def show_curve(self,
radius=0,
band_length=0,
segment_subdivisions=10,
circle_subdivisions=15):
m = self.molecule
if m is None:
return
import tube
s, plist = tube.tube_through_atoms(m.atoms, radius, band_length,
segment_subdivisions,
circle_subdivisions)
if s is None:
return
s.name = 'path tracer curve'
self.curve_parameters = (radius, band_length, segment_subdivisions)
self.curve_model = s
from chimera import addModelClosedCallback
addModelClosedCallback(s, self.curve_model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(s)
def make_model(self, length, thickness, rgb, label, xy_offset, label_rgb,
model_id):
m = chimera.Molecule()
m.name = 'scale bar'
#
# Need to create a residue because atom without residue causes
# unknown C++ exceptions.
#
rid = chimera.MolResId(1)
r = m.newResidue('sb', rid)
atoms = []
for name, pos in (('1', (-length / 2.0, 0, 0)), ('2', (length / 2.0, 0,
0)),
('label', (xy_offset[0],
xy_offset[1] + thickness / 2.0, 0))):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
c = chimera.Coord()
c.x, c.y, c.z = pos
a.setCoord(c) # a.coord = c does not work
a.display = 0
atoms.append(a)
m.atom1, m.atom2, m.label_atom = atoms
m.label_atom.color = background_color()
m.label_atom.display = 1
b = m.newBond(m.atom1, m.atom2)
b.display = b.Always
b.drawMode = b.Stick
b.radius = thickness / 2.0
b.color = chimera_color(rgb)
b.halfbond = 0
m.label_atom.label = label
m.label_atom.labelColor = chimera_color(label_rgb)
self.model = m
if model_id == None:
id, subid = (self.model_id(), chimera.openModels.Default)
else:
id, subid = model_id
chimera.openModels.add([m], baseId=id, subid=subid)
chimera.addModelClosedCallback(m, self.model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(m)
m.openState.active = False
z_near, z_far = clip_plane_positions()
self.set_depth(.5 * (z_near + z_far))
self.set_screen_position(self.screen_position)
self.orientation_cb()
return m
def make_model(self, length, thickness, rgb, label, xy_offset, label_rgb,
model_id):
m = chimera.Molecule()
m.name = 'scale bar'
#
# Need to create a residue because atom without residue causes
# unknown C++ exceptions.
#
rid = chimera.MolResId(1)
r = m.newResidue('sb', rid)
atoms = []
for name, pos in (('1', (-length/2.0, 0, 0)),
('2', (length/2.0, 0, 0)),
('label',
(xy_offset[0], xy_offset[1] + thickness/2.0, 0))):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
c = chimera.Coord()
c.x, c.y, c.z = pos
a.setCoord(c) # a.coord = c does not work
a.display = 0
atoms.append(a)
m.atom1, m.atom2, m.label_atom = atoms
m.label_atom.color = background_color()
m.label_atom.display = 1
b = m.newBond(m.atom1, m.atom2)
b.display = b.Always
b.drawMode = b.Stick
b.radius = thickness/2.0
b.color = chimera_color(rgb)
b.halfbond = 0
m.label_atom.label = label
m.label_atom.labelColor = chimera_color(label_rgb)
self.model = m
if model_id == None:
id, subid = (self.model_id(), chimera.openModels.Default)
else:
id, subid = model_id
chimera.openModels.add([m], baseId = id, subid = subid)
chimera.addModelClosedCallback(m, self.model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(m)
m.openState.active = False
z_near, z_far = clip_plane_positions()
self.set_depth(.5 * (z_near + z_far))
self.set_screen_position(self.screen_position)
self.orientation_cb()
return m
def restoreSession_RibbonStyleEditor(): import SimpleSession import RibbonStyleEditor userScalings = [] userXSections = [] userResidueClasses = [] residueData = [(6, 'Chimera default', 'rounded', 'unknown'), (7, 'Chimera default', 'rounded', 'unknown'), (8, 'Chimera default', 'rounded', 'unknown'), (9, 'Chimera default', 'rounded', 'unknown'), (10, 'Chimera default', 'rounded', 'unknown'), (11, 'Chimera default', 'rounded', 'unknown'), (12, 'Chimera default', 'rounded', 'unknown'), (13, 'Chimera default', 'rounded', 'unknown'), (14, 'Chimera default', 'rounded', 'unknown'), (15, 'Chimera default', 'rounded', 'unknown'), (16, 'Chimera default', 'rounded', 'unknown'), (17, 'Chimera default', 'rounded', 'unknown')] flags = RibbonStyleEditor.NucleicDefault1 SimpleSession.registerAfterModelsCB(RibbonStyleEditor.restoreState, (userScalings, userXSections, userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor():
