def apply_transform(self, xf):
# Apply transform to models.
from chimera import viewer, openModels as om, Point
oslist = list(set([m.openState for m in om.list()]))
# Activate inactive models in fly mode or all models mode.
ialist = []
if self.fly_mode or self.all_models:
ialist = [os for os in set([m.openState for m in om.list()])
if not os.active]
for os in ialist:
os.active = True
if self.fly_mode:
m, c = om.cofrMethod, om.cofr
om.cofrMethod = om.Fixed
view = 0 # TODO: use center between eyes for stereo
e = Point(*viewer.camera.eyePos(view))
om.cofr = e # Rotate about eye position
om.applyXform(xf.inverse())
om.cofr = c # Restore center of rotation
om.cofrMethod = m
else:
om.applyXform(xf)
for os in ialist:
os.active = False
def apply_transform(self, xf):
# Apply transform to models.
from chimera import viewer, openModels as om, Point
oslist = list(set([m.openState for m in om.list()]))
# Activate inactive models in fly mode or all models mode.
ialist = []
if self.fly_mode or self.all_models:
ialist = [
os for os in set([m.openState for m in om.list()])
if not os.active
]
for os in ialist:
os.active = True
if self.fly_mode:
m, c = om.cofrMethod, om.cofr
om.cofrMethod = om.Fixed
view = 0 # TODO: use center between eyes for stereo
e = Point(*viewer.camera.eyePos(view))
om.cofr = e # Rotate about eye position
om.applyXform(xf.inverse())
om.cofr = c # Restore center of rotation
om.cofrMethod = m
else:
om.applyXform(xf)
for os in ialist:
os.active = False
def activateAllCmd():
"""Activate all models. Restore previous activities if called again."""
global _prevActivities
if _prevActivities:
for m in openModels.list():
if _prevActivities.has_key(m.openState):
m.openState.active = _prevActivities[
m.openState]
_prevActivities = None
if _mp:
if 'activate all' in _mp.frequentButtons:
actionButtons = _mp.freqActionButtons
else:
actionButtons = _mp.infreqActionButtons
actionButtons.component('activate all').config(
text='activate all')
else:
_prevActivities = {}
for m in openModels.list():
if _prevActivities.has_key(m.openState):
continue
_prevActivities[m.openState] = m.openState.active
m.openState.active = 1
if _mp:
if 'activate all' in _mp.frequentButtons:
actionButtons = _mp.freqActionButtons
else:
actionButtons = _mp.infreqActionButtons
actionButtons.component('activate all').config(
text='restore activities')
def clip_selected_models():
'Toggle per-model clipping for selected models'
from chimera import selection, openModels
mlist = [m for m in selection.currentGraphs() if m.display]
if len(mlist) == 0:
mlist = [m for m in openModels.list() if m.display and m.useClipPlane]
if len(mlist) == 0:
mlist = [m for m in openModels.list() if m.display]
if len(mlist) == 0:
return
from chimera import tkgui
for m in mlist:
if m.useClipPlane:
m.useClipPlane = False
elif m.bbox()[0]:
tkgui.setClipModel(m) # Set initial clip plane placement.
# Turn off clip adjust mouse mode.
cm = tkgui.getClipModel()
if cm is None or not cm.useClipPlane:
from chimera import dialogs
import ModelClip
cd = dialogs.find(ModelClip.ClipDialog.name)
if cd:
cd.stopMouseClip()
def activateAllCmd():
"""Activate all models. Restore previous activities if called again."""
global _prevActivities
if _prevActivities:
for m in openModels.list():
if _prevActivities.has_key(m.openState):
m.openState.active = _prevActivities[m.openState]
_prevActivities = None
if _mp:
if 'activate all' in _mp.frequentButtons:
actionButtons = _mp.freqActionButtons
else:
actionButtons = _mp.infreqActionButtons
actionButtons.component('activate all').config(text='activate all')
else:
_prevActivities = {}
for m in openModels.list():
if _prevActivities.has_key(m.openState):
continue
_prevActivities[m.openState] = m.openState.active
m.openState.active = 1
if _mp:
if 'activate all' in _mp.frequentButtons:
actionButtons = _mp.freqActionButtons
else:
actionButtons = _mp.infreqActionButtons
actionButtons.component('activate all').config(
text='restore activities')
def write_grasp_surface_file():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes = [SurfaceModel])
if len(mlist) == 0:
from chimera import replyobj
replyobj.status('No displayed surfaces')
return
varray, tarray, narray = surface_geometry(mlist)
if len(tarray) == 0:
from chimera import replyobj
replyobj.status('No displayed triangles')
return
def save_geometry(okay, d, varray=varray, tarray=tarray, narray=narray):
if not okay:
return # User canceled action.
