def sessionRestore(sessionData):
from SimpleSession import idLookup
version = sessionData[0]
if version == 1:
(v, mid, program, name, parserData, serviceData,
tableData) = sessionData
mol = idLookup(mid)
seq = None
showOne = False
elif version == 2:
(v, mid, seq, program, name, parserData, serviceData,
tableData) = sessionData
mol = idLookup(mid)
showOne = False
elif version == 3:
(v, mid, ss, seq, program, name, showOne,
parserData, serviceData, tableData) = sessionData
if mid is not None:
mol = idLookup(mid)
elif ss is not None:
mol = chimera.Sequence.restoreSequence(ss)
else:
mol = None
else:
raise ValueError("unknown blastpdb version: %s" % str(version))
BlastResultsDialog(mol=mol, seq=seq, sessionData=(program, name,
showOne,
parserData,
serviceData,
tableData))
def _sessionRestore(self, info):
from SimpleSession import idLookup
for bondID, anchorID, delta, rotID in info:
bond = idLookup(bondID)
dup = False
for br in self.rotations.values():
if br.bond == bond:
from chimera import replyobj
replyobj.error("Active torsion in session file same as"
" existing active torsion; skipping")
dup = True
break
if dup:
continue
anchorSide = idLookup(anchorID)
if delta:
# need to make rotation have same delta as original
bondRot = BondRot(bond)
bondRot.angle = (-delta, anchorSide)
bondRot.destroy()
if rotID in self.rotations:
rotID = None
br = self.rotationForBond(bond, requestedID=rotID)
br.anchorSide = anchorSide
if delta:
br.set(delta)
def sessionRestore(sessionData):
from SimpleSession import idLookup
version, resID, resType, rotIDs, bbdep, libName, tableInfo = sessionData
from Rotamers import libraries
for lib in libraries:
if lib.displayName == libName:
break
else:
raise ValueError("Cannot find library")
sesData = (bbdep, [idLookup(rot) for rot in rotIDs], tableInfo)
RotamerDialog(idLookup(resID), resType, lib, sessionData=sesData)
def sessionRestore(sessionData):
from SimpleSession import idLookup
version, resID, resType, rotIDs, bbdep, libName, tableInfo = sessionData
from Rotamers import libraries
for lib in libraries:
if lib.displayName == libName:
break
else:
raise ValueError("Cannot find library")
sesData = (bbdep, [idLookup(rot) for rot in rotIDs], tableInfo)
RotamerDialog(idLookup(resID), resType, lib, sessionData=sesData)
def _restoreNMTSession_v1(self, data):
from SimpleSession import idLookup
self.molecule = idLookup(data["molecule"])
self.title = "Normal Modes for %s" % self.molecule.name
self.atoms = [idLookup(sid) for sid in data["atoms"]]
self.modeData = list()
for index, (active, freq, dl) in enumerate(data["modeData"]):
self.modeData.append(
_NormalModeProxy(index, active, freq, [Vector(*v) for v in dl],
self))
self._restoreHandler = chimera.triggers.addHandler(
END_RESTORE_SESSION, self._restoreMovieDialog, None)
def _restoreSession(self, targetMap, version=1): from SimpleSession import idLookup if version == 1: for info, atomIDs in targetMap.items(): rgba, anisoParams = info scale, smoothing = anisoParams self.showAniso([idLookup(atomID) for atomID in atomIDs], color=rgba, scale=scale, smoothing=smoothing) return if version == 2: for info, atomIDs in targetMap.items(): anisoParams, colors = info scale, smoothing, axisFactor = anisoParams ellipsoidColor, axisColor, ellipseColor = colors if ellipseColor: ellipseFactor = 1.0 else: ellipseFactor = None self.showAniso([idLookup(atomID) for atomID in atomIDs], color=ellipsoidColor, showEllipsoid=ellipsoidColor, axisColor=axisColor, axisFactor=axisFactor, ellipseColor=ellipseColor, ellipseFactor=ellipseFactor, scale=scale, smoothing=smoothing) return if version == 3: for info, atomIDs in targetMap.items(): anisoParams, colors = info scale, smoothing, axisFactor, ellipseFactor = anisoParams ellipsoidColor, axisColor, ellipseColor = colors self.showAniso([idLookup(atomID) for