import SimpleSession
import RibbonStyleEditor
userScalings = [('licorice', [[0.35, 0.35], [0.35, 0.35], [0.35, 0.35], [0.35, 0.35, 0.35, 0.35], [0.35, 0.35]])]
userXSections = []
userResidueClasses = []
residueData = [(6, 'Chimera default', 'rounded', u'unknown'), (7, 'Chimera default', 'rounded', u'unknown'), (8, 'Chimera default', 'rounded', u'unknown'), (9, 'Chimera default', 'rounded', u'unknown'), (10, 'Chimera default', 'rounded', u'unknown'), (11, 'Chimera default', 'rounded', u'unknown')]
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(RibbonStyleEditor.restoreState,
(userScalings, userXSections,
userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor():
import SimpleSession
import RibbonStyleEditor
userScalings = []
userXSections = []
userResidueClasses = []
residueData = []
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(
RibbonStyleEditor.restoreState,
(userScalings, userXSections, userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor(): import SimpleSession import RibbonStyleEditor userScalings = [] userXSections = [] userResidueClasses = [] residueData = [(13, 'Chimera default', 'rounded', 'unknown'), (14, 'Chimera default', 'rounded', 'unknown'), (15, 'Chimera default', 'rounded', 'unknown'), (16, 'Chimera default', 'rounded', 'unknown'), (17, 'Chimera default', 'rounded', 'unknown'), (18, 'Chimera default', 'rounded', 'unknown'), (19, 'Chimera default', 'rounded', 'unknown'), (20, 'Chimera default', 'rounded', 'unknown'), (21, 'Chimera default', 'rounded', 'unknown'), (22, 'Chimera default', 'rounded', 'unknown'), (23, 'Chimera default', 'rounded', 'unknown'), (24, 'Chimera default', 'rounded', 'unknown'), (25, 'Chimera default', 'rounded', 'unknown'), (26, 'Chimera default', 'rounded', 'unknown'), (27, 'Chimera default', 'rounded', 'unknown'), (28, 'Chimera default', 'rounded', 'unknown'), (29, 'Chimera default', 'rounded', 'unknown'), (30, 'Chimera default', 'rounded', 'unknown'), (31, 'Chimera default', 'rounded', 'unknown'), (32, 'Chimera default', 'rounded', 'unknown'), (33, 'Chimera default', 'rounded', 'unknown'), (34, 'Chimera default', 'rounded', 'unknown'), (35, 'Chimera default', 'rounded', 'unknown'), (36, 'Chimera default', 'rounded', 'unknown'), (37, 'Chimera default', 'rounded', 'unknown'), (38, 'Chimera default', 'rounded', 'unknown')] flags = RibbonStyleEditor.NucleicDefault1 SimpleSession.registerAfterModelsCB(RibbonStyleEditor.restoreState, (userScalings, userXSections, userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor():
import SimpleSession
import RibbonStyleEditor
userScalings = []
userXSections = []
userResidueClasses = []
residueData = [(2, 'Chimera default', 'rounded', u'unknown'),
(3, 'Chimera default', 'rounded', u'unknown')]
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(
RibbonStyleEditor.restoreState,
(userScalings, userXSections, userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor():
import SimpleSession
import RibbonStyleEditor
userScalings = [('licorice', [[0.35, 0.35], [0.35, 0.35], [0.35, 0.35],
[0.35, 0.35, 0.35, 0.35], [0.35, 0.35]])]
userXSections = []
userResidueClasses = []
residueData = [(1, 'licorice', 'rounded', u'amino acid'),
(2, 'licorice', 'rounded', u'amino acid'),
(3, 'licorice', 'rounded', u'amino acid'),
(4, 'licorice', 'rounded', u'amino acid'),
(5, 'licorice', 'rounded', u'amino acid'),
(6, 'licorice', 'rounded', u'amino acid'),
(7, 'licorice', 'rounded', u'amino acid'),
(8, 'licorice', 'rounded', u'amino acid'),
(9, 'licorice', 'rounded', u'amino acid'),
(10, 'licorice', 'rounded', u'amino acid'),
(11, 'licorice', 'rounded', u'amino acid'),
(12, 'licorice', 'rounded', u'amino acid'),
(13, 'licorice', 'rounded', u'amino acid'),
(14, 'licorice', 'rounded', u'amino acid'),
(15, 'licorice', 'rounded', u'amino acid'),
(16, 'licorice', 'rounded', u'amino acid'),
(17, 'licorice', 'rounded', u'amino acid'),
(18, 'licorice', 'rounded', u'amino acid'),
(19, 'licorice', 'rounded', u'amino acid'),
(20, 'licorice', 'rounded', u'amino acid'),
(21, 'licorice', 'rounded', u'amino acid'),
(22, 'licorice', 'rounded', u'amino acid'),
(23, 'licorice', 'rounded', u'amino acid'),
