def restoreMolecules(srcMolInfo, defRadii, radiiExceptions):
from tempfile import mktemp
import os
from SimpleSession import modelMap, modelOffset
for mid, subid, name, fileContents in srcMolInfo:
fname = mktemp()
f = file(fname, "w")
f.write(fileContents)
f.close() # force a flush
mols = chimera.openModels.open(fname, type="session PDB",
baseId=mid+modelOffset, subid=subid, identifyAs=name)
os.unlink(fname)
if mols:
globals.atomIDs.update(mols[0].sessionIDs)
delattr(mols[0], 'sessionIDs')
modelMap.setdefault((mid, subid), []).extend(mols)
for mList in modelMap.values():
for m in mList:
for a in m.atoms:
try:
a.radius = defRadii[a.idatmType]
except KeyError:
continue
for aID, rad in radiiExceptions:
idLookup(aID).radius = float(rad)
def restoreVRML(vrmlInfo):
sm = globals.sessionMap
for id, subid, name, display, vrmlString in zip(
expandSummary(vrmlInfo['id']),
expandSummary(vrmlInfo['subid']),
expandSummary(vrmlInfo['name']),
expandSummary(vrmlInfo['display']),
vrmlInfo['vrmlString']
):
from SimpleSession import modelMap, modelOffset
if (id, subid) in modelMap:
model = modelMap[(id, subid)][0]
mapId, mapSubid = model.id, model.subid
else:
mapId, mapSubid = id+modelOffset, subid
if not vrmlString.startswith("#VRML"):
# BILD object
from Bld2VRML.bld2vrml import Environment
env = Environment()
for line in vrmlString.splitlines():
env.handleLine(line)
env.finish()
vrmlString = env.buildVRML()
vrmlModels = chimera.openModels.open(vrmlString, type="VRML",
baseId=mapId, subid=mapSubid, identifyAs=name)
for vrml in vrmlModels:
vrml.display = display
sm[len(sm)] = vrml
modelMap.setdefault((id, subid), []).extend(vrmlModels)
def restoreVRML(vrmlInfo):
sm = globals.sessionMap
for id, subid, name, display, vrmlString in zip(
expandSummary(vrmlInfo['id']), expandSummary(vrmlInfo['subid']),
expandSummary(vrmlInfo['name']),
expandSummary(vrmlInfo['display']), vrmlInfo['vrmlString']):
from SimpleSession import modelMap, modelOffset
if (id, subid) in modelMap:
model = modelMap[(id, subid)][0]
mapId, mapSubid = model.id, model.subid
else:
mapId, mapSubid = id + modelOffset, subid
if not vrmlString.startswith("#VRML"):
# BILD object
from Bld2VRML.bld2vrml import Environment
env = Environment()
for line in vrmlString.splitlines():
env.handleLine(line)
env.finish()
vrmlString = env.buildVRML()
vrmlModels = chimera.openModels.open(vrmlString,
type="VRML",
baseId=mapId,
subid=mapSubid,
identifyAs=name)
for vrml in vrmlModels:
vrml.display = display
sm[len(sm)] = vrml
modelMap.setdefault((id, subid), []).extend(vrmlModels)
def restore_state(self, model):
model.name = self.name
model.display = self.display
model.openState.xform = self.xform.create_object()
