def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c],
serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(
serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def parse_surface_pieces(spec):
from chimera.specifier import evalSpec
sel = evalSpec(spec)
import Surface
plist = Surface.selected_surface_pieces(sel)
return plist
def inertia(operation, objects, showEllipsoid = True, color = None,
perChain = False):
from chimera import specifier
try:
sel = specifier.evalSpec(objects)
except:
raise CommandError, 'Bad object specifier "%s"' % objects
if not color is None:
from Commands import parse_color
color = parse_color(color)
atoms = sel.atoms()
if atoms:
import inertia
if perChain:
xf = atoms[0].molecule.openState.xform
mname = molecules_name(list(set([a.molecule for a in atoms])))
s = inertia.surface_model(None, xf, 'ellipsoids ' + mname)
for achain in atoms_by_chain(atoms):
p = inertia.atoms_inertia_ellipsoid(achain, showEllipsoid,
color, s)
if p:
p.oslName = achain[0].residue.id.chainId
else:
inertia.atoms_inertia_ellipsoid(atoms, showEllipsoid, color)
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes = False)
if plist:
import inertia
inertia.surface_inertia_ellipsoid(plist, showEllipsoid, color)
def split_molecules(cmdname, args):
fields = args.split()
from chimera import openModels, Molecule
if len(fields) >= 1:
from chimera import specifier
sel = specifier.evalSpec(fields[0])
mlist = sel.molecules()
else:
mlist = openModels.list(modelTypes=[Molecule])
if len(mlist) == 0:
from Midas.midas_text import error
error('%s: No molecules to split.' % cmdname)
return
slist = []
for m in mlist:
clist = split_molecule(m)
if clist:
openModels.add(clist, baseId=m.id, noprefs=True)
for c in clist:
c.openState.xform = m.openState.xform
slist.append(m)
from chimera import makeLongBondsDashed, makePseudoBondsToMetals
makePseudoBondsToMetals(clist)
makeLongBondsDashed(clist)
openModels.close(slist)
def parse_surface_pieces(spec):
from chimera.specifier import evalSpec
sel = evalSpec(spec)
import Surface
plist = Surface.selected_surface_pieces(sel)
return plist
def parse_object_specifier(spec, name='object'):
from chimera import specifier
try:
sel = specifier.evalSpec(spec)
except:
raise CommandError('Bad %s specifier "%s"' % (name, spec))
return sel
def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c], serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def validate(self, query):
try:
sel = evalSpec(query)
if sel:
current = getattr(sel, self.mode)()
if len(current) == 1:
return current[0]
except: # Syntax error, etc
return
def model_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
mlist = sel.models()
if len(mlist) == 0:
raise CommandError, 'No models specified'
elif len(mlist) > 1:
raise CommandError, 'Multiple models specified'
return mlist[0]
def model_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
mlist = sel.models()
if len(mlist) == 0:
raise CommandError, 'No models specified'
elif len(mlist) > 1:
raise CommandError, 'Multiple models specified'
return mlist[0]
def parse_model_spec(mspec):
if mspec.lower() == 'all':
from chimera import openModels as om
mlist = om.list()
else:
from chimera.specifier import evalSpec
try:
mlist = evalSpec(mspec).models()
except:
mlist = []
return mlist
def segmentation_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
mlist = sel.models()
from regions import Segmentation
slist = [s for s in mlist if isinstance(s, Segmentation)]
if len(slist) == 0:
raise CommandError, 'No segmentation specified'
elif len(slist) > 1:
raise CommandError, 'Multiple segmentations specified'
return slist[0]
def regions_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
import Surface
plist = Surface.selected_surface_pieces(sel)
from Segger import Region
rlist = [
p.region for p in plist
if hasattr(p, 'region') and isinstance(p.region, Region)
]
if len(rlist) == 0:
raise CommandError, 'No segmentation regions specified'
return rlist
def createHelices(m, **kw):
from chimera.specifier import evalSpec
sel = evalSpec(":/isHelix & backbone.minimal", models=[m])
residues = sel.residues()
if not residues:
return []
from chimera.misc import oslCmp
residues.sort(lambda r1, r2: oslCmp(r1.oslIdent(), r2.oslIdent()))
from chimera import bondsBetween
from chimera.selection import INTERSECT, ItemizedSelection
curHelix = []
axes = []
from Geometry import geomManager
geomManager.suspendUpdates()
while residues:
if not curHelix:
r = residues.pop(0)
curHelix.append(r)
helixNum = r.ssId
continue
if helixNum > -1:
if helixNum == residues[0].ssId:
curHelix.append(residues.pop(0))
continue
elif bondsBetween(curHelix[-1], residues[0], True):
curHelix.append(residues.pop(0))
continue
resSel = ItemizedSelection()
resSel.add(curHelix)
resSel.merge(INTERSECT, sel)
atoms = resSel.atoms()
if helixNum < 0:
created += 1
helixNum = created
hname = "%s H%d" % (m.name, helixNum)
axes.append(axisManager.createAxis(hname, atoms, **kw))
curHelix = []
if curHelix:
resSel = ItemizedSelection()
resSel.add(curHelix)
resSel.merge(INTERSECT, sel)
atoms = resSel.atoms()
if helixNum < 0:
created += 1
helixNum = created
hname = "%s H%d" % (m.name, helixNum)
axes.append(axisManager.createAxis(hname, atoms, **kw))
geomManager.enableUpdates()
