def makeAfterModelsCBs():
for cb, data in globals.afterModelsCBs:
try:
if data is not None:
cb(data)
else:
cb()
except:
replyobj.reportException("Error in after-models callback")
def makeAfterModelsCBs(): for cb, data in _afterModelsCBs: try: if data is not None: cb(data) else: cb() except: replyobj.reportException( "Error in after-models callback")
def makeAfterModelsCBs(): for cb, data in globals.afterModelsCBs: try: if data is not None: cb(data) else: cb() except: from chimera import replyobj replyobj.reportException( "Error in after-models callback")
def invoke(self, triggerName, triggerData):
import chimera
try:
return self._func(triggerName, self._funcData, triggerData)
except chimera.ChimeraSystemExit:
raise
except chimera.UserError:
from chimera.replyobj import reportException
reportException()
except:
from chimera.replyobj import reportException
reportException('Error processing trigger "%s"' % triggerName)
def _endRecording(self, *args):
from Midas import MidasError
try:
from chimera import runCommand
runCommand("movie stop")
self.status("Compiling frames into animation", blankAfter=5)
runCommand("movie encode " + self.encodeArgs)
except:
self.status("Error stopping/encoding movie", color="red")
from chimera.replyobj import reportException
reportException("Error stopping/encoding movie")
from chimera.triggerSet import ONESHOT
return ONESHOT
def invoke(self, triggerName, triggerData):
import chimera
try:
return self._func(triggerName,
self._funcData, triggerData)
except chimera.ChimeraSystemExit:
raise
except chimera.UserError:
from chimera.replyobj import reportException
reportException()
except:
from chimera.replyobj import reportException
reportException('Error processing trigger "%s"'
% triggerName)
def _endRecording(self, *args):
from Midas import MidasError
try:
from chimera import runCommand
runCommand("movie stop")
self.status("Compiling frames into animation",
blankAfter=5)
runCommand("movie encode " + self.encodeArgs)
except:
self.status("Error stopping/encoding movie",
color="red")
from chimera.replyobj import reportException
reportException("Error stopping/encoding movie")
from chimera.triggerSet import ONESHOT
return ONESHOT
def Apply(self):
states = {}
for but in self.buttonWidgets.values():
states[but] = but.cget('state')
but.config(state='disabled')
try:
self._Apply()
finally:
for but, state in states.items():
but.config(state=state)
for cb in self.callbacks:
try:
cb()
except:
replyobj.reportException("H-bond callback function")
self.callbacks = []
def Apply(self):
states = {}
for but in self.buttonWidgets.values():
states[but] = but.cget('state')
but.config(state='disabled')
try:
self._Apply()
finally:
for but, state in states.items():
but.config(state=state)
for cb in self.callbacks:
try:
cb()
except:
replyobj.reportException(
"H-bond callback function")
self.callbacks = []
def load_accelerators(self):
from Accelerators import default_accelerator_file
path = self.accelerator_file.get()
if path == '':
path = default_accelerator_file()
self.accelerator_file.set(path)
if path == default_accelerator_file():
self.preferences['path'] = None
else:
self.preferences['path'] = path
dict = {'__file__':path}
try:
execfile(path, dict)
except:
from chimera import replyobj
replyobj.reportException('Error executing accelerators file ' + path)
return
if not dict.has_key('register_accelerators'):
from chimera import replyobj
replyobj.error('Accelerators file ' + path +
' has no register_accelerators() function.')
return
register_accelerators = dict['register_accelerators']
try:
register_accelerators()
except:
from chimera import replyobj
replyobj.reportException('Error running register_accelerators() from accelerators file ' + path)
return
self.fill_listbox()
or saverFile[-3:] != ".py":
continue
saverType = saverFile[4:-3]
try:
exec \
"from formatters.%s import extension, globs, save, fileType" \
% saverFile[:-3]
except ImportError:
replyobj.error("Formatter for %s multi-sequence file "
"does not contain default file-name extension, "
"list of acceptable file name patterns, "
"file type description, and/or save() "
" function\n" % saverType)
continue
except:
replyobj.reportException("Error in %s formatter" % saverType)
continue
saverFunc[fileType] = save
extensions[fileType] = extension
fileGlobs[fileType] = globs
if not saverFunc:
raise ImportError, "No working multi-sequence file formatters found."
