def restorePseudoBondGroups(pbInfo): for category, groupInfo in pbInfo.items(): modelID, attrs, bonds, grpColor = groupInfo grp = getPseudoBondGroup(category, modelID) for attr, val in attrs.items(): if attr == "wireStipple": if val[0]: grp.lineType = chimera.Dash continue setattr(grp, attr, val) grp.color = getColor(grpColor) for bondInfo in bonds: osl1, osl2, bondColor, labelColor, attrs = bondInfo try: a1 = oslLookup(osl1) a2 = oslLookup(osl2) except ValueError: continue pb = grp.newPseudoBond(a1, a2) v1._oslItemMap[getOSL(pb)] = pb if bondColor: pb.color = getColor(bondColor) if labelColor: pb.labelColor = getColor(labelColor) for attr, val in attrs.items(): setattr(pb, attr, val)
def restorePseudoBondGroups(pbInfo):
for category, groupInfo in pbInfo.items():
modelID, attrs, bonds, grpColor = groupInfo
grp = getPseudoBondGroup(category, modelID)
for attr, val in attrs.items():
if attr == "wireStipple":
if val[0]:
grp.lineType = chimera.Dash
continue
setattr(grp, attr, val)
grp.color = getColor(grpColor)
for bondInfo in bonds:
osl1, osl2, bondColor, labelColor, attrs = bondInfo
try:
a1 = oslLookup(osl1)
a2 = oslLookup(osl2)
except ValueError:
continue
pb = grp.newPseudoBond(a1, a2)
v1._oslItemMap[getOSL(pb)] = pb
if bondColor:
pb.color = getColor(bondColor)
if labelColor:
pb.labelColor = getColor(labelColor)
for attr, val in attrs.items():
setattr(pb, attr, val)
def _addGroup(category, color): g = getPseudoBondGroup(category, modelID=-2, hidden=1) if not hasattr(g, 'fixedLabels'): def _setColor(color=color, g=g): from chimera.colorTable import getColorByName g.color = getColorByName(color) g.lineType = chimera.Dash # delay setting the color until colors are set up chimera.registerPostGraphicsFunc(_setColor) g.fixedLabels = 0 g.updateCallbacks = [] return g
def _addGroup(category, color):
g = getPseudoBondGroup(category, modelID=-2, hidden=1)
if not hasattr(g, 'fixedLabels'):
def _setColor(color=color, g=g):
from chimera.colorTable import getColorByName
g.color = getColorByName(color)
g.lineType = chimera.Dash
# delay setting the color until colors are set up
chimera.registerPostGraphicsFunc(_setColor)
g.fixedLabels = 0
g.updateCallbacks = []
return g
def processClashes(residue, rotamers, overlap, hbondAllow, scoreMethod,
makePBs, pbColor, pbWidth, ignoreOthers):
testAtoms = []
for rot in rotamers:
testAtoms.extend(rot.atoms)
from DetectClash import detectClash
clashInfo = detectClash(testAtoms,
clashThreshold=overlap,
interSubmodel=True,
hbondAllowance=hbondAllow)
if makePBs:
from chimera.misc import getPseudoBondGroup
from DetectClash import groupName
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = pbWidth
pbg.color = pbColor
else:
import DetectClash
DetectClash.nukeGroup()
resAtoms = set(residue.atoms)
for rot in rotamers:
score = 0
for ra in rot.atoms:
if ra.name in ("CA", "N", "CB"):
# any clashes of CA/N/CB are already clashes of
# base residue (and may mistakenly be thought
# to clash with "bonded" atoms in nearby
# residues
continue
if ra not in clashInfo:
continue
for ca, clash in clashInfo[ra].items():
if ca in resAtoms:
continue
if ignoreOthers \
and ca.molecule.id != residue.molecule.id:
continue
if scoreMethod == "num":
score += 1
else:
score += clash
if makePBs:
pbg.newPseudoBond(ra, ca)
rot.clashScore = score
if scoreMethod == "num":
return "%2d"
return "%4.2f"
def restorePseudoBondGroups(pbInfo):
from chimera.misc import getPseudoBondGroup
mgr = chimera.PseudoBondMgr.mgr()
sm = globals.sessionMap
groups = []
for category, id, color, showStubBonds, lineWidth, stickScale, \
lineType, bondInfo in zip(
pbInfo['category'],
pbInfo['id'],
expandSummary(pbInfo['color']),
expandSummary(pbInfo['showStubBonds']),
expandSummary(pbInfo['lineWidth']),
expandSummary(pbInfo['stickScale']),
expandSummary(pbInfo['lineType']),
pbInfo['bondInfo']
):