(24, 'licorice', 'rounded', u'amino acid'),
(25, 'licorice', 'rounded', u'amino acid'),
(26, 'licorice', 'rounded', u'amino acid'),
(27, 'licorice', 'rounded', u'amino acid'),
(28, 'licorice', 'rounded', u'amino acid'),
(29, 'licorice', 'rounded', u'amino acid'),
(30, 'licorice', 'rounded', u'amino acid'),
(31, 'licorice', 'rounded', u'amino acid'),
(32, 'licorice', 'rounded', u'amino acid'),
(33, 'licorice', 'rounded', u'amino acid'),
(34, 'licorice', 'rounded', u'amino acid'),
(35, 'licorice', 'rounded', u'amino acid'),
(36, 'licorice', 'rounded', u'amino acid'),
(37, 'licorice', 'rounded', u'amino acid'),
(38, 'licorice', 'rounded', u'amino acid'),
(39, 'licorice', 'rounded', u'amino acid'),
(40, 'licorice', 'rounded', u'amino acid'),
(41, 'licorice', 'rounded', u'unknown')]
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(
RibbonStyleEditor.restoreState,
(userScalings, userXSections, userResidueClasses, residueData, flags))
def restoreSession_RibbonStyleEditor():
import RibbonStyleEditor
import SimpleSession
userScalings = []
userXSections = []
userResidueClasses = []
residueData = [
(1, "Chimera default", "rounded", u"unknown"),
(2, "Chimera default", "rounded", u"unknown"),
]
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(
RibbonStyleEditor.restoreState,
(userScalings, userXSections, userResidueClasses, residueData, flags),
)
def restoreState(mdata, sdata={}):
for name, info in sdata.items():
addStyle(name, info)
for mid in mdata:
m = SimpleSession.idLookup(mid)
md = _molDict(m)
smd = mdata[mid]
for k in smd:
if k.endswith('params'):
md[k] = smd[k]
rds = md[RESIDUES]
srds = smd[RESIDUES]
for rid in srds:
r = SimpleSession.idLookup(rid)
rd = rds[r] = srds[rid]
rd[SUGAR] = []
rd[BASE] = []
_needRebuild[m] = None
def restoreSession_RibbonStyleEditor():
import SimpleSession
import RibbonStyleEditor
userScalings = []
userXSections = []
userResidueClasses = []
residueData = [
(3, "Chimera default", "rounded", "unknown"),
(4, "Chimera default", "rounded", "unknown"),
(5, "Chimera default", "rounded", "unknown"),
(6, "Chimera default", "rounded", "unknown"),
(7, "Chimera default", "rounded", "unknown"),
(8, "Chimera default", "rounded", "unknown"),
]
flags = RibbonStyleEditor.NucleicDefault1
SimpleSession.registerAfterModelsCB(
RibbonStyleEditor.restoreState, (userScalings, userXSections, userResidueClasses, residueData, flags)
)
def _sessionCB(self, trigger, myData, sesFile):
import SimpleSession
if self.reference:
if isinstance(self.reference, StructureSequence):
mid = None
ss = self.reference.saveInfo()
elif isinstance(self.reference, Molecule):
mid = SimpleSession.sessionID(self.reference)
ss = None
else:
mid = None
ss = None
else:
mid = None
ss = None
if self.parser:
parserData = self.parser.sessionData()
else:
parserData = None
if self.service:
serviceData = self.service.sessionData()
else:
serviceData = None
data = (3, # version
mid, # molecule
ss, # StructureSeq
self.sequence, # input seq
self.program, # program
self.basename, # name
self.showOne, # one hit per PDB
parserData, # parser
serviceData, # service
self.blastTable.getRestoreInfo()) # GUI
print >> sesFile, """
try:
from blastpdb.gui import sessionRestore
sessionRestore(%s)
except:
reportRestoreError("Error restoring Blast dialog")
""" % SimpleSession.sesRepr(data)
def save_session(trigger, closure, file):
"""convert data to session data"""
if not _data:
return
# molecular data
mdata = {}
for m in _data:
md = _data[m]
mid = SimpleSession.sessionID(m)
smd = mdata[mid] = {}
for k in md:
if k.endswith('params'):
smd[k] = md[k]
rds = md[RESIDUES]
srds = smd[RESIDUES] = {}
for r in rds:
rid = SimpleSession.sessionID(r)
rd = rds[r]
srd = srds[rid] = {}
for k in rd:
if k.endswith('params'):
srd[k] = rd[k]
srd['side'] = rd['side']
# save restoring code in session
restoring_code = (
"""
def restoreNucleotides():
import NucleicAcids as NA
NA.restoreState(%s, %s)
try:
restoreNucleotides()
except:
reportRestoreError('Error restoring Nucleotides')
""")
file.write(restoring_code % (
SimpleSession.sesRepr(mdata),
SimpleSession.sesRepr(userStyles)
))
def restoreAnimation():
"A method to unpickle and restore animation objects"