def saveFile(mav, modal=False):
filters = []
for fileType in saverFunc.keys():
filters.append([fileType, fileGlobs[fileType],
extensions[fileType]])
filters.sort()
def LoadFrame(self):
from chimera import UserError
if hasattr(self, 'frameEntry') and not self.frameEntry.valid():
raise UserError("Bad frame number text: %s" %
self.frameEntry.getvalue())
currentFrame = self.currentFrame.get()
if currentFrame < self.startFrame \
or currentFrame > self.endFrame:
self.currentFrame.set(self.startFrame)
raise UserError("Frame %d out of range!" % currentFrame)
self._LoadFrame(currentFrame, makeCurrent=True)
if self.holdingSteady:
atoms, steadySel, steadyCS, inverse = self.holdingSteady
baseXform = self.model.openState.xform
baseXform.multiply(inverse)
try:
xform, inverse = self.transforms[currentFrame]
except:
xform, inverse = self.steadyXform()
self.transforms[currentFrame] = (xform, inverse)
baseXform.multiply(xform)
self.model.openState.xform = baseXform
self.holdingSteady = (atoms, steadySel, steadyCS,
inverse)
if self.script:
if self.scriptType == SCRIPT_PYTHON:
scriptGlobals = {
'chimera': chimera
}
if self.frameSubst \
and self.frameSubst.isalnum():
scriptGlobals[self.frameSubst] = {
'mol': self.model._mol,
'startFrame': self.startFrame,
'endFrame': self.endFrame,
'frame': self.currentFrame.get()
}
else:
from Midas.midas_text import processCommandFile
# activate lines that begin with
# "#<currentframe>:"
processedLines = []
curFrame = self.currentFrame.get()
sigil = "#%d:" % curFrame
for line in self.script.splitlines(True):
if line.startswith(sigil):
processedLines.append(
line[len(sigil):])
else:
processedLines.append(line)
script = "".join(processedLines)
if self.frameSubst \
and not self.frameSubst.isspace():
fn = str(curFrame)
if self.zeroPad:
lf = len(self.ensemble)
digits = len(str(lf))
fn = "0" * (digits-len(fn)) + fn
script = script.replace(
self.frameSubst, fn)
try:
if self.scriptType == SCRIPT_PYTHON:
exec self.script in scriptGlobals, {}
else:
processCommandFile(script,
emulateRead=True,
usingString=True)
except:
from chimera.replyobj import reportException
reportException("Problem in per-frame script")
self.stopMovieCallback()
if self.recording \
and currentFrame + self.recordStep > self.recordEnd:
self.recording = False
self.stopMovieCallback()
# stop recording after next frame appears...
chimera.triggers.addHandler('new frame',
self._endRecording, None)
if script: sys.argv = [script] + args args = [script] return_value = 0 for a in args: try: try: chimera.openModels.open(a, prefixableType=1) except IOError, value: # so that we don't get bug reports when # people mistype file names raise chimera.UserError(value) except SystemExit, value: return value except: replyobj.reportException( "Error while processing %s" % a) return_value = 1 if nogui: from chimera import triggers, APPQUIT, fileInfo if not script: if args: fileType = fileInfo.processName(args[-1])[0] else: fileType = None if fileInfo.category(fileType) != fileInfo.SCRIPT: extension.startup(["ReadStdin"]) triggers.activateTrigger(APPQUIT, None) return return_value if eventloop: # run user interface
def LoadFrame(self):
from chimera import UserError
if hasattr(self, 'frameEntry') and not self.frameEntry.valid():
raise UserError("Bad frame number text: %s" %
self.frameEntry.getvalue())
currentFrame = self.currentFrame.get()
if currentFrame < self.startFrame \
or currentFrame > self.endFrame:
self.currentFrame.set(self.startFrame)
raise UserError("Frame %d out of range!" % currentFrame)
self._LoadFrame(currentFrame, makeCurrent=True)
if self.holdingSteady:
atoms, steadySel, steadyCS, inverse = self.holdingSteady
baseXform = self.model.openState.xform
baseXform.multiply(inverse)
try:
xform, inverse = self.transforms[currentFrame]
except:
xform, inverse = self.steadyXform()
self.transforms[currentFrame] = (xform, inverse)
baseXform.multiply(xform)
self.model.openState.xform = baseXform
self.holdingSteady = (atoms, steadySel, steadyCS, inverse)
if self.script:
if self.scriptType == SCRIPT_PYTHON:
scriptGlobals = {'chimera': chimera}
if self.frameSubst \
and self.frameSubst.isalnum():
scriptGlobals[self.frameSubst] = {
'mol': self.model._mol,
'startFrame': self.startFrame,
'endFrame': self.endFrame,
'frame': self.currentFrame.get()
}
else:
from Midas.midas_text import processCommandFile
# activate lines that begin with
# "#<currentframe>:"
processedLines = []
curFrame = self.currentFrame.get()
sigil = "#%d:" % curFrame
for line in self.script.splitlines(True):
if line.startswith(sigil):
processedLines.append(line[len(sigil):])
else:
processedLines.append(line)
script = "".join(processedLines)
if self.frameSubst \
and not self.frameSubst.isspace():
fn = str(curFrame)
if self.zeroPad:
lf = len(self.ensemble)
digits = len(str(lf))
fn = "0" * (digits - len(fn)) + fn
script = script.replace(self.frameSubst, fn)
try:
if self.scriptType == SCRIPT_PYTHON:
exec self.script in scriptGlobals, {}
else:
processCommandFile(script,
emulateRead=True,
usingString=True)
except:
from chimera.replyobj import reportException
reportException("Problem in per-frame script")
self.stopMovieCallback()
if self.recording \
and currentFrame + self.recordStep > self.recordEnd:
self.recording = False
self.stopMovieCallback()