return axes
def parse_atom_specifier(atom_spec, cmdname):
# Parse atoms
from chimera import specifier
try:
asel = specifier.evalSpec(atom_spec)
except:
from Midas.midas_text import error
error('%s: Bad atom specifier %s' % (cmdname, atom_spec))
return []
atoms = asel.atoms()
if len(atoms) == 0:
from Midas.midas_text import error
error('%s: No atoms specified by specifier %s' % (cmdname, atom_spec))
return []
return atoms
def parse_atom_specifier(atom_spec, cmdname):
# Parse atoms
from chimera import specifier
try:
asel = specifier.evalSpec(atom_spec)
except:
from Midas.midas_text import error
error('%s: Bad atom specifier %s' % (cmdname, atom_spec))
return []
atoms = asel.atoms()
if len(atoms) == 0:
from Midas.midas_text import error
error('%s: No atoms specified by specifier %s' % (cmdname, atom_spec))
return []
return atoms
def parse_multiscale_models(surf_spec, cmdname):
# Parse multiscale models
from chimera import specifier
try:
ssel = specifier.evalSpec(surf_spec)
except:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, surf_spec))
return []
ms_models = multiscale_models(ssel.models())
if len(ms_models) == 0:
from Midas.midas_text import error
error('%s: No multiscale models specified by %s' % (cmdname, surf_spec))
return []
return ms_models
def parse_multiscale_models(surf_spec, cmdname):
# Parse multiscale models
from chimera import specifier
try:
ssel = specifier.evalSpec(surf_spec)
except:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, surf_spec))
return []
ms_models = multiscale_models(ssel.models())
if len(ms_models) == 0:
from Midas.midas_text import error
error('%s: No multiscale models specified by %s' %
(cmdname, surf_spec))
return []
return ms_models
def volumes_from_specifier(spec):
from chimera import specifier
try:
sel = specifier.evalSpec(spec)
except:
return []
from volume import Volume, volume_list
vlist = [m for m in sel.models() if isinstance(m, Volume)]
# Translate solid volume models to volume models.
from _volume import Volume_Model
svlist = [m for m in sel.models() if isinstance(m, Volume_Model)]
for s in svlist:
for v in volume_list():
if s in v.models():
if not v in vlist:
vlist.append(v)
break
return vlist
def volumes_from_specifier(spec):
from chimera import specifier
try:
sel = specifier.evalSpec(spec)
except:
return []
from volume import Volume, volume_list
vlist = [m for m in sel.models() if isinstance(m, Volume)]
# Translate solid volume models to volume models.
from _volume import Volume_Model
svlist = [m for m in sel.models() if isinstance(m, Volume_Model)]
for s in svlist:
for v in volume_list():
if s in v.models():
if not v in vlist:
vlist.append(v)
break
return vlist
def inertia(operation,
objects,
showEllipsoid=True,
color=None,
perChain=False):
from chimera import specifier
try:
sel = specifier.evalSpec(objects)
except:
raise CommandError, 'Bad object specifier "%s"' % objects
if not color is None:
from Commands import parse_color
color = parse_color(color)
atoms = sel.atoms()
if atoms:
import inertia
if perChain:
xf = atoms[0].molecule.openState.xform
mname = molecules_name(list(set([a.molecule for a in atoms])))
s = inertia.surface_model(None, xf, 'ellipsoids ' + mname)
for achain in atoms_by_chain(atoms):
p = inertia.atoms_inertia_ellipsoid(achain, showEllipsoid,
color, s)
if p:
p.oslName = achain[0].residue.id.chainId
else:
inertia.atoms_inertia_ellipsoid(atoms, showEllipsoid, color)
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes=False)
if plist:
import inertia
inertia.surface_inertia_ellipsoid(plist, showEllipsoid, color)
def molecules_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
mlist = sel.molecules()
return mlist
# Show unit cell outline for a molecule. Usage "runscript showoutline.py #0" import UnitCell d = UnitCell.show_unit_cell_dialog() from chimera import specifier m = specifier.evalSpec(arguments[0]).molecules()[0] d.show_outline_model(m)
def cmdDetectClash(testAtoms,
overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE],
test="others",
setAttrs=defaults[ACTION_ATTR],
selectClashes=defaults[ACTION_SELECT],
colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR],
nonclashColor=defColors[NONCLASH_COLOR],
makePseudobonds=defaults[ACTION_PSEUDOBONDS],
pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH],
bondSeparation=defaults[BOND_SEPARATION],
saveFile=None,
namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES],
interSubmodel=False,
log=defaults[ACTION_REPLYLOG],
summary=True,
continuous=False):
global _continuousID
from Midas import MidasError
if continuous:
if setAttrs or saveFile != None or log:
raise MidasError("log/setAttrs/saveFile not allowed"
" with continuous detection")
if _continuousID == None:
from inspect import getargvalues, currentframe
argNames, fArgs, fKw, frameDict = getargvalues(currentframe())
callData = [frameDict[an] for an in argNames]
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
return _motionCB(myData)
_continuousID = chimera.triggers.addHandler(
'OpenState', preCB, callData)
elif _continuousID != None:
chimera.triggers.deleteHandler('OpenState', _continuousID)
_continuousID = None
if isinstance(test, basestring):
if test.startswith("other"):
test = "others"
elif test not in ('self', 'model'):