g = getPseudoBondGroup(category, id)
groups.append(g)
g.color = getColor(color)
g.showStubBonds = showStubBonds
g.lineWidth = lineWidth
g.stickScale = stickScale
g.lineType = lineType
for atoms, drawMode, display, halfbond, label, color, \
labelColor in zip(
bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['halfbond']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['color']),
expandSummary(bondInfo['labelColor'])
):
a1, a2 = [idLookup(a) for a in atoms]
pb = g.newPseudoBond(a1, a2)
pb.drawMode = drawMode
pb.display = display
pb.halfbond = halfbond
pb.label = label
pb.color = getColor(color)
pb.labelColor = getColor(labelColor)
sm[len(sm)] = pb
for g in groups:
sm[len(sm)] = g
def restorePseudoBondGroups(pbInfo): from chimera.misc import getPseudoBondGroup mgr = chimera.PseudoBondMgr.mgr() sm = globals.sessionMap groups = [] for category, id, color, showStubBonds, lineWidth, stickScale, \ lineType, bondInfo in zip( pbInfo['category'], pbInfo['id'], expandSummary(pbInfo['color']), expandSummary(pbInfo['showStubBonds']), expandSummary(pbInfo['lineWidth']), expandSummary(pbInfo['stickScale']), expandSummary(pbInfo['lineType']), pbInfo['bondInfo'] ): g = getPseudoBondGroup(category, id) groups.append(g) g.color = getColor(color) g.showStubBonds = showStubBonds g.lineWidth = lineWidth g.stickScale = stickScale g.lineType = lineType for atoms, drawMode, display, halfbond, label, color, \ labelColor in zip( bondInfo['atoms'], expandSummary(bondInfo['drawMode']), expandSummary(bondInfo['display']), expandSummary(bondInfo['halfbond']), expandSummary(bondInfo['label']), expandSummary(bondInfo['color']), expandSummary(bondInfo['labelColor']) ): a1, a2 = [idLookup(a) for a in atoms] pb = g.newPseudoBond(a1, a2) pb.drawMode = drawMode pb.display = display pb.halfbond = halfbond pb.label = label pb.color = getColor(color) pb.labelColor = getColor(labelColor) sm[len(sm)] = pb for g in groups: sm[len(sm)] = g
def restorePseudoBondGroups(pbInfo): from chimera.misc import getPseudoBondGroup mgr = chimera.PseudoBondMgr.mgr() for category, id, color, showStubBonds, lineWidth, stickScale, \ wireStipple, bondInfo in zip( pbInfo['category'], pbInfo['id'], expandSummary(pbInfo['color']), expandSummary(pbInfo['showStubBonds']), expandSummary(pbInfo['lineWidth']), expandSummary(pbInfo['stickScale']), expandSummary(pbInfo['wireStipple']), pbInfo['bondInfo'] ): g = getPseudoBondGroup(category, id) g.color = getColor(color) g.showStubBonds = showStubBonds g.lineWidth = lineWidth g.stickScale = stickScale if wireStipple[0]: g.lineType = chimera.Dash for atoms, drawMode, display, halfbond, label, color, \ labelColor in zip( bondInfo['atoms'], expandSummary(bondInfo['drawMode']), expandSummary(bondInfo['display']), expandSummary(bondInfo['halfbond']), expandSummary(bondInfo['label']), expandSummary(bondInfo['color']), expandSummary(bondInfo['labelColor']) ): a1, a2 = [idLookup(a) for a in atoms] pb = g.newPseudoBond(a1, a2) pb.drawMode = drawMode pb.display = display pb.halfbond = halfbond pb.label = label pb.color = getColor(color) pb.labelColor = getColor(labelColor)
def draw_bond_orders(molecule, error_spring=True):
pbg = getPseudoBondGroup('Bond order errors', associateWith=[molecule])
pbg.lineWidth, pbg.lineType, pbg.color = 2, 1, getColorByName('red')
def draw_spring(bond):
pbg = getPseudoBondGroup('Bond order errors')
pb = pbg.newPseudoBond(*bond.atoms)
pb.drawMode = 2
pb.radius = bond.radius + 0.1
for bond in molecule.bonds:
order = getattr(bond, 'order', None)
if not order:
print('! Invalid order for bond', bond)
if error_spring:
draw_spring(bond)
continue
if not hasattr(bond, '_oldradius'):
bond._oldradius = bond.radius
bond.radius = bond._oldradius * order * 0.5
return pbg
def restorePseudoBondGroups(pbInfo):
from chimera.misc import getPseudoBondGroup
mgr = chimera.PseudoBondMgr.mgr()