# stop recording after next frame appears...
chimera.triggers.addHandler('new frame', self._endRecording, None)
or parserFile[-3:] != ".py":
continue
parserType = parserFile[4:-3]
try:
exec \
"from parsers.%s import extensions, prefixes, parse, fileType" \
% parserFile[:-3]
except ImportError:
replyobj.error("Parser for %s multi-sequence file "
"does not contain file-name extension list, "
"command-line prefix list, "
"file type description, and/or parse() "
"function\n" % parserType)
continue
except:
replyobj.reportException("Error in %s parser"
% parserType)
continue
parseFunc[fileType] = parse
exts[fileType] = extensions
prefs[fileType] = prefixes
extensions = exts
prefixes = prefs
if not parseFunc:
raise ImportError, "No working multi-sequence file parsers found."
def parseFile(filename, fileType, minSeqs=2):
seqs = None
if isinstance(filename, basestring) \
and not filename.startswith("http:") \
and not os.path.exists(filename):
or parserFile[-3:] != ".py":
continue
parserType = parserFile[4:-3]
try:
exec \
"from parsers.%s import extensions, prefixes, parse, fileType" \
% parserFile[:-3]
except ImportError:
replyobj.error("Parser for %s multi-sequence file "
"does not contain file-name extension list, "
"command-line prefix list, "
"file type description, and/or parse() "
"function\n" % parserType)
continue
except:
replyobj.reportException("Error in %s parser" % parserType)
continue
parseFunc[fileType] = parse
exts[fileType] = extensions
prefs[fileType] = prefixes
extensions = exts
prefixes = prefs
if not parseFunc:
raise ImportError, "No working multi-sequence file parsers found."
def parseFile(filename, fileType, minSeqs=2):
seqs = None
if isinstance(filename, basestring) \
and not filename.startswith("http:") \
if script:
sys.argv = [script] + args
args = [script]
return_value = 0
for a in args:
try:
try:
chimera.openModels.open(a, prefixableType=1)
except IOError, value:
# so that we don't get bug reports when
# people mistype file names
raise chimera.UserError(value)
except SystemExit, value:
return value
except:
replyobj.reportException("Error while processing %s" % a)
return_value = 1
if nogui:
from chimera import triggers, APPQUIT, fileInfo
if not script:
if args:
fileType = fileInfo.processName(args[-1])[0]
else:
fileType = None
if fileInfo.category(fileType) != fileInfo.SCRIPT:
extension.startup(["ReadStdin"])
triggers.activateTrigger(APPQUIT, None)
return return_value
if eventloop:
# run user interface
or saverFile[-3:] != ".py":
continue
saverType = saverFile[4:-3]
try:
exec \
"from formatters.%s import extension, globs, save, fileType" \
% saverFile[:-3]
except ImportError:
replyobj.error("Formatter for %s multi-sequence file "
"does not contain default file-name extension, "
"list of acceptable file name patterns, "
"file type description, and/or save() "
" function\n" % saverType)
continue
except:
replyobj.reportException("Error in %s formatter" % saverType)
continue
saverFunc[fileType] = save
extensions[fileType] = extension
fileGlobs[fileType] = globs
if not saverFunc:
raise ImportError, "No working multi-sequence file formatters found."
def saveFile(mav, modal=False):
filters = []
for fileType in saverFunc.keys():
filters.append([fileType, fileGlobs[fileType], extensions[fileType]])
filters.sort()
def reportRestoreError(msg=None): try: from chimera.replyobj import reportException reportException(msg) except: print "Error reporting session extension restore error!"