# atom spec
from chimera.specifier import evalSpec
try:
test = evalSpec(test).atoms()
except:
raise MidasError("Could not parse atom spec '%s'" % test)
clashes = detectClash(testAtoms,
test=test,
hbondAllowance=hbondAllowance,
clashThreshold=overlapCutoff,
bondSeparation=bondSeparation,
intraRes=not ignoreIntraRes,
interSubmodel=interSubmodel)
if selectClashes:
chimera.selection.setCurrent(clashes.keys())
if test == "self":
outputGrouping = set()
else:
outputGrouping = testAtoms
info = (overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes,
clashes, outputGrouping)
if log:
import sys
# put a separator in the Reply Log
print >> sys.stdout, ""
_fileOutput(sys.stdout, info, namingStyle=namingStyle)
if saveFile == '-':
from FindHBond.MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(info,
_fileOutput,
initialfile="overlaps",
title="Choose Overlap Info Save File",
historyID="Overlap info")
elif saveFile is not None:
_fileOutput(saveFile, info, namingStyle=namingStyle)
if summary == True:
def _summary(msg):
from chimera import replyobj
replyobj.status(msg + '\n')
replyobj.info(msg + '\n')
summary = _summary
if summary:
if clashes:
total = 0
for clashList in clashes.values():
total += len(clashList)
summary("%d contacts" % (total / 2))
else:
summary("No contacts")
if not (setAttrs or colorClashes or makePseudobonds):
nukeGroup()
return clashes
if test in ("others", "model"):
atoms = [
a for m in chimera.openModels.list(modelTypes=[chimera.Molecule])
for a in m.atoms
]
else:
atoms = testAtoms
if setAttrs:
# delete the attribute in _all_ atoms...
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if hasattr(a, attrName):
delattr(a, attrName)
for a in atoms:
if a in clashes:
clashVals = clashes[a].values()
clashVals.sort()
setattr(a, attrName, clashVals[-1])
if colorClashes:
for a in atoms:
a.surfaceColor = None
if a in clashes:
a.color = clashColor
else:
a.color = nonclashColor
if makePseudobonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
pbg.color = pbColor
seen = set()
for a in atoms:
if a not in clashes:
continue
seen.add(a)
for clasher in clashes[a].keys():
if clasher in seen:
continue
pbg.newPseudoBond(a, clasher)
else:
nukeGroup()
return clashes
def testTutorial(self):
subUnitFrame = self.g.configFrame.subUnitFrame
self.assertEqual(0, len(subUnitFrame.frames))
self.assertEqual(0, len(self.g.configFrame.config.subunits))
activeItemFrame = subUnitFrame.activeItemFrame
activeItemFrame.fields["name"][1].insert(0, "Rvb1")
activeItemFrame.fields["chainIds"][1].insert(0, "A,C,E")
activeItemFrame.fields["color"][1].set(chimera.MaterialColor(0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.subunits))
self.assertEqual(1, len(subUnitFrame.frames))
activeItemFrame.fields["name"][1].insert(0, "Rvb2")
activeItemFrame.fields["chainIds"][1].insert(0, "B,D,F")
activeItemFrame.fields["color"][1].set(chimera.MaterialColor(0.392, 0.584, 0.929))
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.subunits))
self.assertEqual(2, len(subUnitFrame.frames))
configfilename = tempfile.mkstemp()[1]
self.g.configFrame.resMngr._saveAssembly(configfilename)
self.assertEqual(configfilename, xla.getRecentPaths()[0])
self.g.Subunits.table.colorAll.invoke()
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:.{1}".format(self.model.id, chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:.{1}".format(self.model.id, chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0.392, 0.584, 0.929))
ctable = self.g.Subunits.table
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ["A", "C", "E"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ["B", "D", "F"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
for chain in ["A", "C", "E"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ["B", "D", "F"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.show.invoke()
for chain in ["B", "D", "F"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.showOnly.invoke()
for chain in ["A", "C", "E"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ["B", "D", "F"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
chimera.selection.clearCurrent()
ctable.select.invoke()
self.assertListEqual(["A", "C", "E"], [s.chain for s in chimera.selection.currentChains()])
chimera.selection.clearCurrent()
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.chainVar.set(1)
self.assertEqual(6, len(ctable.table._sortedData()))
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ["A"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ["C", "E"]:
ribbonDisplay = evalSpec("#{0}:.{1}".format(self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
ctable.table.tixTable.hlist.selection_set(2)
ctable.hide.invoke()
ctable.chainVar.set(0)
self.assertEqual(False, self.g.configFrame.config.subunits[0].show)
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.showAll.invoke()
self.assertEqual(True, self.g.configFrame.config.subunits[0].show)
dataFrame = self.g.configFrame.dataFrame
activeItemFrame = dataFrame.activeItemFrame
activeItemFrame.fields["name"][1].insert(0, "xlinks")
paths = ["xlinks/inter.csv", "xlinks/intra.csv", "xlinks/monolinks.csv"]
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields["fileGroup"][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields["type"][3].set("xquest")