atomID in atomIDs], color=ellipsoidColor, showEllipsoid=ellipsoidColor, axisColor=axisColor, axisFactor=axisFactor, ellipseColor=ellipseColor, ellipseFactor=ellipseFactor, scale=scale, smoothing=smoothing) return for info, atomIDs in targetMap.items(): anisoParams, colors = info scale, smoothing, axisFactor, ellipseFactor, \ axisThickness, ellipseThickness = anisoParams ellipsoidColor, axisColor, ellipseColor = colors self.showAniso([idLookup(atomID) for atomID in atomIDs], color=ellipsoidColor, showEllipsoid=ellipsoidColor, axisColor=axisColor, axisFactor=axisFactor, axisThickness=axisThickness, ellipseColor=ellipseColor, ellipseFactor=ellipseFactor, ellipseThickness=ellipseThickness, scale=scale, smoothing=smoothing)
def sessionRestore(sessionData):
from SimpleSession import idLookup
version = sessionData[0]
if version == 1:
ignore, name, molIdList, infoList, tableData = sessionData
molList = [ idLookup(mid) for mid in molIdList ]
for m, info in zip(molList, infoList):
assignModbaseInfo(m, info)
else:
raise ValueError("unknown ModBase version: %s" % str(version))
ModBaseDialog(name, molList, tableData=tableData)
def _restoreSession(self, planeData, fromGeom=False): from SimpleSession import getColor, idLookup maxNumber = 0 for data, atomIDs in planeData.items(): number, name, cmpVal, radius, thickness, colorID, origin, normal\ = data atoms = [idLookup(a) for a in atomIDs] self._instantiatePlane(number, name, self.planeOrdinal + number, getColor(colorID), radius, thickness, self._getSourceModel(atoms), atoms, chimera.Plane(Point(*origin), Vector(*normal))) maxNumber = max(number, maxNumber) self.planeOrdinal += maxNumber
def _restoreSession(self, axisData, fromGeom=False):
from SimpleSession import getColor, idLookup
for i, data in enumerate(axisData.keys()):
atomIDs = axisData[data]
try:
number, name, cmpVal, radius, colorID, extents, center,\
direction = data
except ValueError:
number = i + 1
name, cmpVal, radius, colorID, extents, center,\
direction = data
atoms = [idLookup(a) for a in atomIDs]
self._instantiateAxis(number, name, getColor(colorID), radius,
self._getSourceModel(atoms), atoms,
Point(*center), Vector(*direction), extents)
def create_object(self, id_to_marker):
m1 = id_to_marker[self.marker_id_1]
m2 = id_to_marker[self.marker_id_2]
if self.version >= 2:
from SimpleSession import idLookup
bond = idLookup(self.bond_session_id)
else:
bond = None
import markerset
l = markerset.Link(m1, m2, self.rgba, self.radius, bond = bond)
l.bond.display = self.displayed
if self.extra_attributes:
m.extra_attributes = self.extra_attributes
return l
def id_to_model(id):
model = None
if isinstance(id, tuple) and len(id) == 3:
from SimpleSession import modelMap
mlist = [m for m in modelMap.get(id[:2], []) if m.name == id[2]]
if len(mlist) == 1:
model = mlist[0]
else:
global id_to_model_failed
id_to_model_failed.add(id)
elif not id is None:
from SimpleSession import idLookup
model = idLookup(id)
return model
def create_object(self, id_to_marker):
m1 = id_to_marker[self.marker_id_1]
m2 = id_to_marker[self.marker_id_2]
if self.version >= 2:
from SimpleSession import idLookup
bond = idLookup(self.bond_session_id)
else:
bond = None
import markerset
l = markerset.Link(m1, m2, self.rgba, self.radius, bond=bond)
l.bond.display = self.displayed
if self.extra_attributes:
m.extra_attributes = self.extra_attributes
return l
def restoreSeqInspectors(info):
global _seqInspectors
from SimpleSession import idLookup
for seqName, molID, seqsInfo, mavInfo in info:
mol = idLookup(molID)
for seq in mol.sequences():
if seq.name == seqName:
break
else:
continue
if seq in _seqInspectors:
continue
from MultAlignViewer.MAViewer import restoreMAV
from chimera.Sequence import restoreSequence
mav = restoreMAV([restoreSequence(seqInfo) for seqInfo in seqsInfo],