for category, id, color, showStubBonds, lineWidth, stickScale, \
wireStipple, bondInfo in zip(
pbInfo['category'],
pbInfo['id'],
expandSummary(pbInfo['color']),
expandSummary(pbInfo['showStubBonds']),
expandSummary(pbInfo['lineWidth']),
expandSummary(pbInfo['stickScale']),
expandSummary(pbInfo['wireStipple']),
pbInfo['bondInfo']
):
g = getPseudoBondGroup(category, id)
g.color = getColor(color)
g.showStubBonds = showStubBonds
g.lineWidth = lineWidth
g.stickScale = stickScale
if wireStipple[0]:
g.lineType = chimera.Dash
for atoms, drawMode, display, halfbond, label, color, \
labelColor in zip(
bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['halfbond']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['color']),
expandSummary(bondInfo['labelColor'])
):
a1, a2 = [idLookup(a) for a in atoms]
pb = g.newPseudoBond(a1, a2)
pb.drawMode = drawMode
pb.display = display
pb.halfbond = halfbond
pb.label = label
pb.color = getColor(color)
pb.labelColor = getColor(labelColor)
def cmdDetectClash(testAtoms,
overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE],
test="others",
setAttrs=defaults[ACTION_ATTR],
selectClashes=defaults[ACTION_SELECT],
colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR],
nonclashColor=defColors[NONCLASH_COLOR],
makePseudobonds=defaults[ACTION_PSEUDOBONDS],
pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH],
bondSeparation=defaults[BOND_SEPARATION],
saveFile=None,
namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES],
interSubmodel=False,
log=defaults[ACTION_REPLYLOG],
summary=True,
continuous=False):
global _continuousID
from Midas import MidasError
if continuous:
if setAttrs or saveFile != None or log:
raise MidasError("log/setAttrs/saveFile not allowed"
" with continuous detection")
if _continuousID == None:
from inspect import getargvalues, currentframe
argNames, fArgs, fKw, frameDict = getargvalues(currentframe())
callData = [frameDict[an] for an in argNames]
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
return _motionCB(myData)
_continuousID = chimera.triggers.addHandler(
'OpenState', preCB, callData)
elif _continuousID != None:
chimera.triggers.deleteHandler('OpenState', _continuousID)
_continuousID = None
if isinstance(test, basestring):
if test.startswith("other"):
test = "others"
elif test not in ('self', 'model'):
# atom spec
from chimera.specifier import evalSpec
try:
test = evalSpec(test).atoms()
except:
raise MidasError("Could not parse atom spec '%s'" % test)
clashes = detectClash(testAtoms,
test=test,
hbondAllowance=hbondAllowance,
clashThreshold=overlapCutoff,
bondSeparation=bondSeparation,
intraRes=not ignoreIntraRes,
interSubmodel=interSubmodel)
if selectClashes:
chimera.selection.setCurrent(clashes.keys())
if test == "self":
outputGrouping = set()
else:
outputGrouping = testAtoms
info = (overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes,
clashes, outputGrouping)
if log:
import sys
# put a separator in the Reply Log
print >> sys.stdout, ""
_fileOutput(sys.stdout, info, namingStyle=namingStyle)
if saveFile == '-':
from FindHBond.MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(info,
_fileOutput,
initialfile="overlaps",
title="Choose Overlap Info Save File",
historyID="Overlap info")
elif saveFile is not None:
_fileOutput(saveFile, info, namingStyle=namingStyle)
if summary == True:
def _summary(msg):
from chimera import replyobj
replyobj.status(msg + '\n')
replyobj.info(msg + '\n')
summary = _summary
if summary:
if clashes:
total = 0
for clashList in clashes.values():
total += len(clashList)
summary("%d contacts" % (total / 2))
else:
summary("No contacts")
if not (setAttrs or colorClashes or makePseudobonds):
nukeGroup()
return clashes
if test in ("others", "model"):
atoms = [
a for m in chimera.openModels.list(modelTypes=[chimera.Molecule])
for a in m.atoms
]
else:
atoms = testAtoms
if setAttrs:
# delete the attribute in _all_ atoms...
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if hasattr(a, attrName):
delattr(a, attrName)
for a in atoms:
if a in clashes:
clashVals = clashes[a].values()
clashVals.sort()
setattr(a, attrName, clashVals[-1])
if colorClashes:
for a in atoms:
a.surfaceColor = None
if a in clashes:
a.color = clashColor
else:
a.color = nonclashColor
if makePseudobonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
pbg.color = pbColor
seen = set()
for a in atoms:
if a not in clashes:
continue
seen.add(a)
for clasher in clashes[a].keys():
if clasher in seen:
continue
pbg.newPseudoBond(a, clasher)
else:
nukeGroup()
return clashes
def combine(mols, refMol, newChainIDs=True, log=False, returnMapping=False):
from chimera import replyobj
# figure out residue chain/number remapping
origChainIDs = {}
numChains = 0
minNums = {}
maxNums = {}
for m in mols:
seenIDs = set()
for r in m.residues:
chainID = r.id.chainId
num = r.id.position
key = (m, chainID)
if key in minNums:
if num > maxNums[key]:
maxNums[key] = num
elif num < minNums[key]:
minNums[key] = num
else:
minNums[key] = maxNums[key] = num
if chainID in seenIDs:
continue
numChains += 1
seenIDs.add(chainID)
origChainIDs.setdefault(chainID, []).append(m)
resMap = {}
if newChainIDs:
if numChains > 62:
raise CombineError("More than 62 chains; cannot"
" uniquely identify with single characters")
from string import uppercase, lowercase, digits
possibleIDs = uppercase + lowercase + digits
usedChainIDs = set(origChainIDs.keys())
chainIDmap = {}
for chainID, idMols in origChainIDs.items():
if len(chainID) > 1:
continue
chainIDmap[(idMols[0], chainID)] = chainID
usedChainIDs.add(chainID)
for m in idMols[1:]:
for c in possibleIDs:
if c not in usedChainIDs:
break
if log:
replyobj.info("Remapping %s chain %s"
" to %s\n" % (m, chainID, c))
usedChainIDs.add(c)
chainIDmap[(m, chainID)] = c
for m in mols:
for r in m.residues:
chainID = r.id.chainId
if len(chainID) > 1:
continue
resMap[r] = (chainIDmap[(m, chainID)],
r.id.position)
# handle renumbering for all chains if newChainIDs False,
# otherwise just water/het chains
offsets = {}
for chainID, idMols in origChainIDs.items():
if newChainIDs and len(chainID) < 2:
continue
minMaxs = []
for m in idMols:
mmin = minNums[(m, chainID)]
mmax = maxNums[(m, chainID)]
for omin, omax in minMaxs:
if omin < mmin < omax or omin < mmax < omax:
gmax = max([mm[1] for mm in minMaxs])
offset = gmax - mmin + 1
break
else:
offset = 0
offsets[(m, chainID)] = offset
minMaxs.append((mmin+offset, mmax+offset))
if log and offset:
replyobj.info("Adding %d to %s chain %s"
" numbering\n" % (offset, m, chainID))
for m in mols:
for r in m.residues:
chainID = r.id.chainId
try:
offset = offsets[(m, chainID)]
except KeyError:
continue
resMap[r] = (chainID, r.id.position + offset)