path = d.getPaths()[0]
f = grasp_surface_file(varray, tarray, narray)
file = open(path, 'wb')
file.write(f)
file.close()
from OpenSave import SaveModeless
SaveModeless(title = "Save Surface",
filters = [('GRASP surface', ['*.srf'], '.srf')],
command = save_geometry)
def setModelFieldOnly(models, field, onVal=1, offVal=0, openState=0): # turn off first, then on, so that models not in the models list # that nonetheless have shared openStates get the 'on' value for m in openModels.list(): _setAttr(m, field, offVal, openState) for m in models: _setAttr(m, field, onVal, openState)
def save_surface_state(file):
slist = []
from chimera import openModels as om
from _surface import SurfaceModel
for s in om.list(modelTypes = [SurfaceModel]):
plist = [p for p in s.surfacePieces
if hasattr(p, 'save_in_session') and p.save_in_session]
if plist:
slist.append((s,plist))
if len(slist) == 0:
return
smslist = []
for s,plist in slist:
sms = Surface_Model_State()
sms.state_from_surface_model(s,plist)
smslist.append(sms)
from SessionUtil import objecttree
t = objecttree.instance_tree_to_basic_tree(smslist)
file.write('\n')
file.write('def restore_surfaces():\n')
file.write(' surface_state = \\\n')
objecttree.write_basic_tree(t, file, indent = ' ')
file.write('\n')
file.write(' from Surface import session\n')
file.write(' session.restore_surface_state(surface_state)\n')
file.write('\n')
file.write('try:\n')
file.write(' restore_surfaces()\n')
file.write('except:\n')
file.write(" reportRestoreError('Error restoring surfaces')\n")
file.write('\n')
def color_sphere(radius=1, pattern='circle'):
from chimera import openModels as om
from _surface import SurfaceModel
cs = [
m for m in om.list(modelTypes=[SurfaceModel])
if m.name == 'Direction colors'
]
if cs:
p = cs[0].surfacePieces[0]
else:
from Shape.shapecmd import sphere_shape
p = sphere_shape(radius=radius, modelName='Direction colors')
v, t = p.geometry
#vmask = [1 if z >= 0 else 0 for x,y,z in v]
#p.triangleAndEdgeMask = None
#p.setTriangleMaskFromVertexMask(vmask)
from numpy import empty, float32
c = empty((p.vertexCount, 4), float32)
for i, axis in enumerate(v):
c[i, :] = direction_color(axis, pattern)
p.vertexColors = c
p.useLighting = False
# f = s.addPiece(c[:,:3], t, (0.5,0.5,0.5,1))
# f.displayStyle = f.Mesh
# f.setTriangleMaskFromVertexMask(vmask)
return p
def cal_SASA(input_pdb, output_prefix):
print "pdb inputs = " + input_pdb
print "output prefix = " + output_prefix
model = openModels.open(input_pdb)
runCommand("surf :all")
out = open(output_prefix + "sasa.txt", "w")
x = '---------------------------------------------------------------------------------\n'
print "list " + str(list(model))
for m in openModels.list(modelTypes=[Molecule]):
msas = 0
for r in m.residues:
try:
sas = r.areaSAS
except AttributeError:
continue
msas = msas + sas
out.write('%s,%f\n' % (r, sas))
out.write(x)
out.write('%s,%f\n' % (m, msas))
out.write('\n')
out.close()
runCommand("del")
print msas
return msas
def write_grasp_surface_file():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes=[SurfaceModel])
if len(mlist) == 0:
from chimera import replyobj
replyobj.status('No displayed surfaces')
return
varray, tarray, narray = surface_geometry(mlist)
if len(tarray) == 0:
from chimera import replyobj
replyobj.status('No displayed triangles')
return
def save_geometry(okay, d, varray=varray, tarray=tarray, narray=narray):
if not okay:
return # User canceled action.
