def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True,
lib=lib,
resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule,
hidden=True,
noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'), ('H-Bonds', 'hbond'),
('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(SAVE_SESSION,
self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True, lib=lib, resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule, hidden=True, noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'),
('H-Bonds', 'hbond'), ('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def addVolumeColumn(self, columnName, *args): from Rotamers import processVolume format = processVolume(self.rotamers, columnName, *args) self.rotTable.addColumn(columnName, "lambda r: r.volumeScores[%s]" % repr(columnName), format=format, display=True) registerAttribute(chimera.Molecule, "volumeScores")
def addHbondColumn(self, *args):
from Rotamers import processHbonds
processHbonds(self.residue, self.rotamers, *args)
self.rotTable.addColumn("H-Bonds",
"numHbonds",
format="%d",
display=True)
registerAttribute(chimera.Molecule, "numHbonds")
def addClashColumn(self, *args):
from Rotamers import processClashes
format = processClashes(self.residue, self.rotamers, *args)
self.rotTable.addColumn("Clashes",
"clashScore",
format=format,
display=True)
registerAttribute(chimera.Molecule, "clashScore")
def addVolumeColumn(self, columnName, *args):
from Rotamers import processVolume
format = processVolume(self.rotamers, columnName, *args)
self.rotTable.addColumn(columnName,
"lambda r: r.volumeScores[%s]" %
repr(columnName),
format=format,
display=True)
registerAttribute(chimera.Molecule, "volumeScores")
def Apply(self):
liveModels = [m for m in self.models if not m.__destroyed__]
if not liveModels:
return
note = self.text.getvalue().strip()
track = chimera.TrackChanges.get()
for m in liveModels:
if note:
m.note = note
elif hasattr(m, "note"):
delattr(m, "note")
track.addModified(m, "note changed")
if note:
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "note")
from base import _mp
_mp._confDialog.showColumn("Note", True)
def Apply(self):
liveModels = [m for m in self.models if not m.__destroyed__]
if not liveModels:
return
note = self.text.getvalue().strip()
track = chimera.TrackChanges.get()
for m in liveModels:
if note:
m.note = note
elif hasattr(m, "note"):
delattr(m, "note")
track.addModified(m, "note changed")
if note:
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "note")
from base import _mp
_mp._confDialog.showColumn("Note", True)
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
from SimpleSession import registerAttribute
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain, riCID, aromaticCID, aromaticDisplay, \
aromaticLineType, aromaticMode, hidden in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain']),
expandSummary(molInfo['ribbonInsideColor']),
expandSummary(molInfo['aromaticColor']),
expandSummary(molInfo['aromaticDisplay']),
expandSummary(molInfo['aromaticLineType']),
expandSummary(molInfo['aromaticMode']),
expandSummary(molInfo['hidden'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m], baseId=ids[0]+modelOffset,
subid=ids[1], hidden=hidden)
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
m.ribbonInsideColor = getColor(riCID)
m.aromaticColor = getColor(aromaticCID)
m.aromaticDisplay = aromaticDisplay
m.aromaticLineType = aromaticLineType
m.aromaticMode = aromaticMode
if molInfo['optional']:
for attrName, info in molInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Molecule, attrName,
hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for m, val in zip(items, vals):
if val is not None:
setattr(m, attrName, val)
resStart = len(items)
for mid, name, chain, pos, insert, rcid, lcid, ss, ssId, ribbonDrawMode, \
ribbonDisplay, label, labelOffset, isHet, fillDisplay, fillMode in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
expandSequentialSummary(resInfo['position']),
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ssId']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label']),
expandSummary(resInfo['labelOffset']),
expandSummary(resInfo['isHet']),
expandSummary(resInfo['fillDisplay']),
expandSummary(resInfo['fillMode']),
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ssId = ssId
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
if labelOffset is not None:
r.labelOffset = labelOffset
r.isHet = isHet
r.fillDisplay = fillDisplay
r.fillMode = fillMode
if resInfo['optional']:
residues = items[resStart:]
for attrName, info in resInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Residue, attrName,
hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for r, val in zip(residues, vals):
if val is not None:
setattr(r, attrName, val)
atomStart = len(items)
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, labelOffet, surfaceDisplay, surfaceCategory, surfaceOpacity, \
radius, vdw, idatmType, altLoc in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['labelOffset']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['idatmType']),
expandSummary(atomInfo['altLoc'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
if labelOffset is not None:
a.labelOffset = labelOffset
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if idatmType:
a.idatmType = idatmType
a.altLoc = altLoc
if atomInfo['optional']:
atoms = items[atomStart:]