model.openState.active = self.active
#
# Record how model id number has been remapped.
#
if self.version >= 2:
from SimpleSession import modelMap
modelMap.setdefault((self.id, self.subid), []).append(model)
else:
from SimpleSession import updateOSLmap
updateOSLmap(self.osl_identifier, model.oslIdent())
if self.version >= 3:
p = model.clipPlane
import chimera
p.origin = chimera.Point(*self.clip_plane_origin)
n = chimera.Vector(*self.clip_plane_normal)
if n.length == 0:
n = chimera.Vector(0, 0, -1)
p.normal = n
model.clipPlane = p
model.clipThickness = self.clip_thickness
model.useClipPlane = self.use_clip_plane
if self.version >= 4:
model.useClipThickness = self.use_clip_thickness
def restoreVRML(info):
from SimpleSession import modelOffset
for idInfo, vrmlString in info.items():
id, subid, name = idInfo
from SimpleSession import modelMap
if (id, subid) in modelMap:
model = modelMap[(id, subid)][0]
mapId, mapSubid = model.id, model.subid
else:
mapId, mapSubid = id+modelOffset, subid
vrmlModels = chimera.openModels.open(vrmlString, type="VRML",
baseId=mapId, subid=mapSubid, identifyAs=name)
modelMap.setdefault((id, subid), []).extend(vrmlModels)
def restoreSurfaces(surfDisplayed, surfCategories, surfDict):
for surfDisp in surfDisplayed:
idLookup(surfDisp).surfaceDisplay = 1
for category, atList in surfCategories.items():
for a in atList:
idLookup(a).surfaceCategory = category
for molID, attrs in surfDict.items():
mol = idLookup(molID)
surf = chimera.MSMSModel(mol, attrs['category'])
del attrs['category']
for attr, val in attrs.items():
setattr(surf, attr, val)
chimera.openModels.add([surf], sameAs=mol)
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(surf)
def restoreSurfaces(surfDisplayed, surfCategories, surfDict, surfOpacity): for surfDisp in surfDisplayed: idLookup(surfDisp).surfaceDisplay = 1 for category, atList in surfCategories.items(): for a in atList: idLookup(a).surfaceCategory = category for molID, attrs in surfDict.items(): mol = idLookup(molID) surf = chimera.MSMSModel(mol, attrs['category']) del attrs['category'] for attr, val in attrs.items(): if attr == 'customColors': val = map(getColor, val) setattr(surf, attr, val) chimera.openModels.add([surf], sameAs=mol) from SimpleSession import modelMap modelMap.setdefault((mol.id, mol.subid), []).append(surf) for atomID, opacity in surfOpacity.items(): atom = idLookup(atomID) atom.surfaceOpacity = opacity
def restoreSurfaces(surfDisplayed, surfCategories, surfDict, surfOpacity):
for surfDisp in surfDisplayed:
idLookup(surfDisp).surfaceDisplay = 1
for category, atList in surfCategories.items():
for a in atList:
idLookup(a).surfaceCategory = category
for molID, attrs in surfDict.items():
mol = idLookup(molID)
surf = chimera.MSMSModel(mol, attrs['category'])
del attrs['category']
for attr, val in attrs.items():
if attr == 'customColors':
val = map(getColor, val)
setattr(surf, attr, val)
chimera.openModels.add([surf], sameAs=mol)
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(surf)
for atomID, opacity in surfOpacity.items():
atom = idLookup(atomID)
atom.surfaceOpacity = opacity
def restoreSurfaces(surfInfo):
sm = globals.sessionMap
for mid, category, colorMode, density, name, drawMode, display, \
probeRadius, customColorsSummary, allComponents in zip(
surfInfo['molecule'],
expandSummary(surfInfo['category']),
expandSummary(surfInfo['colorMode']),
expandSummary(surfInfo['density']),
surfInfo['name'],
expandSummary(surfInfo['drawMode']),
expandSummary(surfInfo['display']),
expandSummary(surfInfo['probeRadius']),
surfInfo['customColors'],
expandSummary(surfInfo['allComponents'])
):
mol = idLookup(mid)
s = chimera.MSMSModel(mol, category, allComponents=allComponents)
chimera.openModels.add([s], sameAs=mol)
s.colorMode = colorMode
s.density = density
s.name = name
s.drawMode = drawMode
s.display = display
s.probeRadius = probeRadius
customColors = expandSummary(customColorsSummary)
if customColors:
if len(customColors) != len(s.triangleData()[0]):
from chimera import replyobj
replyobj.error(
"Number of surface vertices for %s (%s) differs from number of colors.\nCustom color scheme not restored\n"
% (mol.oslIdent(), category))
s.colorMode = chimera.MSMSModel.ByAtom
else:
s.customColors = [getColor(c) for c in customColors]