bw["Quit"].config(state="disabled")
def _finish(self, results):
if self.blastTable is None:
# We already quit, so UI is gone
return
from Parser import Parser
import os.path
try:
self.parser = Parser(self.basename, results,
self.program == "psiblast")
except SyntaxError, s:
replyobj.error("BLAST error: %s\n" % s)
return
except:
replyobj.reportException("BLAST error")
return
self.service = None
if self.showOne:
matches = []
seen = set()
for m in self.parser.matches:
if m.pdb is not None:
parts = m.pdb.split('_')
pdb = parts[0]
if pdb in seen:
continue
seen.add(pdb)
matches.append(m)
self.parser.matches = matches
self.blastTable.setData(self.parser.matches)
def saveSession(filename):
replyobj.status("Initializing session save...", blankAfter=0)
from OpenSave import osOpen, tildeExpand
fullName = tildeExpand(filename)
try:
outf = osOpen(fullName, "w")
except:
replyobj.reportException("Error opening %s for writing" % filename)
return
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
class SessionIO:
def __init__(self, stringIO, fileName):
self.fileName = fileName
self.stringIO = stringIO()
def __getattr__(self, attrName):
return getattr(self.stringIO, attrName)
buf = SessionIO(StringIO, fullName)
print >> outf, "import cPickle, base64"
print >> outf, "try:"
print >> outf, "\tfrom SimpleSession.versions.v45 import beginRestore,\\"
print >> outf, "\t registerAfterModelsCB, reportRestoreError, checkVersion"
print >> outf, "except ImportError:"
print >> outf, "\tfrom chimera import UserError"
print >> outf, "\traise UserError('Cannot open session that was saved in a'"
print >> outf, "\t ' newer version of Chimera; update your version')"
print >> outf, "checkVersion(%s)" % repr(version.releaseNum)
print >> outf, "import chimera"
print >> outf, "from chimera import replyobj"
print >> outf, "replyobj.status('Beginning session restore...', \\"
print >> outf, " blankAfter=0)"
print >> outf, "beginRestore()"
print >> outf, """
def restoreCoreModels():
\tfrom SimpleSession.versions.v45 import init, restoreViewer, \\
\t restoreMolecules, restoreColors, restoreSurfaces, \\
\t restoreVRML, restorePseudoBondGroups, restoreModelAssociations"""
global _id2color, _color2id
_id2color = {}
_color2id = {}
molecules = [
m for m in chimera.openModels.list(modelTypes=[chimera.Molecule],
all=True) if autoRestorable(m)
]
allSurfaces = chimera.openModels.list(modelTypes=[chimera.MSMSModel])
allVrmls = [
m for m in chimera.openModels.list(modelTypes=[chimera.VRMLModel])
if autoRestorable(m)
]
surfaces = [s for s in allSurfaces if s.molecule]
if surfaces != allSurfaces:
replyobj.warning(
"Cannot save surfaces without associated structure.\nSurface will not be saved.\n"
)
vrmls = []
for v in allVrmls:
source = v.openedAs[0]
if not source.startswith('#VRML')\
and not os.path.exists(source):
replyobj.warning("Source file for VRML model '%s' no"
" longer exists.\nThe model will not be"
" saved.\n" % v.name)
else:
vrmls.append(v)
atoms = []
bonds = []
residues = []
for m in molecules:
atoms.extend(m.atoms)
bonds.extend(m.bonds)
residues.extend(m.residues)
mgr = chimera.PseudoBondMgr.mgr()
pbGroups = []
for g in mgr.pseudoBondGroups:
if g.category.startswith("internal-chain-"):
noAutoRestore(g)
else:
pbGroups.append(g)
pseudobonds = []
pbMap = {}
for pbg in pbGroups:
pbs = [
pb for pb in pbg.pseudoBonds
if autoRestorable(pb.atoms[0].molecule)
and autoRestorable(pb.atoms[1].molecule)
]
pseudobonds.extend(pbs)
pbMap[pbg] = pbs
setSessionIDparams(molecules, residues, atoms, bonds, surfaces, vrmls,
pseudobonds, pbGroups)
replyobj.status("Gathering molecule information...", blankAfter=0)
molInfo = {}
molInfo['ids'] = summarizeVals([(m.id, m.subid) for m in molecules])
molInfo['name'] = summarizeVals([m.name for m in molecules])
molInfo['color'] = summarizeVals([colorID(m.color) for m in molecules])
molInfo['display'] = summarizeVals([m.display for m in molecules])
molInfo['lineWidth'] = summarizeVals([m.lineWidth for m in molecules])
molInfo['pointSize'] = summarizeVals([m.pointSize for m in molecules])
molInfo['stickScale'] = summarizeVals([m.stickScale for m in molecules])
molInfo['pdbHeaders'] = [m.pdbHeaders for m in molecules]
molInfo['surfaceOpacity'] = summarizeVals(