for attrName, info in atomInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Atom, attrName,
hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for a, val in zip(atoms, vals):
if val is not None:
setattr(a, attrName, val)
bondStart = len(items)
for atoms, drawMode, display, label, labelOffset, radius in zip(
bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['labelOffset']),
expandSummary(bondInfo['radius'])
):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
b.label = label
if labelOffset is not None:
b.labelOffset = labelOffset
b.radius = radius
if bondInfo.get('optional', {}):
bonds = items[bondStart:]
for attrName, info in bondInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Bond, attrName,
hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for b, val in zip(bonds, vals):
if val is not None:
setattr(b, attrName, val)
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(Point(*tuple([float(c)
for c in crdString.split()])), coordSet)
if key == active:
m.activeCoordSet = coordSet
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
from SimpleSession import registerAttribute
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain, riCID, aromaticCID, aromaticDisplay, \
aromaticLineType, aromaticMode, hidden in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain']),
expandSummary(molInfo['ribbonInsideColor']),
expandSummary(molInfo['aromaticColor']),
expandSummary(molInfo['aromaticDisplay']),
expandSummary(molInfo['aromaticLineType']),
expandSummary(molInfo['aromaticMode']),
expandSummary(molInfo['hidden'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m],
baseId=ids[0] + modelOffset,
subid=ids[1],
hidden=hidden)
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
m.ribbonInsideColor = getColor(riCID)
m.aromaticColor = getColor(aromaticCID)
m.aromaticDisplay = aromaticDisplay
m.aromaticLineType = aromaticLineType
m.aromaticMode = aromaticMode
if molInfo['optional']:
for attrName, info in molInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Molecule, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for m, val in zip(items, vals):
if val is not None:
setattr(m, attrName, val)
resStart = len(items)
for mid, name, chain, pos, insert, rcid, lcid, ss, ssId, ribbonDrawMode, \
ribbonDisplay, label, labelOffset, isHet, fillDisplay, fillMode in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
expandSequentialSummary(resInfo['position']),
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ssId']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label']),
expandSummary(resInfo['labelOffset']),
expandSummary(resInfo['isHet']),
expandSummary(resInfo['fillDisplay']),
expandSummary(resInfo['fillMode']),
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ssId = ssId
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
if labelOffset is not None:
r.labelOffset = labelOffset
r.isHet = isHet
r.fillDisplay = fillDisplay
r.fillMode = fillMode
if resInfo['optional']:
residues = items[resStart:]
for attrName, info in resInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Residue, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for r, val in zip(residues, vals):
if val is not None:
setattr(r, attrName, val)
atomStart = len(items)
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, labelOffet, surfaceDisplay, surfaceCategory, surfaceOpacity, \
radius, vdw, idatmType, altLoc in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['labelOffset']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['idatmType']),
expandSummary(atomInfo['altLoc'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
if labelOffset is not None:
a.labelOffset = labelOffset
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if idatmType:
a.idatmType = idatmType
a.altLoc = altLoc
if atomInfo['optional']:
atoms = items[atomStart:]
for attrName, info in atomInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Atom, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for a, val in zip(atoms, vals):
if val is not None:
setattr(a, attrName, val)
bondStart = len(items)
for atoms, drawMode, display, label, labelOffset, radius in zip(
bondInfo['atoms'], expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['labelOffset']),
expandSummary(bondInfo['radius'])):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
b.label = label
if labelOffset is not None:
b.labelOffset = labelOffset
b.radius = radius
if bondInfo.get('optional', {}):
bonds = items[bondStart:]
for attrName, info in bondInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Bond, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for b, val in zip(bonds, vals):
if val is not None:
setattr(b, attrName, val)
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(
Point(*tuple([float(c) for c in crdString.split()])),
coordSet)
if key == active:
m.activeCoordSet = coordSet
def addStandardCharges(models=None,
status=None,
phosphorylation=None,
chargeModel=None,
nogui=False,
showCharges=False):
"""add AMBER charges to well-known residues
'models' restricts the addition to the specified models
'status' is where status messages go (e.g. replyobj.status)
'phosphorylation' controls whether chain-terminal nucleic acids
will have their phosphorylation state changed to correspond to
AMBER charge files (3' phosphorylated, 5' not). A value of None
means that the user will be queried if possible [treated as True
if not possible].