path = d.getPaths()[0]
f = grasp_surface_file(varray, tarray, narray)
file = open(path, 'wb')
file.write(f)
file.close()
from OpenSave import SaveModeless
SaveModeless(title="Save Surface",
filters=[('GRASP surface', ['*.srf'], '.srf')],
command=save_geometry)
def parse_surface_id(sid, cmdname):
if sid[:1] == '#':
sid = sid[1:]
fields = sid.split('.')
if len(fields) == 1:
fields.append('0')
try:
id, subid = int(fields[0]), int(fields[1])
except ValueError:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, sid))
return None
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(id = id, subid = subid, modelTypes = [SurfaceModel])
if len(mlist) == 0:
from Midas.midas_text import error
error('%s: No surface with id %d.%d' % (cmdname, id, subid))
return None
return mlist[0]
def fit_object_models():
from VolumeViewer import Volume
from chimera import openModels as om, Molecule
mlist = om.list(modelTypes=[Molecule, Volume])
folist = ['selected atoms'] + mlist
return folist
def setModelFieldOnly(models, field, onVal=1, offVal=0, openState=0):
# turn off first, then on, so that models not in the models list
# that nonetheless have shared openStates get the 'on' value
for m in openModels.list():
_setAttr(m, field, offVal, openState)
for m in models:
_setAttr(m, field, onVal, openState)
def close_current_models(self):
self.selected_neurons = OrderedDict([])
self.colors = []
current_models = set(openModels.list())
models_to_close = current_models - self.init_models
openModels.close(models_to_close)
update.checkForChanges() # to avoid memory leaks (see: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html)
def aniso(targets=None, color=None, smoothing=3, scale=1.0,
showEllipsoid=True, transparency=None,
axisFactor=None, axisColor=None, axisThickness=0.01,
ellipseFactor=None, ellipseColor=None, ellipseThickness=0.02):
from Midas import MidasError
if targets is None:
targets = openModels.list(modelTypes=[Molecule])
if smoothing < 1:
raise MidasError("'smoothing' must be at least 1")
if transparency is not None:
try:
transparency /= 100.0
if transparency < 0.0 or transparency > 1.0:
raise TypeError("out of range")
except TypeError:
raise MidasError(
"transparency must be a number between zero and one")
numShown = mgr().showAniso(targets, color=color,
smoothing=smoothing, scale=scale,
showEllipsoid=showEllipsoid, ellipsoidTransparency=transparency,
axisFactor=axisFactor, axisColor=axisColor, axisThickness=axisThickness,
ellipseColor=ellipseColor, ellipseFactor=ellipseFactor,
ellipseThickness=ellipseThickness)
if not numShown:
raise MidasError("No atoms chosen or none had anisotropic"
" information")
def setZoom(self):
self.writeMessageToLog("Setting zoom")
surf = self.surfaces[0]
rc = Radial_Color()
try:
rmin, rmax = rc.value_range(surf.surfacePieces[0])
except:
self.writeMessageToLog("using old Chimera radial method")
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
rmin, rmax = rc.value_range(vertices, vertex_xform=None)
while rmax is None:
self.writeMessageToLog("Contour %.2f is too big, no surface is shown"%(self.contour))
self.contour *= 0.9
self.voldata.set_parameters(surface_levels = [self.contour])
self.voldata.show('surface')
self.surfaces = openModels.list(modelTypes=[SurfaceModel])
surf = self.surfaces[0]
try:
rmin, rmax = rc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
rmin, rmax = rc.value_range(vertices, vertex_xform=None)
self.writeMessageToLog("found r_max value of %.3f"%(rmax))
## ten percent bigger to ensure that entire particle is in frame
viewsize = 1.1*rmax/self.zoom
chimera.viewer.viewSize = viewsize
#self.runChimCommand('scale %.3f' % self.zoom)
self.writeMessageToLog("set view size to %.3f"%(viewsize))
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 fit_object_models(): from VolumeViewer import Volume from chimera import openModels as om, Molecule mlist = om.list(modelTypes = [Molecule, Volume]) folist = ['selected atoms'] + mlist return folist
def model(trgt, tmpl8, od):
# open target sequence
rc('open ' + trgt)
# open template structure, and generate sequence
rc('open ' + tmpl8)
rc('sequence #0')
# MAV objects
fmav = findMAVs()
target, template = fmav
tar_seq = target.seqs[0]
temp_seq = copy(template.seqs[0])
seq_name = tmpl8.split('/')[-1]
# align sequences
# get template secondary structure matrix
nb = Pmw.NoteBook()
structPage = nb.add("From Structure")
ssParams = SSParams(structPage, template.prefs)