# combine...
from chimera import Atom, Bond, Residue, Molecule
combined = Molecule()
combined.name = "combination"
from SimpleSession.save import optionalAttributes
from chimera.molEdit import addAtom
atomAttrs = optionalAttributes[Atom].keys() + ['color', 'vdwColor',
'labelColor', 'surfaceColor', 'drawMode', 'display', 'label',
'radius', 'surfaceDisplay', 'surfaceCategory', 'surfaceOpacity',
'vdw']
bondAttrs = optionalAttributes[Bond].keys() + ['drawMode', 'display',
'radius']
resAttrs = optionalAttributes[Residue].keys() + ['ribbonColor',
'labelColor', 'isHelix', 'isSheet', 'isTurn', 'ribbonDrawMode',
'ribbonDisplay', 'label', 'isHet']
serial = 1
atomMap = {}
for m in mols:
if m.openState == refMol.openState:
xform = None
else:
xform = refMol.openState.xform
xform.invert()
for r in m.residues:
chainID, pos = resMap[r]
nr = combined.newResidue(r.type, chainID, pos,
r.id.insertionCode)
for attrName in resAttrs:
try:
setattr(nr, attrName,
getattr(r, attrName))
except AttributeError:
continue
ratoms = r.atoms
ratoms.sort(lambda a1, a2:
cmp(a1.coordIndex, a2.coordIndex))
for a in ratoms:
if xform is None:
crd = a.coord()
else:
crd = xform.apply(a.xformCoord())
na = addAtom(a.name, a.element, nr, crd,
serialNumber=serial)
na.altLoc = a.altLoc
atomMap[a] = na
serial += 1
for attrName in atomAttrs:
try:
setattr(na, attrName,
getattr(a, attrName))
except AttributeError:
continue
for b in m.bonds:
a1, a2 = b.atoms
nb = combined.newBond(atomMap[a1], atomMap[a2])
for attrName in bondAttrs:
try:
setattr(nb, attrName,
getattr(b, attrName))
except AttributeError:
continue
consensusAttrs = ['color', 'display', 'lineWidth', 'pointSize',
'stickScale', 'surfaceOpacity', 'ballScale', 'vdwDensity',
'autochain', 'ribbonHidesMainchain']
for attrName in consensusAttrs:
consensusVal = None
for m in mols:
val = getattr(m, attrName)
if consensusVal == None:
consensusVal = val
elif val != consensusVal:
break
else:
setattr(combined, attrName, consensusVal)
associatedModels = set()
for m in mols:
associatedModels.update(m.associatedModels())
from chimera import PseudoBondMgr
for opbg in PseudoBondMgr.mgr().pseudoBondGroups:
if opbg in associatedModels:
if opbg.category.startswith("internal-chain-"):
continue
assert(opbg.category.startswith("coordination complex"))
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup("coordination complexes of %s"
% combined.name, associateWith=[combined])
for attrName in ['color', 'showStubBonds', 'lineWidth',
'stickScale', 'lineType']:
setattr(pbg, attrName, getattr(opbg, attrName))
else:
pbg = opbg
for opb in opbg.pseudoBonds:
oa1, oa2 = opb.atoms
na1 = atomMap.get(oa1, oa1)
na2 = atomMap.get(oa2, oa2)
if oa1 == na1 and oa2 == na2:
continue
pb = pbg.newPseudoBond(na1, na2)
for attrName in ['drawMode', 'display', 'halfbond',
'label', 'color', 'labelColor']:
setattr(pb, attrName, getattr(opb, attrName))
if returnMapping:
return atomMap, combined
return combined
def draw_spring(bond):
pbg = getPseudoBondGroup('Bond order errors')
pb = pbg.newPseudoBond(*bond.atoms)
pb.drawMode = 2
pb.radius = bond.radius + 0.1
def combine(mols, refMol, newChainIDs=True, log=False, returnMapping=False):
from chimera import replyobj
# figure out residue chain/number remapping
origChainIDs = {}
numChains = 0
minNums = {}
maxNums = {}
for m in mols:
seenIDs = set()
for r in m.residues:
chainID = r.id.chainId
num = r.id.position
key = (m, chainID)
if key in minNums:
if num > maxNums[key]:
maxNums[key] = num
elif num < minNums[key]:
minNums[key] = num
else:
minNums[key] = maxNums[key] = num
if chainID in seenIDs:
continue
numChains += 1
seenIDs.add(chainID)
origChainIDs.setdefault(chainID, []).append(m)
resMap = {}
if newChainIDs:
if numChains > 62:
raise CombineError("More than 62 chains; cannot"
" uniquely identify with single characters")
from string import uppercase, lowercase, digits
possibleIDs = uppercase + lowercase + digits
usedChainIDs = set(origChainIDs.keys())
chainIDmap = {}
for chainID, idMols in origChainIDs.items():
if len(chainID) > 1:
continue
chainIDmap[(idMols[0], chainID)] = chainID
usedChainIDs.add(chainID)
for m in idMols[1:]:
for c in possibleIDs:
if c not in usedChainIDs:
break
if log:
replyobj.info("Remapping %s chain %s"
" to %s\n" % (m, chainID, c))
usedChainIDs.add(c)
chainIDmap[(m, chainID)] = c
for m in mols:
for r in m.residues:
chainID = r.id.chainId
if len(chainID) > 1:
continue
resMap[r] = (chainIDmap[(m, chainID)], r.id.position)
# handle renumbering for all chains if newChainIDs False,
# otherwise just water/het chains
offsets = {}
for chainID, idMols in origChainIDs.items():
if newChainIDs and len(chainID) < 2:
continue
minMaxs = []
for m in idMols:
mmin = minNums[(m, chainID)]
mmax = maxNums[(m, chainID)]
for omin, omax in minMaxs:
if omin < mmin < omax or omin < mmax < omax:
gmax = max([mm[1] for mm in minMaxs])
offset = gmax - mmin + 1
break
else:
offset = 0
offsets[(m, chainID)] = offset
minMaxs.append((mmin + offset, mmax + offset))
if log and offset:
replyobj.info("Adding %d to %s chain %s"
" numbering\n" % (offset, m, chainID))
for m in mols:
for r in m.residues:
chainID = r.id.chainId
try:
offset = offsets[(m, chainID)]
except KeyError:
continue
resMap[r] = (chainID, r.id.position + offset)