'showCharges' controls whether atoms get labeled with their charge.
The return value is a 2-tuple of dictionaries: the first of which
details the residues that did not receive charges [key: residue
type, value: list of residues], and the second lists remaining
uncharged atoms [key: (residue type, atom name), value: list of
atoms]
Hydrogens need to be present.
"""
from AddAttr import addAttributes
import os.path
attrFile = os.path.join(os.path.split(__file__)[0], "amberName.defattr")
if status:
status("Defining AMBER residue types\n")
addAttributes(attrFile, models=models, raiseAttrDialog=False)
if models is None:
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
else:
mols = models
if phosphorylation != False:
if status:
status("Checking phosphorylation of chain-terminal"
" nucleic acids\n")
likeAmber = True
deletes = []
for m in mols:
for r in m.residues:
amberName = getattr(r, 'amberName', "UNK")
if len(amberName) != 2 \
or amberName[0] not in 'DR' \
or amberName[1] not in 'ACGTU' \
or 'P' not in r.atomsMap:
continue
p = r.atomsMap['P'][0]
for nb in p.neighbors:
if nb.residue != r:
break
else:
# trailing phosphate
deletes.append(r)
if deletes:
if phosphorylation is None:
if nogui or chimera.nogui:
phosphorylation = True
else:
from gui import PhosphorylateDialog
phosphorylation = PhosphorylateDialog().run(
chimera.tkgui.app)
if phosphorylation:
_phosphorylate(mols, status, deletes)
if status:
status("Adding standard charges\n")
unchargedResTypes = {}
unchargedAtoms = {}
unchargedResidues = set()
from dict import ffChargeTypeData
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "chargeModel")
registerAttribute(chimera.Atom, "gaffType")
if chargeModel == None:
chargeModel = defaultChargeModel
replyobj.info("Charge model: %s\n" % chargeModel)
chargeTypeData = ffChargeTypeData[chargeModel]
track = chimera.TrackChanges.get()
for m in mols:
m.chargeModel = chargeModel
track.addModified(m, ATTR_SET)
for r in m.residues:
if getattr(r, '_solvateCharged', False):
continue
if not hasattr(r, 'amberName'):
unchargedResidues.add(r)
unchargedResTypes.setdefault(r.type, []).append(r)
for a in m.atoms:
if getattr(a.residue, '_solvateCharged', False):
continue
a.charge = 0.0
track.addModified(a, ATTR_SET)
if a.residue.type in unchargedResTypes:
if showCharges:
a.label = str(a.charge)
continue
atomKeys = [a.name.lower()]
if a.element.number == 1 and a.name.lower()[0] in "dt":
atomKeys.append('h' + a.name.lower()[1:])
atomKeys.append(a.element)
for ak in atomKeys:
key = (a.residue.amberName, ak)
try:
a.charge, a.gaffType = chargeTypeData[key]
except KeyError:
continue
if showCharges:
a.label = "%+g" % a.charge
break
else:
unchargedAtoms.setdefault((a.residue.type, a.name),
[]).append(a)
# merge connected non-standard residues into a "mega" residue.
# also any standard residues directly connected
for urt, urs in unchargedResTypes.items():
for ur in urs[:]:
if urt not in unchargedResTypes:
break
if ur not in unchargedResTypes[urt]:
# connected to residue of same type and
# previously removed
continue
connected = [ur]
queue = [ur]
while queue:
curRes = queue.pop(0)
neighbors = set()
stdConnects = {}
for a in curRes.atoms:
for na in a.neighbors:
naRes = na.residue
if naRes == curRes \
or naRes in connected:
continue
# don't add standard residue
# if connected through chain
# bond
if naRes not in unchargedResidues:
from chimera.misc \
import principalAtom
pa = principalAtom(naRes)
if pa != None:
if pa.name == 'CA':
testNames = ['N', 'C']
else:
testNames = ['P', "O3'"]
if na.name in testNames and na.name not in stdConnects.get(
naRes, set()):
stdConnects.setdefault(naRes,
set()).add(na.name)
continue
neighbors.add(naRes)
neighbors = list(neighbors)
neighbors.sort(lambda r1, r2: cmp(r1.type, r2.type))
connected.extend(neighbors)
queue.extend(
[nb for nb in neighbors if nb in unchargedResidues])