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.dataItems))
self.assertEqual(1, len(dataFrame.frames))
dataMgrTab = self.g.__dict__["Data manager"]
self.assertEqual(3, len(dataMgrTab.winfo_children()))
xFrame = self.g.Xlinks
xFrame.displayDefaultBtn.invoke()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertEqual(216, len(xmgr.pbg.pseudoBonds))
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(75, displayed)
xFrame.ld_score_var.set(30.0)
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideAllXlinksBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
xFrame.displayDefaultBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideIntraXlinksBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.displayDefaultBtn.invoke()
xFrame.hideInterXlinksBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(33, displayed)
xFrame.showAllXlinksBtn.invoke()
xFrame.smartModeBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(162, displayed)
xFrame.smartModeBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.confOligBtn.invoke()
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(18, displayed)
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
activeItemFrame.fields["name"][1].insert(0, "sequences")
paths = ["sequences.yeast.fasta"]
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields["fileGroup"][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields["type"][3].set("sequences")
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.dataItems))
self.assertEqual(2, len(dataFrame.frames))
sequenceFrame = dataFrame.frames[-1]
mapFrame = sequenceFrame.fields["mapping"][1]
mapFrame.mapButton.invoke()
for seqName, subset in mapFrame.subsetframes.iteritems():
if "RUVB1" in seqName:
subset.menus[0].var.set("Rvb1")
if "RUVB2" in seqName:
subset.menus[0].var.set("Rvb2")
mapFrame.onSave()
self.g.configFrame.resMngr._saveAssembly(self.g.configFrame.config.file)
self.assertEqual(5, len(dataMgrTab.winfo_children()))
dataMgrTab.winfo_children()[2].invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
dataMgrTab.winfo_children()[2].invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.showModifiedFrame.showModifiedMap()
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:.{1}".format(self.model.id, chain)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("light gray"))
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:.{1}".format(self.model.id, chain)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("light gray"))
some_red_resi = map(str, [81, 128, 161, 174, 276])
for resi in some_red_resi:
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("red"))
some_red_resi = map(str, [85, 116, 193, 210, 239, 377])
for resi in some_red_resi:
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("red"))
some_yellow_resi = map(str, [15, 130, 201, 285, 438])
for resi in some_yellow_resi:
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("yellow"))
some_blue_resi = map(str, [198, 331, 338, 357])
for resi in some_blue_resi:
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("blue"))
xFrame.ld_score_var.set(0.0)
xFrame.showModifiedFrame.showModifiedMap()
some_blue_resi = map(str, [377])
for resi in some_blue_resi:
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("blue"))
xFrame.ld_score_var.set(30.0)
xFrame.showModifiedFrame.showModifiedMap()
modelStatsTable = self.g.Xlinks.modelStatsTable
modelStatsTable.xlinkToolbar.resetView()
self.g.Subunits.table.colorAll.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, "w") as f:
modelStatsTable._exportTable(f)
with open(csvfilename, "rU") as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ["\t", ","])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual(
["All xlinks", "Satisfied", "Violated", "Satisfied [%]", "Violated [%]", "model"], reader.fieldnames
)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(2, int(row["Violated"]))
self.assertEqual(18, int(row["All xlinks"]))
self.assertEqual(16, int(row["Satisfied"]))
self.assertEqual("88.9", row["Satisfied [%]"])
self.assertEqual("11.1", row["Violated [%]"])
self.assertEqual("yRvb12.hexamer.pdb", row["model"])
modelStatsTable.modelListFrame.winfo_children()[8].invoke()
detailsFrame = modelStatsTable.detailsFrame
self.assertEqual(2, len(detailsFrame.winfo_children()))
detailsFrame.showHistogram()
xlinksSet = detailsFrame.xlinkDataMgr.getXlinksWithDistances(detailsFrame.xlinkStats)
self.assertEqual(18, len(xlinksSet.data))
# TODO: test exportSelectedXlinkList
detailsFrame.byCompViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, "w") as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, "rU") as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ["\t", ","])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
detailsFrame.byPairViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, "w") as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, "rU") as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ["\t", ","])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
modelStatsTable.xlinkToolbar.lengthThreshVar.set(40.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, "w") as f:
modelStatsTable._exportTable(f)