# combine...
from chimera import Atom, Bond, Residue, Molecule
combined = Molecule()
combined.name = "combination"
from SimpleSession.save import optionalAttributes
from chimera.molEdit import addAtom
atomAttrs = optionalAttributes[Atom].keys() + [
'color', 'vdwColor', 'labelColor', 'surfaceColor', 'drawMode',
'display', 'label', 'radius', 'surfaceDisplay', 'surfaceCategory',
'surfaceOpacity', 'vdw'
]
bondAttrs = optionalAttributes[Bond].keys() + [
'drawMode', 'display', 'radius'
]
resAttrs = optionalAttributes[Residue].keys() + [
'ribbonColor', 'labelColor', 'isHelix', 'isSheet', 'isTurn',
'ribbonDrawMode', 'ribbonDisplay', 'label', 'isHet'
]
serial = 1
atomMap = {}
for m in mols:
if m.openState == refMol.openState:
xform = None
else:
xform = refMol.openState.xform
xform.invert()
for r in m.residues:
chainID, pos = resMap[r]
nr = combined.newResidue(r.type, chainID, pos, r.id.insertionCode)
for attrName in resAttrs:
try:
setattr(nr, attrName, getattr(r, attrName))
except AttributeError:
continue
ratoms = r.atoms
ratoms.sort(lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex))
for a in ratoms:
if xform is None:
crd = a.coord()
else:
crd = xform.apply(a.xformCoord())
na = addAtom(a.name, a.element, nr, crd, serialNumber=serial)
na.altLoc = a.altLoc
atomMap[a] = na
serial += 1
for attrName in atomAttrs:
try:
setattr(na, attrName, getattr(a, attrName))
except AttributeError:
continue
for b in m.bonds:
a1, a2 = b.atoms
nb = combined.newBond(atomMap[a1], atomMap[a2])
for attrName in bondAttrs:
try:
setattr(nb, attrName, getattr(b, attrName))
except AttributeError:
continue
consensusAttrs = [
'color', 'display', 'lineWidth', 'pointSize', 'stickScale',
'surfaceOpacity', 'ballScale', 'vdwDensity', 'autochain',
'ribbonHidesMainchain'
]
for attrName in consensusAttrs:
consensusVal = None
for m in mols:
val = getattr(m, attrName)
if consensusVal == None:
consensusVal = val
elif val != consensusVal:
break
else:
setattr(combined, attrName, consensusVal)
associatedModels = set()
for m in mols:
associatedModels.update(m.associatedModels())
from chimera import PseudoBondMgr
for opbg in PseudoBondMgr.mgr().pseudoBondGroups:
if opbg in associatedModels:
if opbg.category.startswith("internal-chain-"):
continue
assert (opbg.category.startswith("coordination complex"))
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup("coordination complexes of %s" %
combined.name,
associateWith=[combined])
for attrName in [
'color', 'showStubBonds', 'lineWidth', 'stickScale',
'lineType'
]:
setattr(pbg, attrName, getattr(opbg, attrName))
else:
pbg = opbg
for opb in opbg.pseudoBonds:
oa1, oa2 = opb.atoms
na1 = atomMap.get(oa1, oa1)
na2 = atomMap.get(oa2, oa2)
if oa1 == na1 and oa2 == na2:
continue
pb = pbg.newPseudoBond(na1, na2)
for attrName in [
'drawMode', 'display', 'halfbond', 'label', 'color',
'labelColor'
]:
setattr(pb, attrName, getattr(opb, attrName))
if returnMapping:
return atomMap, combined
return combined
def processHbonds(residue,
rotamers,
drawHbonds,
bondColor,
lineWidth,
relax,
distSlop,
angleSlop,
twoColors,
relaxColor,
groupName,
ignoreOtherModels,
cacheDA=False):
from FindHBond import findHBonds
if ignoreOtherModels:
targetModels = [residue.molecule] + rotamers
else:
targetModels = chimera.openModels.list(
modelTypes=[chimera.Molecule]) + rotamers
if relax and twoColors:
color = relaxColor
else:
color = bondColor
hbonds = dict.fromkeys(
findHBonds(targetModels,
intramodel=False,
distSlop=distSlop,
angleSlop=angleSlop,
cacheDA=True), color)
if relax and twoColors:
hbonds.update(
dict.fromkeys(findHBonds(targetModels, intramodel=False),
bondColor))
backboneNames = set(['CA', 'C', 'N', 'O'])
# invalid H-bonds: involving residue side chain or rotamer backbone
invalidAtoms = set(
[ra for ra in residue.atoms if ra.name not in backboneNames])
invalidAtoms.update([
ra for rot in rotamers for ra in rot.atoms if ra.name in backboneNames
])
rotAtoms = set(
[ra for rot in rotamers for ra in rot.atoms if ra not in invalidAtoms])
for rot in rotamers:
rot.numHbonds = 0
if drawHbonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
elif groupName:
nukeGroup(groupName)
for hb, color in hbonds.items():
d, a = hb
if (d in rotAtoms) == (a in rotAtoms):
# only want rotamer to non-rotamer
continue
if d in invalidAtoms or a in invalidAtoms:
continue
if d in rotAtoms:
rot = d.molecule
else:
rot = a.molecule
rot.numHbonds += 1
if drawHbonds:
pb = pbg.newPseudoBond(d, a)
pb.color = color
def createHBonds(models=None, intramodel=True, intermodel=True, relax=True,
distSlop=recDistSlop, angleSlop=recAngleSlop, twoColors=False,
selRestrict=None, lineWidth=1.0, saveFile=None, batch=False,
interSubmodel=False, makePseudobonds=True, retainCurrent=False,
reveal=False, namingStyle=None, log=False, cacheDA=None,
color=(0.0, 0.8, 0.9, 1.0), slopColor=(0.95, 0.5, 0.0, 1.0)):
"""Wrapper to be called by gui and command line.
Use findHBonds for other programming applications.
"""
inColors = (color, slopColor)
outColors = []
for c in inColors:
if isinstance(c, basestring):
from chimera.colorTable import getColorByName
try:
outColors.append(getColorByName(c))
except KeyError:
raise "No known color named '%s'" % c
elif isinstance(c, tuple):
oc = chimera.MaterialColor()
oc.ambientDiffuse = c[:3]
if len(c) > 3:
oc.opacity = c[-1]
outColors.append(oc)
else:
outColors.append(c)
bondColor, slopColor = outColors
donors = acceptors = None
if selRestrict is not None:
selAtoms = currentAtoms(asDict=True)
if not selAtoms:
if batch:
return
raise UserError("No atoms in selection.")
if (not intermodel or selRestrict == "both") and models is None:
# intramodel only or both ends in selection
models = currentMolecules()
if selRestrict == "both":
# both ends in selection
donors = acceptors = selAtoms
if models is None:
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
if not relax:
distSlop = angleSlop = 0.0
if cacheDA == None:
# cache trajectories by default
cacheDA = len(models) == 1 and len(models[0].coordSets) > 1
hbonds = findHBonds(models, intermodel=intermodel,
intramodel=intramodel, distSlop=distSlop,
angleSlop=angleSlop, donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
hbonds = _filterBySel(hbonds, selAtoms, selRestrict)
outputInfo = (intermodel, intramodel, relax, distSlop, angleSlop,
models, hbonds)
if log:
import sys
# provide a separator from other output
print>>sys.stdout, ""
_fileOutput(sys.stdout, outputInfo, namingStyle)
if saveFile == '-':
from MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(outputInfo, _fileOutput,
initialfile="hbond.info",
title="Choose H-Bond Save File",
historyID="H-bond info")
elif saveFile is not None:
_fileOutput(saveFile, outputInfo, namingStyle)
replyobj.status("%d hydrogen bonds found\n"
% len(hbonds), log=1, blankAfter=120)
if not makePseudobonds:
return
if twoColors:
# color relaxed constraints differently
precise = findHBonds(models,
intermodel=intermodel, intramodel=intramodel,
donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
precise = _filterBySel(precise, selAtoms, selRestrict)