# avoid using atom names with the trailing "-number"
# distinguisher if possible...
if len(connected) > 1:
fr = FakeRes(connected)
else:
fr = connected[0]
unchargedResTypes.setdefault(fr.type, []).append(fr)
for cr in connected:
if cr in unchargedResidues:
unchargedResTypes[cr.type].remove(cr)
if not unchargedResTypes[cr.type]:
del unchargedResTypes[cr.type]
continue
# remove standard-residue atoms from
# uncharged list
for ca in cr.atoms:
uas = unchargedAtoms.get((cr.type, ca.name), [])
if ca not in uas:
continue
uas.remove(ca)
if not uas:
del unchargedAtoms[(cr.type, ca.name)]
# split isolated atoms (e.g. metals) into separate "residues"
for resType, residues in unchargedResTypes.items():
bondResidues = residues
brType = resType
while True:
if len(bondResidues[0].atoms) == 1:
break
for a in bondResidues[0].atoms:
if a.bonds:
continue
hasIso = [r for r in bondResidues if a.name in r.atomsMap]
if len(hasIso) == len(bondResidues):
rem = []
else:
rem = [r for r in bondResidues if r not in hasIso]
iso = []
nonIso = rem
isoType = "%s[%s]" % (resType, a.name)
brType = "%s[non-%s]" % (brType, a.name)
for r in hasIso:
isoRes = FakeRes(
isoType, [fa for fa in r.atoms if fa.name == a.name])
iso.append(isoRes)
nonIsoAtoms = [fa for fa in r.atoms if fa.name != a.name]
if not nonIsoAtoms:
brType = None
continue
nonIsoRes = FakeRes(brType, nonIsoAtoms)
nonIso.append(nonIsoRes)
unchargedResTypes[isoType] = iso
bondResidues = nonIso
else:
# no isolated atoms
break
if brType != resType:
del unchargedResTypes[resType]
if brType != None:
unchargedResTypes[brType] = bondResidues
# despite same residue type, residues may still differ -- particularly
# terminal vs. non-terminal...
for resType, residues in unchargedResTypes.items():
if len(residues) < 2:
continue
varieties = {}
for r in residues:
key = tuple([a.name for a in r.oslChildren()])
varieties.setdefault(key, []).append(r)
if len(varieties) == 1:
continue
# in order to give the varieties distinguishing names,
# find atoms in common
keys = varieties.keys()
common = set(keys[0])
for k in keys[1:]:
common = common.intersection(set(k))
uncommon = set()
for k in keys:
uncommon = uncommon.union(set(k) - common)
del unchargedResTypes[resType]
for k, residues in varieties.items():
names = set(k)
more = names - common
less = uncommon - names
newKey = resType
if more:
newKey += " (w/%s)" % ",".join(list(more))
if less:
newKey += " (wo/%s)" % ",".join(list(less))
unchargedResTypes[newKey] = residues
if status:
status("Standard charges added\n")
return unchargedResTypes, unchargedAtoms
def _addAttr(attrFile, models, log, raiseAttrDialog):
setAttrs = {}
colors = {}
from CGLutil.annotatedDataFile import readDataFile
control = { 'match mode': _MATCH_MODE_ANY, 'recipient': "atoms" }
for rawControl, data in readDataFile(attrFile):
control.update(rawControl)
legalNames = ["attribute", "match mode", "recipient"]
for name in control.keys():
if name not in legalNames:
raise SyntaxError("Unknown name part of control"
" line: '%s'\nMust be one of: %s" % (
name, ", ".join(legalNames)))
if "attribute" not in control:
raise SyntaxError("No attribute name specified in file")
attrName = control["attribute"]
if not attrName.replace("_", "").isalnum() \
or attrName[0].isdigit():
raise SyntaxError("Attribute name (%s) is bad.\n"
"It must be strictly alphanumeric characters or"
" underscores with no spaces and must not start"
" with a digit." % control["attribute"])
colorAttr = attrName.lower().endswith("color")
matchMode = control["match mode"]
if matchMode not in _matchModes:
raise SyntaxError("Unknown match mode (%s) specified.\n"
"It must be one of: %s" % (
control["match mode"], ", ".join(_matchModes)))
recipient = control["recipient"]
if not hasattr(selection.ItemizedSelection, recipient):
raise SyntaxError("Unknown attribute recipient (%s)"
" specified.\nSuggest using atoms, residues, or"
" molecules" % control["recipient"])
dataErrors = []
for lineNum, d in enumerate(data):
try:
selector, value = d
except ValueError:
dataErrors.append("Data line %d of file either"
" not selector/value or not"
" tab-delimited" % (lineNum+1))
continue
try:
sel = specifier.evalSpec(selector, models)
except:
import sys
dataErrors.append("Mangled selector (%s) on"
" data line %d: %s" % (selector,
lineNum+1, sys.exc_value))
continue
matches = getattr(sel, recipient)()