[m.surfaceOpacity for m in molecules])
molInfo['ballScale'] = summarizeVals([m.ballScale for m in molecules])
molInfo['vdwDensity'] = summarizeVals([m.vdwDensity for m in molecules])
molInfo['autochain'] = summarizeVals([m.autochain for m in molecules])
molInfo['ribbonHidesMainchain'] = summarizeVals(
[m.ribbonHidesMainchain for m in molecules])
molInfo['ribbonInsideColor'] = summarizeVals(
[colorID(m.ribbonInsideColor) for m in molecules])
molInfo['aromaticColor'] = summarizeVals(
[colorID(m.aromaticColor) for m in molecules])
molInfo['aromaticDisplay'] = summarizeVals(
[m.aromaticDisplay for m in molecules])
molInfo['aromaticLineType'] = summarizeVals(
[m.aromaticLineType for m in molecules])
molInfo['aromaticMode'] = summarizeVals(
[m.aromaticMode for m in molecules])
molInfo['hidden'] = summarizeVals(
[m in m.openState.hidden for m in molecules])
molInfo['optional'] = saveOptionalAttrs(chimera.Molecule, molecules)
print >> outf, "\tmolInfo =", pickled(molInfo)
replyobj.status("Gathering residue information...", blankAfter=0)
resInfo = {}
resInfo['molecule'] = summarizeVals(
[sessionID(r.molecule) for r in residues], consecutiveExceptions=True)
resInfo['name'] = summarizeVals([r.type for r in residues])
resInfo['chain'] = summarizeVals([r.id.chainId for r in residues],
consecutiveExceptions=True)
resInfo['insert'] = summarizeVals([r.id.insertionCode for r in residues])
resInfo['position'] = summarizeSequentialVals(
[r.id.position for r in residues])
resInfo['ribbonColor'] = summarizeVals(
[colorID(r.ribbonColor) for r in residues], consecutiveExceptions=True)
resInfo['labelColor'] = summarizeVals(
[colorID(r.labelColor) for r in residues], consecutiveExceptions=True)
resInfo['ss'] = summarizeVals([(r.isHelix, r.isStrand, r.isTurn)
for r in residues],
consecutiveExceptions=True)
resInfo['ssId'] = summarizeVals([r.ssId for r in residues],
consecutiveExceptions=True)
resInfo['ribbonDrawMode'] = summarizeVals(
[r.ribbonDrawMode for r in residues], consecutiveExceptions=True)
resInfo['ribbonDisplay'] = summarizeVals(
[r.ribbonDisplay for r in residues], consecutiveExceptions=True)
resInfo['label'] = summarizeVals([r.label for r in residues])
resInfo['labelOffset'] = summarizeVals([r.labelOffset for r in residues])
resInfo['isHet'] = summarizeVals([r.isHet for r in residues],
consecutiveExceptions=True)
resInfo['fillDisplay'] = summarizeVals([r.fillDisplay for r in residues],
consecutiveExceptions=True)
resInfo['fillMode'] = summarizeVals([r.fillMode for r in residues],
consecutiveExceptions=True)
resInfo['optional'] = saveOptionalAttrs(chimera.Residue, residues)
print >> outf, "\tresInfo =", pickled(resInfo)
replyobj.status("Gathering atom information...", blankAfter=0)
atomInfo = {}
atomInfo['altLoc'] = summarizeVals([a.altLoc for a in atoms])
atomInfo['residue'] = summarizeVals([sessionID(a.residue) for a in atoms],
consecutiveExceptions=True)
atomInfo['element'] = summarizeVals([a.element.number for a in atoms])
atomInfo['name'] = summarizeVals([a.name for a in atoms])
atomInfo['color'] = summarizeVals([colorID(a.color) for a in atoms])
atomInfo['vdwColor'] = summarizeVals([colorID(a.vdwColor) for a in atoms])
atomInfo['labelColor'] = summarizeVals(
[colorID(a.labelColor) for a in atoms])
atomInfo['surfaceColor'] = summarizeVals(
[colorID(a.surfaceColor) for a in atoms])
atomInfo['drawMode'] = summarizeVals([a.drawMode for a in atoms],
consecutiveExceptions=True)
atomInfo['display'] = summarizeVals([a.display for a in atoms],
consecutiveExceptions=True)
atomInfo['label'] = summarizeVals([a.label for a in atoms])
atomInfo['labelOffset'] = summarizeVals([a.labelOffset for a in atoms])
atomInfo['radius'] = summarizeVals([a.radius for a in atoms])
atomInfo['surfaceDisplay'] = summarizeVals(
[a.surfaceDisplay for a in atoms], consecutiveExceptions=True)
atomInfo['surfaceCategory'] = summarizeVals(
[a.surfaceCategory for a in atoms], consecutiveExceptions=True)
atomInfo['surfaceOpacity'] = summarizeVals(
[a.surfaceOpacity for a in atoms], consecutiveExceptions=True)
atomInfo['vdw'] = summarizeVals([a.vdw for a in atoms],
consecutiveExceptions=True)
atomInfo['optional'] = saveOptionalAttrs(chimera.Atom, atoms)