# Scenes must be unpickled after restoring transitions, because each
# scene links to a 'scene' transition. Likewise, keyframes must be
# unpickled after restoring scenes, because each keyframe links to a scene.
# The unpickle process is left to the restore* functions, it's
# important that it doesn't happen prior to calling those functions.
import SimpleSession
from Animate.Session import restoreKeyframes, restoreScenes, restoreTransitions
SimpleSession.registerAfterModelsCB(restoreTransitions, trPickle)
SimpleSession.registerAfterModelsCB(restoreScenes, scPickle)
SimpleSession.registerAfterModelsCB(restoreKeyframes, kfPickle)
def restoreState(args): if len(args) == 4: userScalings, userXSections, userResidueClasses, residueData = args flags = 0 else: userScalings, userXSections, userResidueClasses, residueData, flags = args import scaling, xsection, atoms import chimera, SimpleSession for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): m.updateRibbonData() scData = scaling.sessionRestoreUsed(userScalings) xsData = xsection.sessionRestoreUsed(userXSections) rcData = atoms.sessionRestoreUsed(userResidueClasses) for rId, sc, xs, rc in residueData: r = SimpleSession.idLookup(rId) atoms.sessionRestoreResidue(r, rc, rcData, flags) scaling.sessionRestoreResidue(r, sc, scData) xsection.sessionRestoreResidue(r, xs, xsData)
def restoreAnimation(): 'A method to unpickle and restore animation objects' # Scenes must be unpickled after restoring transitions, because each # scene links to a 'scene' transition. Likewise, keyframes must be # unpickled after restoring scenes, because each keyframe links to a scene. # The unpickle process is left to the restore* functions, it's # important that it doesn't happen prior to calling those functions. import SimpleSession from Animate.Session import restoreTransitions from Animate.Session import restoreScenes from Animate.Session import restoreKeyframes SimpleSession.registerAfterModelsCB(restoreTransitions, trPickle) SimpleSession.registerAfterModelsCB(restoreScenes, scPickle) SimpleSession.registerAfterModelsCB(restoreKeyframes, kfPickle)
for name, fpos in formattedPositions.items():
positions[name] = deformatPosition(fpos)
import Midas
if modelOffset == 0:
Midas.positions.clear()
Midas.positions.update(positions)
positionStack = []
Midas._positionStack = map(deformatPosition, positionStack)
def delayedMidasBase():
try:
restoreMidasBase()
except:
reportRestoreError('Error restoring Midas base state')
import SimpleSession
SimpleSession.registerAfterModelsCB(delayedMidasBase)
try:
import StructMeasure
from StructMeasure.DistMonitor import restoreDistances
registerAfterModelsCB(restoreDistances, 1)
except:
reportRestoreError("Error restoring distances in session")
def restoreRemainder():
from SimpleSession.versions.v45 import restoreWindowSize, \
restoreOpenStates, restoreSelections, restoreFontInfo, \
restoreOpenModelsAttrs, restoreModelClip
except:
reportRestoreError("Error restoring color key")
def restore2DLabelDialog(info):
from chimera.dialogs import find
from Ilabel.gui import IlabelDialog
dlg = find(IlabelDialog.name)
if dlg is not None:
dlg.destroy()
dlg = find(IlabelDialog.name, create=True)
dlg._restoreSession(info)
import SimpleSession
SimpleSession.registerAfterModelsCB(restore2DLabelDialog, {'mouse func': 'labeling', 'sel ranges': (), 'dialog shown': 1})
def restoreRemainder():
from SimpleSession.versions.v65 import restoreWindowSize, \
restoreOpenStates, restoreSelections, restoreFontInfo, \
restoreOpenModelsAttrs, restoreModelClip, restoreSilhouettes
curSelIds = []
savedSels = []