# restrict to models; the "models" argument to evalSpec
# only works if the selector is an OSL
if matches and models is not None:
md = set(models)
level = matches[0].oslLevel()
if level == selection.SelGraph:
filterFunc = lambda x, md=md: x in md
elif level == selection.SelEdge:
filterFunc = lambda x, md=md: \
x.atoms[0].molecule in md
else:
filterFunc = lambda x, md=md: \
x.molecule in md
matches = filter(filterFunc, matches)
if not matches:
if matchMode != _MATCH_MODE_ANY:
dataErrors.append("Selector (%s) on"
" data line %d matched nothing"
% (selector, lineNum+1))
continue
elif len(matches) > 1:
if matchMode == _MATCH_MODE_1_TO_1:
dataErrors.append("Selector (%s) on"
" data line %d matched multiple"
" items: %s" % (selector,
lineNum+1, ", ".join(map(lambda
m: m.oslIdent(), matches))))
if log:
replyobj.info("Selector %s matched " % selector
+ ", ".join(map(misc.chimeraLabel,
matches)) + "\n")
if colorAttr:
if value[0].isalpha():
# color name
from chimera.colorTable \
import getColorByName
try:
value = getColorByName(value)
except KeyError:
dataErrors.append("Unknown"
" color name on data"
" line %d: '%s'" %
(lineNum+1, value))
continue
else:
try:
rgba = tuple(map(float,
value.split()))
except ValueError:
dataErrors.append(
"Unrecognizable color"
" value on data line"
" %d: '%s'; Must be"
" either color name or"
" 3 or 4 numbers"
" between 0 and 1"
" (RGBA)" % (lineNum+1))
continue
if max(rgba) > 1.0 or min(rgba) < 0.0:
dataErrors.append("Color"
" component values on"
" data line %d not"
" in the range 0 to 1"
% (lineNum+1))
continue
if rgba in colors:
value = colors[rgba]
elif len(rgba) in [3, 4]:
value = chimera.MaterialColor(
*rgba)
colors[rgba] = value
else:
dataErrors.append("Bad number"
" of color components"
" on data line %d; Must"
" be either 3 or 4 (was"
" %d)" % (lineNum+1,
len(rgba)))
continue
else:
value = convertType(value)
for match in matches:
setattr(match, attrName, value)
if matches and not colorAttr:
setAttrs[(recipient, attrName)] = value
recipMapping = {
"molecules": chimera.Molecule,
"residues": chimera.Residue,
"bonds": chimera.Bond,
"atoms": chimera.Atom
}
from SimpleSession import registerAttribute
for recipient, attrName in setAttrs:
if recipient in recipMapping:
registerAttribute(recipMapping[recipient], attrName)
if setAttrs and not chimera.nogui and raiseAttrDialog:
from ShowAttr import ShowAttrDialog, screenedAttrs
from chimera import dialogs
showableAttr = False
reasons = []
for recipient, attrName in setAttrs.keys():
if recipient == "molecules":
recipient = "models"
validRecipients = ["atoms", "residues", "models"]
if recipient not in validRecipients:
reasons.append("%s not assigned to atoms,"
" residues, or models" % attrName)
continue
key = [chimera.Atom, chimera.Residue, chimera.Model][
validRecipients.index(recipient)]
if attrName in screenedAttrs[key]:
reasons.append("%s automatically screened out"
" by Render By Attribute" % attrName)
continue
if attrName[0] == '_':
reasons.append("%s considered to be a private"
" variable" % attrName)
continue
if attrName[0].isupper():
reasons.append("%s considered to be a symbolic"
" constant due to initial capital"
" letter" % attrName)
continue
showableAttr = True
break
if showableAttr:
if models is None:
ms = chimera.openModels.list()
else:
ms = models
if colorAttr:
an = None
mode = None
else:
an = attrName
from types import StringTypes
if type(setAttrs[(recipient, attrName)]) in (
bool,) + StringTypes:
mode = "Select"
else:
mode = "Render"
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=[m for m in ms
if isinstance(m, chimera.Molecule)],
attrsOf=recipient, attrName=an, mode=mode)
else:
replyobj.warning("No attributes usable by Render dialog"
" were defined:\n" + "\n".join(reasons) + "\n")
if dataErrors:
raise SyntaxError, "\n".join(dataErrors)
return setAttrs
def addStandardCharges(models=None, status=None, phosphorylation=None,
chargeModel=None, nogui=False, showCharges=False):
"""add AMBER charges to well-known residues
'models' restricts the addition to the specified models
'status' is where status messages go (e.g. replyobj.status)
'phosphorylation' controls whether chain-terminal nucleic acids
will have their phosphorylation state changed to correspond to
AMBER charge files (3' phosphorylated, 5' not). A value of None
means that the user will be queried if possible [treated as True
if not possible].