# setting custom colors seems to implicitly
# set the color mode...
s.colorMode = colorMode
sm[len(sm)] = s
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(s)
def restoreSurfaces(surfInfo):
sm = globals.sessionMap
for mid, category, colorMode, density, name, drawMode, display, \
probeRadius, customColorsSummary, allComponents in zip(
surfInfo['molecule'],
expandSummary(surfInfo['category']),
expandSummary(surfInfo['colorMode']),
expandSummary(surfInfo['density']),
surfInfo['name'],
expandSummary(surfInfo['drawMode']),
expandSummary(surfInfo['display']),
expandSummary(surfInfo['probeRadius']),
surfInfo['customColors'],
expandSummary(surfInfo['allComponents'])
):
mol = idLookup(mid)
s = chimera.MSMSModel(mol, category,
allComponents=allComponents)
chimera.openModels.add([s], sameAs=mol)
s.colorMode = colorMode
s.density = density
s.name = name
s.drawMode = drawMode
s.display = display
s.probeRadius = probeRadius
customColors = expandSummary(customColorsSummary)
if customColors:
if len(customColors) != len(s.triangleData()[0]):
from chimera import replyobj
replyobj.error("Number of surface vertices for %s (%s) differs from number of colors.\nCustom color scheme not restored\n" % (mol.oslIdent(), category))
s.colorMode = chimera.MSMSModel.ByAtom
else:
s.customColors = [getColor(c)
for c in customColors]
# setting custom colors seems to implicitly
# set the color mode...
s.colorMode = colorMode
sm[len(sm)] = s
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(s)
def restoreMolecules(srcMolMap):
from tempfile import mktemp
import os
from SimpleSession import modelOffset
for idInfo, fileContents in srcMolMap.items():
fname = mktemp()
f = file(fname, "w")
f.write(fileContents)
f.close() # force a flush
mid, subid, name = idInfo
mols = chimera.openModels.open(fname,
type="session PDB",
baseId=mid + modelOffset,
subid=subid,
identifyAs=name)
os.unlink(fname)
if mols:
globals.atomIDs.update(mols[0].sessionIDs)
delattr(mols[0], 'sessionIDs')
from SimpleSession import modelMap
modelMap.setdefault((mid, subid), []).extend(mols)
def restoreSurfaces(surfInfo):
sm = globals.sessionMap
si = {}
for n in ('molecule', 'name', 'customColors'):
si[n] = surfInfo[n]
for n in ('category', 'colorMode', 'density', 'drawMode', 'display',
'probeRadius', 'allComponents', 'lineWidth', 'pointSize',
'useLighting', 'twoSidedLighting', 'smoothLines',
'transparencyBlendMode', 'oneTransparentLayer'):
si[n] = expandSummary(surfInfo[n])
for i, mid in enumerate(si['molecule']):
mol = idLookup(mid)
s = chimera.MSMSModel(mol,
si['category'][i],
probeRadius=si['probeRadius'][i],
allComponents=si['allComponents'][i],
vertexDensity=si['density'][i])
chimera.openModels.add([s], sameAs=mol)
for n in ('name', 'colorMode', 'drawMode', 'display', 'lineWidth',
'pointSize', 'useLighting', 'twoSidedLighting',
'smoothLines', 'transparencyBlendMode',
'oneTransparentLayer'):
setattr(s, n, si[n][i])
customColors = expandSummary(si['customColors'][i])
if customColors:
if len(customColors) != len(s.triangleData()[0]):
from chimera import replyobj
replyobj.error(
"Number of surface vertices for %s (%s) differs from number of colors.\nCustom color scheme not restored\n"
% (mol.oslIdent(), category))
s.colorMode = chimera.MSMSModel.ByAtom
else:
s.customColors = [getColor(c) for c in customColors]