with open(csvfilename, "rU") as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ["\t", ","])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual(
["All xlinks", "Satisfied", "Violated", "Satisfied [%]", "Violated [%]", "model"], reader.fieldnames
)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(1, int(row["Violated"]))
self.assertEqual(18, int(row["All xlinks"]))
self.assertEqual(17, int(row["Satisfied"]))
self.assertEqual("94.4", row["Satisfied [%]"])
self.assertEqual("5.6", row["Violated [%]"])
self.assertEqual("yRvb12.hexamer.pdb", row["model"])
modelStatsTable.xlinkToolbar.lengthThreshVar.set(30.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
xFrame.showXlinksFromTabNameCompOptMenuFrom.var.set("Rvb1")
xFrame.showXlinksFromTabNameCompOptMenuTo.var.set("Rvb2")
xFrame.showXlinksFromBtn.invoke()
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.ld_score_var.set(0.0)
displayed = len([pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(27, displayed)
xFrame.ld_score_var.set(30.0)
colorXlinkedFrame = xFrame.colorXlinkedFrame
colorXlinkedFrame.compOptMenuFrom.var.set("Rvb1")
colorXlinkedFrame.compOptMenuTo.var.set("Rvb2")
colorXlinkedFrame.colorOptionVar.set(1)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.colorTable.getColorByName("red"))
display = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ["A", "C", "E"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0.392, 0.584, 0.929))
display = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.compOptMenuFrom.var.set("Rvb2")
colorXlinkedFrame.compOptMenuTo.var.set("Rvb1")
colorXlinkedFrame.uncolorOthersBtn.var.set(True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ["A", "C", "E"]:
display = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, False)
some_test_resi = map(str, [123, 157, 198, 357, 414])
for resi in some_test_resi:
for chain in ["B", "D", "F"]:
color = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
display = evalSpec("#{0}:{2}.{1}".format(self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [
{
'tr3d': Xform.xform(-0.50000042, 0.86602516, 0.00000116, -103.53997515,
-0.86602516, -0.50000042, 0.00000058, 179.33655802,
0.00000108, -0.00000072, 1.00000000, 0.00005125, orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}
]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))] for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j-i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def cmdDetectClash(testAtoms, overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE], test="others",
setAttrs=defaults[ACTION_ATTR], selectClashes=
defaults[ACTION_SELECT], colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR], nonclashColor=
defColors[NONCLASH_COLOR], makePseudobonds=
defaults[ACTION_PSEUDOBONDS], pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH], bondSeparation=
defaults[BOND_SEPARATION], saveFile=None, namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES], interSubmodel=False,
log=defaults[ACTION_REPLYLOG], summary=True,
continuous=False):
global _continuousID
from Midas import MidasError
if continuous:
if setAttrs or saveFile != None or log:
raise MidasError("log/setAttrs/saveFile not allowed"
" with continuous detection")
if _continuousID == None:
from inspect import getargvalues, currentframe
argNames, fArgs, fKw, frameDict = getargvalues(
currentframe())
callData = [frameDict[an] for an in argNames]
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
return _motionCB(myData)
_continuousID = chimera.triggers.addHandler(
'OpenState', preCB, callData)
elif _continuousID != None:
chimera.triggers.deleteHandler('OpenState', _continuousID)
_continuousID = None
if isinstance(test, basestring):
if test.startswith("other"):
test = "others"
elif test not in ('self', 'model'):
# atom spec
from chimera.specifier import evalSpec
try:
test = evalSpec(test).atoms()
except:
raise MidasError("Could not parse atom spec '%s'" % test)
clashes = detectClash(testAtoms, test=test,
hbondAllowance=hbondAllowance, clashThreshold=overlapCutoff,
bondSeparation=bondSeparation, intraRes=not ignoreIntraRes,
interSubmodel=interSubmodel)
if selectClashes:
chimera.selection.setCurrent(clashes.keys())
if test == "self":
outputGrouping = set()
else:
outputGrouping = testAtoms
info = (overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes,
clashes, outputGrouping)
if log:
import sys
# put a separator in the Reply Log
print>>sys.stdout, ""
_fileOutput(sys.stdout, info, namingStyle=namingStyle)
if saveFile == '-':
from FindHBond.MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(info, _fileOutput, initialfile="overlaps",
title="Choose Overlap Info Save File",
historyID="Overlap info")
elif saveFile is not None:
_fileOutput(saveFile, info, namingStyle=namingStyle)
if summary == True:
def _summary(msg):
from chimera import replyobj
replyobj.status(msg + '\n')
replyobj.info(msg + '\n')
summary = _summary
if summary:
if clashes:
total = 0
for clashList in clashes.values():
total += len(clashList)
summary("%d contacts" % (total/2))
else:
summary("No contacts")
if not (setAttrs or colorClashes or makePseudobonds):
nukeGroup()
return clashes
if test in ("others", "model"):
atoms = [a for m in chimera.openModels.list(
modelTypes=[chimera.Molecule]) for a in m.atoms]
else:
atoms = testAtoms
if setAttrs:
# delete the attribute in _all_ atoms...
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if hasattr(a, attrName):
delattr(a, attrName)
for a in atoms:
if a in clashes:
clashVals = clashes[a].values()
clashVals.sort()
setattr(a, attrName, clashVals[-1])
if colorClashes:
for a in atoms:
a.surfaceColor = None
if a in clashes:
a.color = clashColor
else:
a.color = nonclashColor
if makePseudobonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
pbg.color = pbColor
seen = set()
for a in atoms:
if a not in clashes:
continue
seen.add(a)
for clasher in clashes[a].keys():
if clasher in seen:
continue
pbg.newPseudoBond(a, clasher)
else:
nukeGroup()
return clashes
def molecules_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
mlist = sel.molecules()
return mlist
def _addAttr(attrFile, models, log, raiseAttrDialog):
setAttrs = {}
colors = {}
from CGLutil.annotatedDataFile import readDataFile
control = { 'match mode': _MATCH_MODE_ANY, 'recipient': "atoms" }
for rawControl, data in readDataFile(attrFile):
control.update(rawControl)
legalNames = ["attribute", "match mode", "recipient"]
for name in control.keys():
if name not in legalNames:
raise SyntaxError("Unknown name part of control"
" line: '%s'\nMust be one of: %s" % (
name, ", ".join(legalNames)))
if "attribute" not in control:
raise SyntaxError("No attribute name specified in file")
attrName = control["attribute"]
if not attrName.replace("_", "").isalnum() \
or attrName[0].isdigit():
raise SyntaxError("Attribute name (%s) is bad.\n"
"It must be strictly alphanumeric characters or"
" underscores with no spaces and must not start"
" with a digit." % control["attribute"])
colorAttr = attrName.lower().endswith("color")
matchMode = control["match mode"]
if matchMode not in _matchModes:
raise SyntaxError("Unknown match mode (%s) specified.\n"
"It must be one of: %s" % (
control["match mode"], ", ".join(_matchModes)))
recipient = control["recipient"]
if not hasattr(selection.ItemizedSelection, recipient):
raise SyntaxError("Unknown attribute recipient (%s)"
" specified.\nSuggest using atoms, residues, or"
" molecules" % control["recipient"])
dataErrors = []
for lineNum, d in enumerate(data):
try:
selector, value = d
except ValueError:
dataErrors.append("Data line %d of file either"
" not selector/value or not"
" tab-delimited" % (lineNum+1))
continue
try:
sel = specifier.evalSpec(selector, models)
except:
import sys
dataErrors.append("Mangled selector (%s) on"
" data line %d: %s" % (selector,
lineNum+1, sys.exc_value))
continue
matches = getattr(sel, recipient)()
# restrict to models; the "models" argument to evalSpec
# only works if the selector is an OSL
if matches and models is not None:
md = set(models)
level = matches[0].oslLevel()
if level == selection.SelGraph:
filterFunc = lambda x, md=md: x in md
elif level == selection.SelEdge:
filterFunc = lambda x, md=md: \
x.atoms[0].molecule in md
else:
filterFunc = lambda x, md=md: \
x.molecule in md
matches = filter(filterFunc, matches)
if not matches:
if matchMode != _MATCH_MODE_ANY:
dataErrors.append("Selector (%s) on"
" data line %d matched nothing"
% (selector, lineNum+1))
continue
elif len(matches) > 1:
if matchMode == _MATCH_MODE_1_TO_1:
dataErrors.append("Selector (%s) on"
" data line %d matched multiple"
" items: %s" % (selector,
lineNum+1, ", ".join(map(lambda
m: m.oslIdent(), matches))))
if log:
replyobj.info("Selector %s matched " % selector
+ ", ".join(map(misc.chimeraLabel,
matches)) + "\n")
if colorAttr:
if value[0].isalpha():
# color name
from chimera.colorTable \
import getColorByName
try:
value = getColorByName(value)
except KeyError:
dataErrors.append("Unknown"
" color name on data"
" line %d: '%s'" %
(lineNum+1, value))
continue
else:
try:
rgba = tuple(map(float,
value.split()))
except ValueError:
dataErrors.append(
"Unrecognizable color"
" value on data line"
" %d: '%s'; Must be"
" either color name or"
" 3 or 4 numbers"
" between 0 and 1"
" (RGBA)" % (lineNum+1))
continue
if max(rgba) > 1.0 or min(rgba) < 0.0:
dataErrors.append("Color"
" component values on"
" data line %d not"
" in the range 0 to 1"
% (lineNum+1))
continue
if rgba in colors:
value = colors[rgba]
elif len(rgba) in [3, 4]:
value = chimera.MaterialColor(
*rgba)
colors[rgba] = value
else:
dataErrors.append("Bad number"
" of color components"
" on data line %d; Must"
" be either 3 or 4 (was"
" %d)" % (lineNum+1,
len(rgba)))
continue
else:
value = convertType(value)
for match in matches:
setattr(match, attrName, value)
if matches and not colorAttr:
setAttrs[(recipient, attrName)] = value
recipMapping = {
"molecules": chimera.Molecule,
"residues": chimera.Residue,
"bonds": chimera.Bond,
"atoms": chimera.Atom
}
from SimpleSession import registerAttribute
for recipient, attrName in setAttrs:
if recipient in recipMapping:
registerAttribute(recipMapping[recipient], attrName)
if setAttrs and not chimera.nogui and raiseAttrDialog:
from ShowAttr import ShowAttrDialog, screenedAttrs
from chimera import dialogs
showableAttr = False
reasons = []
for recipient, attrName in setAttrs.keys():