'showCharges' controls whether atoms get labeled with their charge.
The return value is a 2-tuple of dictionaries: the first of which
details the residues that did not receive charges [key: residue
type, value: list of residues], and the second lists remaining
uncharged atoms [key: (residue type, atom name), value: list of
atoms]
Hydrogens need to be present.
"""
from AddAttr import addAttributes
import os.path
attrFile = os.path.join(os.path.split(__file__)[0],
"amberName.defattr")
if status:
status("Defining AMBER residue types\n")
addAttributes(attrFile, models=models, raiseAttrDialog=False)
if models is None:
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
else:
mols = models
if phosphorylation != False:
if status:
status("Checking phosphorylation of chain-terminal"
" nucleic acids\n")
likeAmber = True
deletes = []
for m in mols:
for r in m.residues:
amberName = getattr(r, 'amberName', "UNK")
if len(amberName) != 2 \
or amberName[0] not in 'DR' \
or amberName[1] not in 'ACGTU' \
or 'P' not in r.atomsMap:
continue
p = r.atomsMap['P'][0]
for nb in p.neighbors:
if nb.residue != r:
break
else:
# trailing phosphate
deletes.append(r)
if deletes:
if phosphorylation is None:
if nogui or chimera.nogui:
phosphorylation = True
else:
from gui import PhosphorylateDialog
phosphorylation = PhosphorylateDialog(
).run(chimera.tkgui.app)
if phosphorylation:
_phosphorylate(mols, status, deletes)
if status:
status("Adding standard charges\n")
unchargedResTypes = {}
unchargedAtoms = {}
unchargedResidues = set()
from dict import ffChargeTypeData
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "chargeModel")
registerAttribute(chimera.Atom, "gaffType")
if chargeModel == None:
chargeModel = defaultChargeModel
replyobj.info("Charge model: %s\n" % chargeModel)
chargeTypeData = ffChargeTypeData[chargeModel]
track = chimera.TrackChanges.get()
for m in mols:
m.chargeModel = chargeModel
track.addModified(m, ATTR_SET)
for r in m.residues:
if getattr(r, '_solvateCharged', False):
continue
if not hasattr(r, 'amberName'):
unchargedResidues.add(r)
unchargedResTypes.setdefault(r.type,
[]).append(r)
for a in m.atoms:
if getattr(a.residue, '_solvateCharged', False):
continue
a.charge = 0.0
track.addModified(a, ATTR_SET)
if a.residue.type in unchargedResTypes:
if showCharges:
a.label = str(a.charge)
continue
atomKeys = [a.name.lower()]
if a.element.number == 1 and a.name.lower()[0] in "dt":
atomKeys.append('h' + a.name.lower()[1:])
atomKeys.append(a.element)
for ak in atomKeys:
key = (a.residue.amberName, ak)
try:
a.charge, a.gaffType = chargeTypeData[
key]
except KeyError:
continue
if showCharges:
a.label = "%+g" % a.charge
break
else:
unchargedAtoms.setdefault((a.residue.type,
a.name), []).append(a)