# only restore explicitly-set IDATM types...
atomInfo['idatmType'] = summarizeVals([(a.idatmIsExplicit and a.idatmType)
for a in atoms])
print >> outf, "\tatomInfo =", pickled(atomInfo)
replyobj.status("Gathering bond information...", blankAfter=0)
bondInfo = {}
bondInfo['atoms'] = [[sessionID(a) for a in b.atoms] for b in bonds]
bondInfo['drawMode'] = summarizeVals([b.drawMode for b in bonds],
consecutiveExceptions=True)
bondInfo['display'] = summarizeVals([b.display for b in bonds])
bondInfo['label'] = summarizeVals([b.label for b in bonds])
bondInfo['labelOffset'] = summarizeVals([b.labelOffset for b in bonds])
bondInfo['radius'] = summarizeVals([b.radius for b in bonds])
bondInfo['optional'] = saveOptionalAttrs(chimera.Bond, bonds)
print >> outf, "\tbondInfo =", pickled(bondInfo)
replyobj.status("Gathering coordinates...", blankAfter=0)
crdInfo = {}
for m in molecules:
crdSets = {}
crdInfo[sessionID(m)] = crdSets
for key, coordSet in m.coordSets.items():
crdSets[key] = [(sessionID(a), str(a.coord(coordSet)))
for a in m.atoms]
if coordSet == m.activeCoordSet:
crdSets['active'] = key
print >> outf, "\tcrdInfo =", pickled(crdInfo)
replyobj.status("Gathering surface information...", blankAfter=0)
surfInfo = {}
surfInfo['molecule'] = [sessionID(s.molecule) for s in surfaces]
surfInfo['name'] = [s.name for s in surfaces]
surfInfo['customColors'] = surfColors = []
for attrname in ('category', 'colorMode', 'density', 'drawMode', 'display',
'probeRadius', 'allComponents', 'lineWidth', 'pointSize',
'useLighting', 'twoSidedLighting', 'smoothLines',
'transparencyBlendMode', 'oneTransparentLayer'):
values = [getattr(s, attrname) for s in surfaces]
surfInfo[attrname] = summarizeVals(values)
for s in surfaces:
if s.colorMode == chimera.MSMSModel.Custom:
surfColors.append(
summarizeVals([colorID(c) for c in s.customColors]))
else:
surfColors.append(summarizeVals([]))
print >> outf, "\tsurfInfo =", sesRepr(surfInfo)
replyobj.status("Gathering VRML information...", blankAfter=0)
vrmlInfo = {}
vrmlInfo['id'] = summarizeVals([v.id for v in vrmls])
vrmlInfo['subid'] = summarizeVals([v.subid for v in vrmls])
vrmlInfo['name'] = summarizeVals([v.name for v in vrmls])
vrmlInfo['display'] = summarizeVals([v.display for v in vrmls])
vrmlInfo['vrmlString'] = vrmlStrings = []
for v in vrmls:
source = v.openedAs[0]
if source.startswith('#VRML'):
vrmlStrings.append(source)
else:
# source is file name
vrmlFile = open(source, 'r')
vrmlStrings.append(vrmlFile.read())
vrmlFile.close()
print >> outf, "\tvrmlInfo =", sesRepr(vrmlInfo)
replyobj.status("Gathering color information...", blankAfter=0)