mavInfo)
_addSeqInspector(seq, mav=mav)
def restoreSeqInspectors(info): global _seqInspectors from SimpleSession import idLookup for seqName, molID, seqsInfo, mavInfo in info: mol = idLookup(molID) for seq in mol.sequences(): if seq.name == seqName: break else: continue if seq in _seqInspectors: continue from MultAlignViewer.MAViewer import restoreMAV from chimera.Sequence import restoreSequence mav = restoreMAV([restoreSequence(seqInfo) for seqInfo in seqsInfo], mavInfo) _addSeqInspector(seq, mav=mav)
def create_object(self, marker_set):
if self.version >= 2:
from SimpleSession import idLookup
atom = idLookup(self.atom_session_id)
else:
atom = None
import markerset
m = markerset.Marker(marker_set, self.id, self.xyz, self.rgba, self.radius,
atom = atom)
m.atom.display = self.displayed
m.set_note(self.note)
m.set_note_rgba(self.note_rgba)
m.show_note(self.note_shown)
if self.extra_attributes:
m.extra_attributes = self.extra_attributes
return m
def create_object(self):
import markerset
ms = markerset.Marker_Set(self.name)
ms.next_marker_id = self.next_marker_id
ms.file_path = self.file_path
mm = self.marker_model
if mm:
if self.version >= 3:
from SimpleSession import idLookup
m = idLookup(self.molecule_session_id)
ms.set_marker_molecule(m)
import markerset
markerset.msc.open_models_cb(None, None, [m])
else:
from SimpleSession import modelOffset
model_id = (mm.id + modelOffset, mm.subid)
m = ms.marker_model(model_id)
if self.version >= 2:
m.color = markerset.chimera_color(self.color)
id_to_marker = {}
for m in self.markers:
marker = m.create_object(ms)
id_to_marker[marker.id] = marker
for l in self.links:
l.create_object(id_to_marker)
if self.extra_attributes:
ms.extra_attributes = self.extra_attributes
if mm and ms.molecule:
mm.restore_state(ms.molecule)
cm = self.curve_model
if cm:
radius, band_length, subdivisions = self.curve_parameters
ms.show_curve(radius, band_length, subdivisions)
cm.restore_state(ms.curve_model)
return ms
def create_object(self):
import markerset
ms = markerset.Marker_Set(self.name)
ms.next_marker_id = self.next_marker_id
ms.file_path = self.file_path
mm = self.marker_model
if mm:
if self.version >= 3:
from SimpleSession import idLookup
m = idLookup(self.molecule_session_id)
ms.set_marker_molecule(m)
import markerset
markerset.msc.open_models_cb(None, None, [m])
else:
from SimpleSession import modelOffset
model_id = (mm.id + modelOffset, mm.subid)
m = ms.marker_model(model_id)
if self.version >= 2:
m.color = markerset.chimera_color(self.color)
id_to_marker = {}
for m in self.markers:
marker = m.create_object(ms)
id_to_marker[marker.id] = marker
for l in self.links:
l.create_object(id_to_marker)
if self.extra_attributes:
ms.extra_attributes = self.extra_attributes
if mm and ms.molecule:
mm.restore_state(ms.molecule)
cm = self.curve_model
if cm:
radius, band_length, subdivisions = self.curve_parameters
ms.show_curve(radius, band_length, subdivisions)
cm.restore_state(ms.curve_model)
return ms
def create_object(self, marker_set):
if self.version >= 2:
from SimpleSession import idLookup
atom = idLookup(self.atom_session_id)
else:
atom = None
import markerset
m = markerset.Marker(marker_set,
self.id,
self.xyz,
self.rgba,
self.radius,
atom=atom)
m.atom.display = self.displayed
m.set_note(self.note)
m.set_note_rgba(self.note_rgba)
m.show_note(self.note_shown)
if self.extra_attributes:
m.extra_attributes = self.extra_attributes
return m
def restoreTorsions(info): from SimpleSession import idLookup from BondRotMgr import bondRotMgr for bondID, atom1ID, atom2ID in info: br = bondRotMgr.rotationForBond(idLookup(bondID)) br.anchorSide = idLookup(atom1ID)
def restoreAngles(angleInfo): from SimpleSession import idLookup for atomIDs in angleInfo: addAngle([idLookup(aID) for aID in atomIDs])