kw = {'ssMatrix': ssParams.getMatrix()}
# generalize these vars later. tired of hacking rn.
# match target fasta sequence to template pdb sequence
target.alignSeq(temp_seq, displayName=seq_name,
matrix=template.prefs[MATRIX], gapOpenStrand=-18.0,
scoreGap=-1, scoreGapOpen=-12, gapOpenHelix=-18.0,
gapOpenOther=-6.0, gapChar='.', guideSeqs=None,
ssFraction=0.3, **kw)
# run modeller on alignment
kw = {'licenseKey': 'MODELIRANJE'}
ModellerBase.model(target, tar_seq, openModels.list(modelTypes=[Molecule]),
'5', 1, 1, 0, veryFast=0, **kw)
def unclip_command(cmdname, args):
if len(args) == 0:
from chimera import openModels as om
unclip_models(om.list())
else:
from Midas.midas_text import doExtensionFunc
doExtensionFunc(unclip_models, args)
def remove_sphere_key():
from chimera import openModels as om
from _surface import SurfaceModel
om.close([
m for m in om.list(modelTypes=[SurfaceModel])
if m.name == 'Direction colors'
])
def mainchain():
import re
from chimera import openModels, Molecule
mainChain = re.compile("^(N|CA|C)$", re.I)
for m in openModels.list(modelTypes=[Molecule]):
for a in m.atoms:
a.display = mainChain.match(a.name) != None
def find_molecule_by_name(name):
from chimera import openModels, Molecule
mlist = openModels.list(modelTypes=[Molecule])
for m in mlist:
if m.name == name:
return m
return None
def all_atoms():
from chimera import openModels, Molecule
mlist = openModels.list(modelTypes = [Molecule])
atoms = []
for m in mlist:
atoms.extend(m.atoms)
return atoms
def mainchain():
import re
from chimera import openModels, Molecule
mainChain = re.compile("^(N|CA|C)$", re.I)
for m in openModels.list(modelTypes=[Molecule]):
for a in m.atoms:
a.display = mainChain.match(a.name) != None
def find_molecule_by_name(name):
from chimera import openModels, Molecule
mlist = openModels.list(modelTypes = [Molecule])
for m in mlist:
if m.name == name:
return m
return None
def selected_surface_pieces(self):
plist = Surface.selected_surface_pieces()
if len(plist) > 0:
return plist
plist = []
for m in openModels.list(modelTypes = [SurfaceModel]):
plist.extend(m.surfacePieces)
return plist
def marker_sets():
from chimera import openModels as om, Molecule
msets = [
m.marker_set for m in om.list(modelTypes=[Molecule])
if hasattr(m, 'marker_set')
]
return msets
def colorable_surface_models():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes = [SurfaceModel])
from SurfaceCap import is_surface_cap
mlist = [m for m in mlist if not is_surface_cap(m)]
return mlist
def surface_models():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes=[SurfaceModel])
from SurfaceCap import is_surface_cap
mlist = filter(lambda m: not is_surface_cap(m), mlist)
return mlist
def colorable_surface_models():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes=[SurfaceModel])
from SurfaceCap import is_surface_cap
mlist = [m for m in mlist if not is_surface_cap(m)]
return mlist
def activate_models(self, active):
from chimera import openModels
for m in openModels.list():
m.openState.active = active
m = self.box_model.model()
if m:
m.openState.active = True
def undo_symmetry_copies(molecules = None):
mlist = molecules
if mlist is None:
from chimera import openModels as om, Molecule
mlist = om.list(modelTypes = [Molecule])
mlist = [m for m in mlist if hasattr(m, 'symmetry_copies')]
for mol in mlist:
remove_symmetry_copies(mol)
def undo_symmetry_copies(molecules=None):
mlist = molecules
if mlist is None:
from chimera import openModels as om, Molecule
mlist = om.list(modelTypes=[Molecule])
mlist = [m for m in mlist if hasattr(m, 'symmetry_copies')]
for mol in mlist:
remove_symmetry_copies(mol)
def colorBB():
red = getColorByName('red')
yellow = getColorByName('yellow')
# return a list of opened molecules
for mol in openModels.list(modelTypes=[Molecule]):
mol.color = red # change model color to be red