# remember all saved colors/materials...
knownColors = {}
knownMaterials = {}
from chimera import _savedColors, _savedMaterials
for name, material in _savedMaterials.items():
knownMaterials[name] = (material.specular, material.shininess)
for name, color in _savedColors.items():
if not isinstance(color, chimera.MaterialColor):
continue
matName = color.material.name()
if matName is None: # unnamed material
matName = "mat" + str(id(color.material))
knownColors[name] = (color.ambientDiffuse, color.opacity, matName)
if matName not in knownMaterials:
mat = color.material
knownMaterials[matName] = (mat.specular, mat.shininess)
print >> outf, "\tcolors =", sesRepr(knownColors)
print >> outf, "\tmaterials =", sesRepr(knownMaterials)
replyobj.status("Gathering pseudobond information...", blankAfter=0)
pbInfo = {}
pbInfo['category'] = [g.category for g in pbGroups]
pbInfo['id'] = [g.id for g in pbGroups]
pbInfo['color'] = summarizeVals([colorID(g.color) for g in pbGroups])
pbInfo['showStubBonds'] = summarizeVals(
[g.showStubBonds for g in pbGroups])
pbInfo['lineWidth'] = summarizeVals([g.lineWidth for g in pbGroups])
pbInfo['stickScale'] = summarizeVals([g.stickScale for g in pbGroups])
pbInfo['lineType'] = summarizeVals([g.lineType for g in pbGroups])
pbInfo['bondInfo'] = pbBondInfos = []
for g in pbGroups:
pbs = pbMap[g]
info = {}
pbBondInfos.append(info)
info['atoms'] = [[sessionID(a) for a in pb.atoms] for pb in pbs]
info['drawMode'] = summarizeVals([pb.drawMode for pb in pbs])
info['display'] = summarizeVals([pb.display for pb in pbs])
info['halfbond'] = summarizeVals([pb.halfbond for pb in pbs])
info['label'] = summarizeVals([pb.label for pb in pbs])
info['color'] = summarizeVals([colorID(pb.color) for pb in pbs])
info['labelColor'] = summarizeVals(
[colorID(pb.labelColor) for pb in pbs])
print >> outf, "\tpbInfo =", sesRepr(pbInfo)
associations = {}
for m in molecules + surfaces + vrmls + pbGroups:
ams = []
for am in m.associatedModels():
if autoRestorable(am):
ams.append(sessionID(am))
if ams:
associations[sessionID(m)] = ams
print >> outf, "\tmodelAssociations =", sesRepr(associations)
replyobj.status("Gathering font information...", blankAfter=0)
from chimera.bgprefs import BACKGROUND, LABEL_FONT
from chimera import preferences
fontInfo = {'face': preferences.getOption(BACKGROUND, LABEL_FONT).get()}
replyobj.status("Gathering clip plane information...", blankAfter=0)
clipPlaneInfo = {}
for m in molecules + surfaces:
if m.useClipPlane:
pl = m.clipPlane
clipPlaneInfo[sessionID(m)] = (pl.origin.data(), pl.normal.data(),
m.useClipThickness, m.clipThickness)
replyobj.status("Gathering selection information...", blankAfter=0)
curSelIds = []
curSel = selection.copyCurrent()
selMols = curSel.molecules()
badMols = filter(lambda m: not autoRestorable(m), selMols)
if badMols:
curSel.remove(badMols)
for a in curSel.atoms():
curSelIds.append(sessionID(a))
for b in curSel.bonds():
curSelIds.append(sessionID(b))
savedSels = []
from copy import copy
for selName, sel in selection.savedSels.items():
badMols = [m for m in sel.molecules() if not autoRestorable(m)]
filtSel = copy(sel)
if badMols:
filtSel.remove(badMols)
ids = []
for a in filtSel.atoms():
ids.append(sessionID(a))
for b in filtSel.bonds():
ids.append(sessionID(b))
savedSels.append((selName, ids))
replyobj.status("Gathering transformation information...", blankAfter=0)
xfDict = {}
for m in (molecules + vrmls):
xf = m.openState.xform
rotV, angle = xf.getRotation()
rot = tuple([float(v) for v in str(rotV).split()])
trans = tuple([float(v) for v in str(xf.getTranslation()).split()])
xfDict[sessionID(m)] = ((rot, angle), trans, m.openState.active)
replyobj.status("Gathering view information...", blankAfter=0)
viewer = chimera.viewer
camera = viewer.camera
viewerAttrs = {}
for va in ("viewSize", "scaleFactor", "clipping", "highlight", "depthCue",
"depthCueRange", "showSilhouette", "silhouetteColor",
"silhouetteWidth"):
if va.endswith("Color"):
viewerAttrs[va] = colorID(getattr(viewer, va))
else:
viewerAttrs[va] = getattr(viewer, va)