if recipient == "molecules":
recipient = "models"
validRecipients = ["atoms", "residues", "models"]
if recipient not in validRecipients:
reasons.append("%s not assigned to atoms,"
" residues, or models" % attrName)
continue
key = [chimera.Atom, chimera.Residue, chimera.Model][
validRecipients.index(recipient)]
if attrName in screenedAttrs[key]:
reasons.append("%s automatically screened out"
" by Render By Attribute" % attrName)
continue
if attrName[0] == '_':
reasons.append("%s considered to be a private"
" variable" % attrName)
continue
if attrName[0].isupper():
reasons.append("%s considered to be a symbolic"
" constant due to initial capital"
" letter" % attrName)
continue
showableAttr = True
break
if showableAttr:
if models is None:
ms = chimera.openModels.list()
else:
ms = models
if colorAttr:
an = None
mode = None
else:
an = attrName
from types import StringTypes
if type(setAttrs[(recipient, attrName)]) in (
bool,) + StringTypes:
mode = "Select"
else:
mode = "Render"
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=[m for m in ms
if isinstance(m, chimera.Molecule)],
attrsOf=recipient, attrName=an, mode=mode)
else:
replyobj.warning("No attributes usable by Render dialog"
" were defined:\n" + "\n".join(reasons) + "\n")
if dataErrors:
raise SyntaxError, "\n".join(dataErrors)
return setAttrs
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [{
'tr3d':
Xform.xform(-0.50000042,
0.86602516,
0.00000116,
-103.53997515,
-0.86602516,
-0.50000042,
0.00000058,
179.33655802,
0.00000108,
-0.00000072,
1.00000000,
0.00005125,
orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))]
for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j - i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def testTutorial(self):
subUnitFrame = self.g.configFrame.subUnitFrame
self.assertEqual(0, len(subUnitFrame.frames))
self.assertEqual(0, len(self.g.configFrame.config.subunits))
activeItemFrame = subUnitFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'Rvb1')
activeItemFrame.fields['chainIds'][1].insert(0, 'A,C,E')
activeItemFrame.fields['color'][1].set(chimera.MaterialColor(
0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.subunits))
self.assertEqual(1, len(subUnitFrame.frames))
activeItemFrame.fields['name'][1].insert(0, 'Rvb2')
activeItemFrame.fields['chainIds'][1].insert(0, 'B,D,F')
activeItemFrame.fields['color'][1].set(
chimera.MaterialColor(0.392, 0.584, 0.929))
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.subunits))
self.assertEqual(2, len(subUnitFrame.frames))
configfilename = tempfile.mkstemp()[1]
self.g.configFrame.resMngr._saveAssembly(configfilename)
self.assertEqual(configfilename, xla.getRecentPaths()[0])
self.g.Subunits.table.colorAll.invoke()
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0.392, 0.584, 0.929))
ctable = self.g.Subunits.table
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.show.invoke()
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.showOnly.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
chimera.selection.clearCurrent()
ctable.select.invoke()
self.assertListEqual(
['A', 'C', 'E'],
[s.chain for s in chimera.selection.currentChains()])
chimera.selection.clearCurrent()
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.chainVar.set(1)
self.assertEqual(6, len(ctable.table._sortedData()))
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ['A']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ['C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
ctable.table.tixTable.hlist.selection_set(2)
ctable.hide.invoke()
ctable.chainVar.set(0)
self.assertEqual(False, self.g.configFrame.config.subunits[0].show)
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.showAll.invoke()
self.assertEqual(True, self.g.configFrame.config.subunits[0].show)
dataFrame = self.g.configFrame.dataFrame
activeItemFrame = dataFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'xlinks')
paths = [
'xlinks/inter.csv', 'xlinks/intra.csv', 'xlinks/monolinks.csv'
]
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields['fileGroup'][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields['type'][3].set('xquest')
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.dataItems))
self.assertEqual(1, len(dataFrame.frames))
dataMgrTab = self.g.__dict__['Data manager']
self.assertEqual(3, len(dataMgrTab.winfo_children()))
xFrame = self.g.Xlinks
xFrame.displayDefaultBtn.invoke()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertEqual(216, len(xmgr.pbg.pseudoBonds))
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(75, displayed)
xFrame.ld_score_var.set(30.0)
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideAllXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
xFrame.displayDefaultBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideIntraXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.displayDefaultBtn.invoke()
xFrame.hideInterXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(33, displayed)
xFrame.showAllXlinksBtn.invoke()