atoms = mol.atoms
for atom in atoms:
if atom.name == 'CA':
atom.color = yellow
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 chosen_atoms(self):
m = self.molecule_menu.getvalue()
from chimera import Molecule, openModels, selection
if isinstance(m, Molecule):
return [m], False
elif m == 'selected atoms':
mlist = list(set([a.molecule for a in selection.currentAtoms()]))
return mlist, True
elif m == 'all molecules':
mlist = openModels.list(modelTypes=[Molecule])
return mlist, False
return [], False
def default_molecule():
from chimera import openModels, Molecule
mlist = openModels.list(modelTypes = [Molecule])
mlist = [m for m in mlist if not hasattr(m, 'symmetry_xform')]
if len(mlist) == 0:
from Midas import MidasError
raise MidasError, 'No molecules are opened'
elif len(mlist) > 1:
from Midas import MidasError
raise MidasError, 'Multiple molecules opened, must specify one'
mol = mlist[0]
return mol
def default_molecule():
from chimera import openModels, Molecule
mlist = openModels.list(modelTypes=[Molecule])
mlist = [m for m in mlist if not hasattr(m, 'symmetry_xform')]
if len(mlist) == 0:
from Midas import MidasError
raise MidasError, 'No molecules are opened'
elif len(mlist) > 1:
from Midas import MidasError
raise MidasError, 'Multiple molecules opened, must specify one'
mol = mlist[0]
return mol
def chosen_atoms(self):
m = self.molecule_menu.getvalue()
from chimera import Molecule, openModels, selection
if isinstance(m, Molecule):
return [m], False
elif m == 'selected atoms':
mlist = list(set([a.molecule for a in selection.currentAtoms()]))
return mlist, True
elif m == 'all molecules':
mlist = openModels.list(modelTypes = [Molecule])
return mlist, False
return [], False
def getChains():
"""Get the chain names in a protein molecule"""
#TODO, check if there is a quick method to get the list of chains
mols = openModels.list(modelTypes=[Molecule])
chains = []
m = mols[0] # get the first model
for residue in m.residues:
if residue.id.chainId not in chains:
chains.append(str(residue.id.chainId))
chains = sorted(chains)
return chains
def alignModels(preexistingModels): """Transform session models so model with lowest id has the same transform as the preexisting model with lowest id.""" from chimera import openModels pset = set(preexistingModels) newModels = [m for m in openModels.list() if not m in pset] pxf = lowestIdXform(preexistingModels) nxf = lowestIdXform(newModels) if pxf is None or nxf is None: return xf = nxf.inverse() xf.premultiply(pxf) for os in set([m.openState for m in newModels]): os.globalXform(xf)
def selection_surface_distance():
from chimera import selection
alist = selection.currentAtoms()
if len(alist) == 0:
from chimera.replyobj import status
status('No atoms or markers selected')
return
from chimera import openModels
from _surface import SurfaceModel
smlist = openModels.list(modelTypes = [SurfaceModel])
write_surface_distances(alist, smlist)
def find_surface_model(model_id):
from chimera import openModels as om
if model_id is None or model_id == (om.Default, om.Default):
return
from _surface import SurfaceModel
id, subid = model_id
slist = om.list(id = id, subid = subid, modelTypes = [SurfaceModel])
if len(slist) > 1:
raise CommandError, 'multiple surfaces with model id %d' % model_id
if len(slist) == 1:
return slist[0]
return None
def all_surface_pieces(include_outline_boxes=True):
from _surface import SurfacePiece, SurfaceModel
from chimera import openModels as om
slist = om.list(modelTypes=[SurfaceModel])
plist = []
if include_outline_boxes:
for s in slist:
plist.extend(s.surfacePieces)
else:
for s in slist:
plist.extend(
[p for p in s.surfacePieces if not hasattr(p, 'outline_box')])
return plist
def alignModels(preexistingModels):
"""Transform session models so model with lowest id has the
same transform as the preexisting model with lowest id."""
