagSimulation argument can be used to specify a Simulation in
which to place the new tag atoms, or it can be one of three string
values. For a value of "tagged" (the default), the tag atoms are
placed in the TagTool's taggedSim Simulation. A value of "current",
means the current Simulation is used, and a value of "new" causes a
separate newly-created XplorSimulation to be used. Whatever its value.
the tagSimulation is specified in the returned TagInfo's simulation
member.
As a side-effect, the [tagResidues] atomSelLang abbrevation is
updated to include all tag residue atoms, and the [fixedReference]
abbreviation is updated, if necessary, to contain the [tagResidues]
entries.
This method returns a TagInfo object
If tag weights are present for tagName, these are set in the weights
member of the object.
By default, if tagSimulation != "new" all added atoms are designated
as pseudo atoms for the atomSelLang specifications. The behavior
can be forced by setting makePseudo to True or False.
- addTag(self, selection, tagName, numCopies=None, useCoordLibrary=True, randomizeTorsions=False, atomResid=None, atomsExist=False, segid=None, verbose=False)
- Add atoms to a simulation, and anchor the tag to an existing
residue identified by the selection argument.
This method calls addAtoms if atomsExist=False, and then attachTag.
If atomResid==None, the resid of the generated tag is that
corresponding to the selection argument.
- create_TagRepel(self, selection='all', termName='tagRepel', bbSel='name CA C N O HN HA* HT* OT*')
- Create a repelPot.RepelPot term to prevent intra-tag overlap
and overlap of tag atoms with backbone atoms. The selection argument
can be used to further restrict included atoms.
- extendedCoords(self)
- Generate random, extended initial coords
- loadCoords(self, tagNum, tagInfo, inTagNum, loadSim, verbose)
- Load PDB record number inTagNum from from tagInfo.coords, and
copy these to the new tag (with new segid/resid, Simulation).
- loadParameters(self, tagInfo, verbose)
- loadTopologyIfNeeded(self, tagInfo, simulation=None, force=False, verbose=False)
- If force=True, load topology info unconditionally. As a side-effect,
residue names are initialized for tagInfo.systemType by
psfGen.initResidueNames.
- placeInFrame(self, tagInfo)
- For each tag copy,
put in canonical reference frame
attachAtoms[0] is at the origin
z is along the attachAtoms[1]-attachAtoms[0] vector
v is along the attachAtoms[2]-attachAtoms[0] vector
- potName(self)
- rigidTopologySetup(self, ivm)
- segidsResids(self)
- Return list of (segid,resid) pairs for all added tags.
- simulation(self)
- return fullSim
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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