# setting custom colors seems to implicitly
# set the color mode...
s.colorMode = si['colorMode'][i]
sm[len(sm)] = s
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(s)
def restoreSurfaces(surfInfo):
sm = globals.sessionMap
si = {}
for n in ('molecule', 'name', 'customColors'):
si[n] = surfInfo[n]
for n in ('category', 'colorMode', 'density', 'drawMode',
'display', 'probeRadius', 'allComponents',
'lineWidth', 'pointSize', 'useLighting',
'twoSidedLighting', 'smoothLines',
'transparencyBlendMode', 'oneTransparentLayer'):
si[n] = expandSummary(surfInfo[n])
for i, mid in enumerate(si['molecule']):
mol = idLookup(mid)
s = chimera.MSMSModel(mol, si['category'][i],
probeRadius = si['probeRadius'][i],
allComponents = si['allComponents'][i],
vertexDensity = si['density'][i])
chimera.openModels.add([s], sameAs=mol)
for n in ('name', 'colorMode', 'drawMode', 'display',
'lineWidth', 'pointSize', 'useLighting',
'twoSidedLighting', 'smoothLines',
'transparencyBlendMode', 'oneTransparentLayer'):
setattr(s, n, si[n][i])
customColors = expandSummary(si['customColors'][i])
if customColors:
if len(customColors) != len(s.triangleData()[0]):
from chimera import replyobj
replyobj.error("Number of surface vertices for %s (%s) differs from number of colors.\nCustom color scheme not restored\n" % (mol.oslIdent(), category))
s.colorMode = chimera.MSMSModel.ByAtom
else:
s.customColors = [getColor(c)
for c in customColors]
# setting custom colors seems to implicitly
# set the color mode...
s.colorMode = si['colorMode'][i]
sm[len(sm)] = s
from SimpleSession import modelMap
modelMap.setdefault((mol.id, mol.subid), []).append(s)
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
openModelsArgs = {}
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain 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'])
):
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])
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
if molInfo['optional']:
for attrName, info in molInfo['optional'].items():
for a, val in zip(items, expandSummary(info)):
if val is not None:
setattr(a, attrName, val)
resStart = len(items)
for mid, name, chain, pos, insert, rcid, lcid, ss, ribbonDrawMode, \
ribbonDisplay, label in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
resInfo['position'],
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label'])
):
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.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
if resInfo['optional']:
residues = items[resStart:]
for attrName, info in resInfo['optional'].items():
for a, val in zip(residues, expandSummary(info)):
if val is not None:
setattr(a, attrName, val)
atomStart = len(items)
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, surfaceDisplay, surfaceCategory, surfaceOpacity, radius, vdw, \
idatmType 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['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['idatmType'])
):
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
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if idatmType:
a.idatmType = idatmType
if atomInfo['optional']:
atoms = items[atomStart:]
for attrName, info in atomInfo['optional'].items():
for a, val in zip(atoms, expandSummary(info)):
if val is not None:
setattr(a, attrName, val)
for atoms, drawMode, display in zip(
bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display'])
):
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
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 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):
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
openModelsArgs = {}
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain 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'])
):
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])
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
for mid, name, chain, pos, insert, rcid, lcid, ss, ribbonDrawMode, \
ribbonDisplay, label in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
resInfo['position'],
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label'])
):
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.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, surfaceDisplay, surfaceCategory, surfaceOpacity, radius, vdw, \
bfactor, occupancy, charge, idatmType 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['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['bfactor']),
expandSummary(atomInfo['occupancy']),
expandSummary(atomInfo['charge']),
expandSummary(atomInfo['idatmType'])
):
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
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if bfactor is not None:
a.bfactor = bfactor
if occupancy is not None:
a.occupancy = occupancy
if charge is not None:
a.charge = charge
if idatmType:
a.idatmType = idatmType
for atoms, drawMode, display in zip(bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display'])):
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
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