from chimera import openModels
pset = set(preexistingModels)
newModels = [m for m in openModels.list() if not m in pset]
pxf = lowestIdXform(preexistingModels)
nxf = lowestIdXform(newModels)
if pxf is None or nxf is None:
return
xf = nxf.inverse()
xf.premultiply(pxf)
for os in set([m.openState for m in newModels]):
os.globalXform(xf)
def model(tmpl8, loops):
# open template structure, and generate sequence
rc('open ' + tmpl8)
rc('sequence #0; wait')
# MAV objects
fmav = findMAVs()
template = fmav[0]
temp_seq = template.seqs[0]
seq_name = tmpl8.split('/')[-1]
# run modeller on alignment
kw = {'licenseKey': 'MODELIRANJE'}
ModellerBase.model(template, temp_seq, openModels.list(modelTypes=[Molecule]),
'10', 1, 1, 0, veryFast=0, loopInfo=('', loops), **kw)
def destroy(self): if self.cavities: cav1 = self.cavities[0] atoms = (cav1.mouthInfo["atoms"].atoms() or cav1.pocketInfo["atoms"].atoms()) if atoms: # close surface too... from chimera import openModels mol = atoms[0].molecule openModels.close(openModels.list( id=mol.id, subid=mol.subid)) for chk in [self.doSelect, self.doColor, self.doSurface, self.doZoom, self.excludeMouth]: chk.destroy() chimera.extension.manager.deregisterInstance(self) ModelessDialog.destroy(self)
def beginRestore():
# temporarily make these names available in the SimpleSession module
import SimpleSession
from SimpleSession import BEGIN_RESTORE_SESSION
chimera.triggers.activateTrigger(BEGIN_RESTORE_SESSION, None)
SimpleSession.registerAfterModelsCB = registerAfterModelsCB
SimpleSession.reportRestoreError = reportRestoreError
SimpleSession.findFile = findFile
SimpleSession.getColor = getColor
SimpleSession.idLookup = idLookup
SimpleSession.modelMap = {}
from SimpleSession.versions import highestOpenID
SimpleSession.modelOffset = highestOpenID() + 1
from chimera import openModels
SimpleSession.preexistingModels = openModels.list()
SimpleSession.mergedSession = (len(SimpleSession.preexistingModels) > 0)
def beginRestore(): # temporarily make these names available in the SimpleSession module import SimpleSession SimpleSession.updateOSLmap = updateOSLmap SimpleSession.registerAfterModelsCB = registerAfterModelsCB SimpleSession.oslMap = oslMap SimpleSession.reportRestoreError = reportRestoreError SimpleSession.findFile = findFile SimpleSession.oslLookup = oslLookup SimpleSession.getColor = getColor SimpleSession.weedOSLlist = weedOSLlist SimpleSession.weedOSLdict = weedOSLdict from SimpleSession.versions import highestOpenID SimpleSession.modelOffset = highestOpenID() + 1 from chimera import openModels SimpleSession.preexistingModels = openModels.list() SimpleSession.mergedSession = (len(SimpleSession.preexistingModels) > 0)
def __init__(self, movie):
self.movie = movie
self.data = numpy.load('gtm.dat')
self.k = self.data['k'] # number of cells of the map
self.nx = self.data['nx'] # Number of cells of the map for dimension x
self.ny = self.data['ny'] # Number of cells of the map for dimension y
self.logR = self.data['logR']
R = numpy.exp(self.logR)
mask = (R.sum(axis=1).reshape(self.nx, self.ny) ==0)
self.matrix = -self.data['log_density']
self.matrix[mask] = numpy.nan
self.min_value = numpy.nanmin(self.matrix)