# merge connected non-standard residues into a "mega" residue.
# also any standard residues directly connected
for urt, urs in unchargedResTypes.items():
for ur in urs[:]:
if urt not in unchargedResTypes:
break
if ur not in unchargedResTypes[urt]:
# connected to residue of same type and
# previously removed
continue
connected = [ur]
queue = [ur]
while queue:
curRes = queue.pop(0)
neighbors = set()
stdConnects = {}
for a in curRes.atoms:
for na in a.neighbors:
naRes = na.residue
if naRes == curRes \
or naRes in connected:
continue
# don't add standard residue
# if connected through chain
# bond
if naRes not in unchargedResidues:
from chimera.misc \
import principalAtom
pa = principalAtom(
naRes)
if pa != None:
if pa.name == 'CA':
testNames = ['N', 'C']
else:
testNames = ['P', "O3'"]
if na.name in testNames and na.name not in stdConnects.get(naRes, set()):
stdConnects.setdefault(naRes, set()).add(na.name)
continue
neighbors.add(naRes)
neighbors = list(neighbors)
neighbors.sort(lambda r1, r2:
cmp(r1.type, r2.type))
connected.extend(neighbors)
queue.extend([nb for nb in neighbors
if nb in unchargedResidues])
# avoid using atom names with the trailing "-number"
# distinguisher if possible...
if len(connected) > 1:
fr = FakeRes(connected)
else:
fr = connected[0]
unchargedResTypes.setdefault(fr.type, []).append(fr)
for cr in connected:
if cr in unchargedResidues:
unchargedResTypes[cr.type].remove(cr)
if not unchargedResTypes[cr.type]:
del unchargedResTypes[cr.type]
continue
# remove standard-residue atoms from
# uncharged list
for ca in cr.atoms:
uas = unchargedAtoms.get((cr.type,
ca.name), [])
if ca not in uas:
continue
uas.remove(ca)
if not uas:
del unchargedAtoms[(cr.type,
ca.name)]
# split isolated atoms (e.g. metals) into separate "residues"
for resType, residues in unchargedResTypes.items():
bondResidues = residues
brType = resType
while True:
if len(bondResidues[0].atoms) == 1:
break
for a in bondResidues[0].atoms:
if a.bonds:
continue
hasIso = [r for r in bondResidues
if a.name in r.atomsMap]
if len(hasIso) == len(bondResidues):
rem = []
else:
rem = [r for r in bondResidues
if r not in hasIso]
iso = []
nonIso = rem
isoType = "%s[%s]" % (resType, a.name)
brType = "%s[non-%s]" % (brType, a.name)
for r in hasIso:
isoRes = FakeRes(isoType, [fa
for fa in r.atoms
if fa.name == a.name])
iso.append(isoRes)
nonIsoAtoms = [fa for fa in r.atoms
if fa.name != a.name]
if not nonIsoAtoms:
brType = None
continue
nonIsoRes = FakeRes(brType, nonIsoAtoms)
nonIso.append(nonIsoRes)
unchargedResTypes[isoType] = iso
bondResidues = nonIso
else:
# no isolated atoms
break
if brType != resType:
del unchargedResTypes[resType]
if brType != None:
unchargedResTypes[brType] = bondResidues
# despite same residue type, residues may still differ -- particularly
# terminal vs. non-terminal...
for resType, residues in unchargedResTypes.items():
if len(residues) < 2:
continue
varieties = {}
for r in residues:
key = tuple([a.name for a in r.oslChildren()])
varieties.setdefault(key, []).append(r)
if len(varieties) == 1:
continue
# in order to give the varieties distinguishing names,
# find atoms in common
keys = varieties.keys()
common = set(keys[0])
for k in keys[1:]:
common = common.intersection(set(k))
uncommon = set()
for k in keys:
uncommon = uncommon.union(set(k) - common)
del unchargedResTypes[resType]
for k, residues in varieties.items():
names = set(k)
more = names - common
less = uncommon - names
newKey = resType
if more:
newKey += " (w/%s)" % ",".join(list(more))
if less:
newKey += " (wo/%s)" % ",".join(list(less))
unchargedResTypes[newKey] = residues
if status:
status("Standard charges added\n")
return unchargedResTypes, unchargedAtoms
def addHbondColumn(self, *args):
from Rotamers import processHbonds
processHbonds(self.residue, self.rotamers, *args)
self.rotTable.addColumn("H-Bonds", "numHbonds", format="%d",
display=True)
registerAttribute(chimera.Molecule, "numHbonds")
def addClashColumn(self, *args):
from Rotamers import processClashes
format = processClashes(self.residue, self.rotamers, *args)
self.rotTable.addColumn("Clashes", "clashScore", format=format,
display=True)
registerAttribute(chimera.Molecule, "clashScore")