xFrame.smartModeBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(162, displayed)
xFrame.smartModeBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.confOligBtn.invoke()
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(18, displayed)
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
activeItemFrame.fields['name'][1].insert(0, 'sequences')
paths = ['sequences.yeast.fasta']
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields['fileGroup'][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields['type'][3].set('sequences')
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.dataItems))
self.assertEqual(2, len(dataFrame.frames))
sequenceFrame = dataFrame.frames[-1]
mapFrame = sequenceFrame.fields['mapping'][1]
mapFrame.mapButton.invoke()
for seqName, subset in mapFrame.subsetframes.iteritems():
if 'RUVB1' in seqName:
subset.menus[0].var.set('Rvb1')
if 'RUVB2' in seqName:
subset.menus[0].var.set('Rvb2')
mapFrame.onSave()
self.g.configFrame.resMngr._saveAssembly(
self.g.configFrame.config.file)
self.assertEqual(5, len(dataMgrTab.winfo_children()))
dataMgrTab.winfo_children()[2].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
dataMgrTab.winfo_children()[2].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.showModifiedFrame.showModifiedMap()
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('light gray'))
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('light gray'))
some_red_resi = map(str, [81, 128, 161, 174, 276])
for resi in some_red_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
some_red_resi = map(str, [85, 116, 193, 210, 239, 377])
for resi in some_red_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
some_yellow_resi = map(str, [15, 130, 201, 285, 438])
for resi in some_yellow_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('yellow'))
some_blue_resi = map(str, [198, 331, 338, 357])
for resi in some_blue_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('blue'))
xFrame.ld_score_var.set(0.0)
xFrame.showModifiedFrame.showModifiedMap()
some_blue_resi = map(str, [377])
for resi in some_blue_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('blue'))
xFrame.ld_score_var.set(30.0)
xFrame.showModifiedFrame.showModifiedMap()
modelStatsTable = self.g.Xlinks.modelStatsTable
modelStatsTable.xlinkToolbar.resetView()
self.g.Subunits.table.colorAll.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
modelStatsTable._exportTable(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual([
'All xlinks', 'Satisfied', 'Violated', 'Satisfied [%]',
'Violated [%]', 'model'
], reader.fieldnames)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(2, int(row['Violated']))
self.assertEqual(18, int(row['All xlinks']))
self.assertEqual(16, int(row['Satisfied']))
self.assertEqual('88.9', row['Satisfied [%]'])
self.assertEqual('11.1', row['Violated [%]'])
self.assertEqual('yRvb12.hexamer.pdb', row['model'])
modelStatsTable.modelListFrame.winfo_children()[8].invoke()
detailsFrame = modelStatsTable.detailsFrame
self.assertEqual(2, len(detailsFrame.winfo_children()))
detailsFrame.showHistogram()
xlinksSet = detailsFrame.xlinkDataMgr.getXlinksWithDistances(
detailsFrame.xlinkStats)
self.assertEqual(18, len(xlinksSet.data))
#TODO: test exportSelectedXlinkList
detailsFrame.byCompViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
detailsFrame.byPairViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
modelStatsTable.xlinkToolbar.lengthThreshVar.set(40.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
modelStatsTable._exportTable(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual([
'All xlinks', 'Satisfied', 'Violated', 'Satisfied [%]',
'Violated [%]', 'model'
], reader.fieldnames)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(1, int(row['Violated']))
self.assertEqual(18, int(row['All xlinks']))
self.assertEqual(17, int(row['Satisfied']))
self.assertEqual('94.4', row['Satisfied [%]'])
self.assertEqual('5.6', row['Violated [%]'])
self.assertEqual('yRvb12.hexamer.pdb', row['model'])
modelStatsTable.xlinkToolbar.lengthThreshVar.set(30.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
xFrame.showXlinksFromTabNameCompOptMenuFrom.var.set('Rvb1')
xFrame.showXlinksFromTabNameCompOptMenuTo.var.set('Rvb2')
xFrame.showXlinksFromBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.ld_score_var.set(0.0)
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(27, displayed)
xFrame.ld_score_var.set(30.0)
colorXlinkedFrame = xFrame.colorXlinkedFrame
colorXlinkedFrame.compOptMenuFrom.var.set('Rvb1')
colorXlinkedFrame.compOptMenuTo.var.set('Rvb2')
colorXlinkedFrame.colorOptionVar.set(1)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.MaterialColor(0.392, 0.584, 0.929))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.compOptMenuFrom.var.set('Rvb2')
colorXlinkedFrame.compOptMenuTo.var.set('Rvb1')
colorXlinkedFrame.uncolorOthersBtn.var.set(True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, False)
some_test_resi = map(str, [123, 157, 198, 357, 414])
for resi in some_test_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