PlotDialog.__init__(self, self.min_value, numpy.nanmax(self.matrix))
self.master = self._master
self.displayed_matrix = self.matrix
self.selection_mode = 'Cell'
self.bmus = numpy.asarray([numpy.unravel_index(e, (self.nx,self.ny))
for e in range(self.k)])
self.selected_neurons = OrderedDict([])
self.colors = [] # colors of the dot in the map
self.subplot = self.add_subplot(1, 1, 1)
self.colorbar = None
self.cluster_map = None
self.highlighted_cluster = None
self._displayData()
movie.triggers.addHandler(self.movie.NEW_FRAME_NUMBER, self.update_bmu, None)
self.registerPickHandler(self.onPick)
self.figureCanvas.mpl_connect("key_press_event", self.onKey)
self.figureCanvas.mpl_connect("key_release_event", self.offKey)
self.keep_selection = False
self.init_models = set(openModels.list())
self.movie_id = movie.model.id
self.i, self.j = None, None # current neuron
self.rmsd_list = None
self.rep_rmsd = None
self.experimental_data_filename = None
self.data_driven_clusters = None
self.ctrl_pressed = False
self.motion_notify_event = None
self.slice_id = 0 # slice of the matrix to display for high dimensional data
self.plot1D = None # 1D plot for multidimensional features
self.clustermode = (1,'Frames') # to display either Density map or ensemble of frames
self.rep_map = numpy.zeros((self.nx, self.ny))
for i in range(self.nx):
for j in range(self.ny):
self.rep_map[i,j] = numpy.ravel_multi_index((i,j), (self.nx, self.ny))
def focusCmd(models):
from chimera import openModels, viewer, update
shown = {}
for m in openModels.list():
shown[m] = m.display
if m in models:
m.display = 1
else:
m.display = 0
update.checkForChanges()
viewer.viewAll()
if chimera.openModels.cofrMethod != chimera.OpenModels.Independent:
openModels.cofrMethod = openModels.CenterOfView
viewer.clipping = True
for m,disp in shown.items():
m.display = disp
update.checkForChanges()
def create_volume_plane_surface(volume, height, interpolate = 'cubic',
mesh = 'isotropic', colormap = 'rainbow',
smoothing_factor = 0.3,
smoothing_iterations = 0,
color = (.7, .7, .7, 1),
replace = True):
m = volume.matrix()
axes = [a for a in range(3) if m.shape[2-a] == 1]
if len(axes) != 1:
from chimera.replyobj import warning
warning('Volume %s has more than one plane shown (%d,%d,%d)' %
((volume.name,) + tuple(reversed(m.shape))))
return
axis = axes[0]
m = m.squeeze() # Convert 3d array to 2d
tf = volume.matrix_indices_to_xyz_transform()
perm = {0: ((0,0,1,0),(1,0,0,0),(0,1,0,0)), # 2d matrix xyh -> 3d yzx
1: ((1,0,0,0),(0,0,1,0),(0,1,0,0)), # 2d matrix xyh -> 3d xzy
2: ((1,0,0,0),(0,1,0,0),(0,0,1,0))}[axis]
from Matrix import multiply_matrices
tf = multiply_matrices(tf, perm)
s = create_surface(m, height, tf, color, interpolate, mesh,
smoothing_factor, smoothing_iterations)
s.name = volume.name + ' height'
if colormap == 'rainbow':
invert = not height is None and height < 0
tf = volume.data.ijk_to_xyz_transform
normal = [tf[i][axis] for i in range(3)]
colormap_surface(s, normal, rainbow_colormap(invert))
from chimera import openModels
if replace:
openModels.close([m for m in openModels.list()
if getattr(m, 'topography_volume', None) == volume])
openModels.add([s])
s.openState.xform = volume.model_transform()
s.topography_volume = volume
return s