openModelsAttrs = { 'cofrMethod': 2 }
windowSize = (1024, 781)
xformMap = {0: (((-0.34821455627968, 0.82726846257295, 0.44087811652103), 9.9995089373332), (0.0076537672682732, 0.0083331466146478, -0.0095913043915013), False), 1: (((-0.99040907112338, 0.13815836179107, 0.0014624991412663), 109.62935189875), (8.9189222591104, -0.045770457294621, -0.032931556893357), False), 2: (((-0.20080631594196, -0.92498261478313, 0.32262049815036), 18.985788096111), (17.497129733092, -0.68455407611151, -0.47980035902674), False), 3: (((0.99205523056863, 0.020289399059421, -0.12415619109504), 170.88474103051), (-0.1169711633136, -8.6869766220186, 0.11207397706245), True), 4: (((0.23529125830917, 0.94204993508282, 0.23912328112031), 96.859237242746), (8.9195514371968, -9.2219927891895, -0.28512231169757), False), 5: (((0.73008849334292, 0.68289739957367, 0.024938595465521), 170.41609346508), (18.067194686271, -9.1650094893277, -1.4626137937459), False)}
fontInfo = {'face': (u'Sans Serif', 'Bold', 12)}
clipPlaneInfo = {}
def _rebuild(triggerName, closure, changes):
"""'monitor changes' trigger handler"""
global _rebuilding
if _block or not _needRebuild or _rebuilding:
return
_rebuilding = True
for mol in _needRebuild:
md = _molDict(mol)
try:
if md[VRML]:
v = md[VRML]
md[VRML] = None
chimera.openModels.close(v)
except (KeyError, chimera.error):
# Either there's no previous VRML
# model to close or it has already
# been closed.
pass
# figure out which residues are of which type because
# ladder needs knowledge about the whole molecule
rds = md[RESIDUES]
sides = {}
for k in SideOptions:
sides[k] = []
for r in rds.keys():
if r.__destroyed__:
# Sometimes the residues are gone,
# but there's a still reference to them.
del rds[r]
continue
sides[rds[r]['side']].append(r)
if not rds:
# no residues to track in molecule
v = md[VRML]
if v:
chimera.openModels.close(v)
del _data[mol]
continue
allResidues = set(rds.keys())
# make new VRML nodes
hideSugars = set()
hideBases = set()
residues = sides['ladder']
if not residues:
md.pop('ladder params', None)
else:
# redo all ladder nodes
hideSugars.update(residues)
hideBases.update(residues)
make_ladder(mol, residues, rds, **md['ladder params'])
residues = sides['fill/slab']
if residues:
hideBases.update(make_slab(mol, residues, rds))
residues = sides['tube/slab']
if residues:
hideSugars.update(residues)
make_tube(mol, residues, rds)
hideBases.update(make_slab(mol, residues, rds))
residues = sides['orient']
if residues:
make_orient(mol, residues, rds)
# make sure sugar/base atoms are hidden/shown
showSugars = allResidues - hideSugars
showBases = allResidues - hideBases
showResidues = showSugars - hideBases
showSugars.difference_update(showResidues)
showBases.difference_update(showResidues)
setHideAtoms(False, AlwaysRE, NeverRE, showResidues)
setHideAtoms(False, BackboneSugarRE, NeverRE, showSugars)
nonRibbonSugars = [r for r in hideSugars
if not r.ribbonDisplay or not r.hasRibbon()]
setHideAtoms(False, BackboneRE, NeverRE, nonRibbonSugars)
setHideAtoms(False, BaseAtomsRE, BaseExceptRE, showBases)
# open VRML model
nodes = sum((rds[r][SUGAR] + rds[r][BASE] for r in rds), [])
if nodes:
vrml = nodesToVRML(nodes)
vList = chimera.openModels.open(vrml, type='VRML',
sameAs=mol, hidden=True,
identifyAs='%s - Nucleotides' % mol.name)
assert(len(vList) == 1)
v = vList[0]
mol.addAssociatedModel(v)
md[VRML] = v
SimpleSession.noAutoRestore(v)
_needRebuild.clear()
# Since changing hide bits doesn't cause a rebuilding
# of the molecule's display list, rebuild them all!
chimera.viewer.invalidateCache()
_rebuilding = False