# give another opportunity to read the result...
replyobj.status("%d hydrogen bonds found\n" % len(hbonds),
blankAfter=120)
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup("hydrogen bonds", issueHint=True)
if not retainCurrent:
pbg.deleteAll()
pbg.lineWidth = lineWidth
for don, acc in hbonds:
if don.associated(acc, "hydrogen bonds"):
continue
pb = pbg.newPseudoBond(don, acc)
if twoColors:
if (don, acc) in precise:
color = bondColor
else:
color = slopColor
else:
color = bondColor
pb.color = color
if reveal:
for end in [don, acc]:
if end.display:
continue
for ea in end.residue.oslChildren():
ea.display = True
from chimera import runCommand
runCommand("findhbond linewidth 2 color yellow")
from chimera.misc import getPseudoBondGroup
hbonds = len(getPseudoBondGroup("hydrogen bonds").pseudoBonds)
runCommand("2dlabels change mylabel text '%d H-bonds'" % hbonds)
def cmdDetectClash(testAtoms, overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE], test="others",
setAttrs=defaults[ACTION_ATTR], selectClashes=
defaults[ACTION_SELECT], colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR], nonclashColor=
defColors[NONCLASH_COLOR], makePseudobonds=
defaults[ACTION_PSEUDOBONDS], pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH], bondSeparation=
defaults[BOND_SEPARATION], saveFile=None, namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES], interSubmodel=False,
log=defaults[ACTION_REPLYLOG], summary=True,
continuous=False):
global _continuousID
from Midas import MidasError
if continuous:
if setAttrs or saveFile != None or log:
raise MidasError("log/setAttrs/saveFile not allowed"
" with continuous detection")
if _continuousID == None:
from inspect import getargvalues, currentframe
argNames, fArgs, fKw, frameDict = getargvalues(
currentframe())
callData = [frameDict[an] for an in argNames]
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
return _motionCB(myData)
_continuousID = chimera.triggers.addHandler(
'OpenState', preCB, callData)
elif _continuousID != None:
chimera.triggers.deleteHandler('OpenState', _continuousID)
_continuousID = None
if isinstance(test, basestring):
if test.startswith("other"):
test = "others"
elif test not in ('self', 'model'):
# atom spec
from chimera.specifier import evalSpec
try:
test = evalSpec(test).atoms()
except:
raise MidasError("Could not parse atom spec '%s'" % test)
clashes = detectClash(testAtoms, test=test,
hbondAllowance=hbondAllowance, clashThreshold=overlapCutoff,
bondSeparation=bondSeparation, intraRes=not ignoreIntraRes,
interSubmodel=interSubmodel)
if selectClashes:
chimera.selection.setCurrent(clashes.keys())
if test == "self":
outputGrouping = set()
else:
outputGrouping = testAtoms
info = (overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes,
clashes, outputGrouping)
if log:
import sys
# put a separator in the Reply Log
print>>sys.stdout, ""
_fileOutput(sys.stdout, info, namingStyle=namingStyle)
if saveFile == '-':
from FindHBond.MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(info, _fileOutput, initialfile="overlaps",
title="Choose Overlap Info Save File",
historyID="Overlap info")
elif saveFile is not None:
_fileOutput(saveFile, info, namingStyle=namingStyle)
if summary == True:
def _summary(msg):
from chimera import replyobj
replyobj.status(msg + '\n')
replyobj.info(msg + '\n')
summary = _summary
if summary:
if clashes:
total = 0
for clashList in clashes.values():
total += len(clashList)
summary("%d contacts" % (total/2))
else:
summary("No contacts")
if not (setAttrs or colorClashes or makePseudobonds):
nukeGroup()
return clashes
if test in ("others", "model"):
atoms = [a for m in chimera.openModels.list(
modelTypes=[chimera.Molecule]) for a in m.atoms]
else:
atoms = testAtoms
if setAttrs:
# delete the attribute in _all_ atoms...
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if hasattr(a, attrName):
delattr(a, attrName)
for a in atoms:
if a in clashes:
clashVals = clashes[a].values()
clashVals.sort()
setattr(a, attrName, clashVals[-1])
if colorClashes:
for a in atoms:
a.surfaceColor = None
if a in clashes:
a.color = clashColor
else:
a.color = nonclashColor
if makePseudobonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
pbg.color = pbColor
seen = set()
for a in atoms:
if a not in clashes:
continue
seen.add(a)
for clasher in clashes[a].keys():
if clasher in seen:
continue
pbg.newPseudoBond(a, clasher)
else:
nukeGroup()
return clashes