cameraAttrs = {}
for ca in ("ortho", "nearFar", "focal", "center", "fieldOfView",
"eyeSeparation"):
cameraAttrs[ca] = getattr(camera, ca)
viewerInfo = {
"detail": chimera.LODControl.get().quality,
"viewerFog": colorID(viewer.depthCueColor),
"viewerBG": colorID(viewer.background),
"viewerHL": colorID(viewer.highlightColor),
"viewerAttrs": viewerAttrs,
"cameraAttrs": cameraAttrs,
"cameraMode": camera.mode(),
}
# start printing into buffer so that color map can be inserted here
replyobj.status("Writing preliminary session info...", blankAfter=0)
print >> buf, "\tviewerInfo =", sesRepr(viewerInfo)
print >> buf, """
\treplyobj.status("Initializing session restore...", blankAfter=0)
\tinit(colorInfo)
\treplyobj.status("Restoring colors...", blankAfter=0)
\trestoreColors(colors, materials)
\treplyobj.status("Restoring molecules...", blankAfter=0)
\trestoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo)
\treplyobj.status("Restoring surfaces...", blankAfter=0)
\trestoreSurfaces(surfInfo)
\treplyobj.status("Restoring VRML models...", blankAfter=0)
\trestoreVRML(vrmlInfo)
\treplyobj.status("Restoring pseudobond groups...", blankAfter=0)
\trestorePseudoBondGroups(pbInfo)
\treplyobj.status("Restoring model associations...", blankAfter=0)
\trestoreModelAssociations(modelAssociations)
\treplyobj.status("Restoring camera...", blankAfter=0)
\trestoreViewer(viewerInfo)
try:
restoreCoreModels()
except:
reportRestoreError("Error restoring core models")
\treplyobj.status("Restoring extension info...", blankAfter=0)
"""
replyobj.status("Writing extension session info...", blankAfter=0)
chimera.triggers.activateTrigger(SAVE_SESSION, buf)
replyobj.status("Writing remaining session info...", blankAfter=0)
print >> buf, """
def restoreRemainder():
\tfrom SimpleSession.versions.v45 import restoreWindowSize, \\
\t restoreOpenStates, restoreSelections, restoreFontInfo, \\
\t restoreOpenModelsAttrs, restoreModelClip
"""
# any use of colors below have to have those colors also run through
# colorID() before init() gets printed, so that the color map contains
# those colors
print >> buf, "\tcurSelIds = ", sesRepr(curSelIds)
print >> buf, "\tsavedSels =", sesRepr(savedSels)
print >> buf, "\topenModelsAttrs = { 'cofrMethod': %d }" % (
chimera.openModels.cofrMethod)
if chimera.openModels.cofrMethod == chimera.openModels.Fixed:
cofr = chimera.openModels.cofr
print >> buf, "\tfrom chimera import Point"
print>> buf, "\topenModelsAttrs['cofr'] = Point(%g, %g, %g)" \
% (cofr.x, cofr.y, cofr.z)
print >> buf, "\twindowSize =", sesRepr(chimera.viewer.windowSize)
print >> buf, "\txformMap =", sesRepr(xfDict)
print >> buf, "\tfontInfo =", sesRepr(fontInfo)
print >> buf, "\tclipPlaneInfo =", sesRepr(clipPlaneInfo)
print >> buf, """
\treplyobj.status("Restoring window...", blankAfter=0)
\trestoreWindowSize(windowSize)
\treplyobj.status("Restoring open states...", blankAfter=0)
\trestoreOpenStates(xformMap)
\treplyobj.status("Restoring font info...", blankAfter=0)
\trestoreFontInfo(fontInfo)
\treplyobj.status("Restoring selections...", blankAfter=0)
\trestoreSelections(curSelIds, savedSels)
\treplyobj.status("Restoring openModel attributes...", blankAfter=0)
\trestoreOpenModelsAttrs(openModelsAttrs)
\treplyobj.status("Restoring model clipping...", blankAfter=0)
\trestoreModelClip(clipPlaneInfo)
\treplyobj.status("Restoring remaining extension info...", blankAfter=0)
try:
restoreRemainder()
except:
reportRestoreError("Error restoring post-model state")
from SimpleSession.versions.v45 import makeAfterModelsCBs
makeAfterModelsCBs()
"""
print >> buf, "from SimpleSession.versions.v45 import endRestore"
print >> buf, "replyobj.status('Finishing restore...', blankAfter=0)"
print >> buf, "endRestore()"
print >> buf, "replyobj.status('Restore finished.')"
# insert color map
print >> outf, "\tcolorInfo =", sesRepr(_id2color)
# print buffered output
print >> outf, buf.getvalue()
buf.close()
outf.close()
from versions import globals
del globals.sessionMap
_id2color = _color2id = None
replyobj.status("Session written")