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 make_molecule_map(atoms, resolution, step, pad, cutoff_range, sigma_factor,
display_threshold, model_id, replace, show_dialog):
atoms = tuple(atoms)
grid, molecules = molecule_grid_data(atoms, resolution, step, pad,
cutoff_range, sigma_factor)
from chimera import openModels as om
if replace:
from VolumeViewer import volume_list
vlist = [
v for v in volume_list()
if getattr(v, 'molmap_atoms', None) == atoms
]
om.close(vlist)
from VolumeViewer import volume_from_grid_data
v = volume_from_grid_data(grid, open_model=False, show_dialog=show_dialog)
v.initialize_thresholds(mfrac=(display_threshold, 1), replace=True)
v.show()
v.molmap_atoms = tuple(atoms) # Remember atoms used to calculate volume
v.molmap_parameters = (resolution, step, pad, cutoff_range, sigma_factor)
if len(molecules) == 1 and model_id is None:
om.add([v], sameAs=tuple(molecules)[0])
else:
if model_id is None:
model_id = (om.Default, om.Default)
om.add([v], baseId=model_id[0], subid=model_id[1])
v.openState.xform = atoms[0].molecule.openState.xform
return v
def removeAniso(self, targets):
if isinstance(targets, dict):
molMap = targets
else:
molMap = self._makeMolMap(targets)
someShowing = bool(self._surfMap)
for m, atoms in molMap.items():
if m not in self._surfMap:
continue
surfMap = self._surfMap[m]
for a in atoms:
try:
pieceInfo = surfMap[a]
except KeyError:
continue
if not a.__destroyed__:
a.labelOffset = None
for key, pieces in pieceInfo.items():
if key == "anisoParams" or not pieces:
continue
for piece in pieces:
piece.model.removePiece(piece)
del surfMap[a]
del self._atomMolLookup[a]
if len(surfMap) == 1:
openModels.close([surfMap.pop("model")])
del self._surfMap[m]
if someShowing and not self._surfMap:
triggers.deleteHandler('Atom', self._handlerID)
def make_molecule_map(atoms, resolution, step, pad, cutoff_range,
sigma_factor, display_threshold, model_id, replace,
show_dialog):
atoms = tuple(atoms)
grid, molecules = molecule_grid_data(atoms, resolution, step, pad,
cutoff_range, sigma_factor)
from chimera import openModels as om
if replace:
from VolumeViewer import volume_list
vlist = [v for v in volume_list()
if getattr(v, 'molmap_atoms', None) == atoms]
om.close(vlist)
from VolumeViewer import volume_from_grid_data
v = volume_from_grid_data(grid, open_model = False,
show_dialog = show_dialog)
v.initialize_thresholds(mfrac = (display_threshold, 1), replace = True)
v.show()
v.molmap_atoms = tuple(atoms) # Remember atoms used to calculate volume
v.molmap_parameters = (resolution, step, pad, cutoff_range, sigma_factor)
if len(molecules) == 1 and model_id is None:
om.add([v], sameAs = tuple(molecules)[0])
else:
if model_id is None:
model_id = (om.Default, om.Default)
om.add([v], baseId = model_id[0], subid = model_id[1])
v.openState.xform = atoms[0].molecule.openState.xform
return v
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 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 close(self):
if self.molecule:
from chimera import openModels
openModels.close([self.molecule])
if self.curve_model:
from chimera import openModels
openModels.close([self.curve_model])
self.curve_model = None
def remove_extra_copies(m, nkeep):
clist = []
while True:
name = m.name + (' #%d' % (len(clist)+nkeep+1))
c = find_model_by_name(name)
if c is None:
break
clist.append(c)
from chimera import openModels
openModels.close(clist)
def remove_extra_copies(m, nkeep):
clist = []
while True:
name = m.name + (' #%d' % (len(clist) + nkeep + 1))
c = find_model_by_name(name)
if c is None:
break
clist.append(c)
from chimera import openModels
openModels.close(clist)
def show_outline_cb(self):
m = self.menu_molecule()
if m == None:
return
name = self.outline_model_name(m)
om = find_model_by_name(name) # Close outline if shown
if om:
from chimera import openModels
openModels.close([om])
else:
self.show_outline_model(m)
def show_outline_cb(self):
m = self.menu_molecule()
if m == None:
return
name = self.outline_model_name(m)
om = find_model_by_name(name) # Close outline if shown
if om:
from chimera import openModels
openModels.close([om])
else:
self.show_outline_model(m)
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 generate_images(cubs, pdbs):
if 'CHIMERA' not in os.environ:
sys.exit("To render movies, you must run the script with "
"pychimera: pychimera wfnmovie.py [...]")
from chimera import runCommand as rc, openModels
print('Generating .png images for {} cub/pdb files'.format(len(cubs)))
for i, (cub, pdb) in tqdm(enumerate(zip(cubs, pdbs))):
cubmodel = openModels.open(cub)[0]
pdbmodel = openModels.open(pdb)[0]
rc('vol #0 level 0.70')
rc('scolor #0 gradient #0 cmap rainbow')
rc('transp 50 #0')
rc('turn y 180')
rc('turn x -60')
rc('focus')
rc('copy file {}.png width 1280 height 720'.format(cub.split('.')[0]))
openModels.close([cubmodel, pdbmodel])
def show_crystal_contacts(
molecule,
dist,
make_copies=False,
angle_tolerance=pi / 1800, # 0.1 degrees
shift_tolerance=0.1, # Angstroms
replace=False):
if not hasattr(molecule, 'pdbHeaders'):
return None
# Find all unique pairs of contacting asymmetric units.
clist = report_crystal_contacts(molecule, dist, angle_tolerance,
shift_tolerance)
crystal = Crystal(molecule.pdbHeaders)
# Incorrect matrices in PDB header may not be orthogonal. Check.
check_orthogonality(crystal.ncs_matrices, 'NCS', tolerance=1e-3)
check_orthogonality(crystal.smtry_matrices, 'SMTRY', tolerance=1e-3)
# Get list of clashing asymmetric units.
asu_list = contacting_asymmetric_units(clist,
crystal,
include_000_unit_cell=True)
# Place markers representing each asym unit.
marker_set = contact_marker_model(molecule, crystal, clist, asu_list)
cmodels = [marker_set.marker_model()]
if make_copies:
# Make molecule copies.
cm = make_asu_copies(molecule, contacting_asu(clist), crystal)
cmodels.extend(cm)
# Zoom to show all asym units.
zoom_to_fit(padding=0.05)
# Remember contact models so they can be replaced if recalculated.
if replace and hasattr(molecule, 'crystal_contact_models'):
from chimera import openModels
openModels.close(molecule.crystal_contact_models)
molecule.crystal_contact_models = cmodels
return cmodels
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
def show_crystal_contacts(molecule, dist,
make_copies = False,
angle_tolerance = pi/1800, # 0.1 degrees
shift_tolerance = 0.1, # Angstroms
replace = False):
if not hasattr(molecule, 'pdbHeaders'):
return None
# Find all unique pairs of contacting asymmetric units.
clist = report_crystal_contacts(molecule, dist,
angle_tolerance, shift_tolerance)
crystal = Crystal(molecule.pdbHeaders)
# Incorrect matrices in PDB header may not be orthogonal. Check.
check_orthogonality(crystal.ncs_matrices, 'NCS', tolerance = 1e-3)
check_orthogonality(crystal.smtry_matrices, 'SMTRY', tolerance = 1e-3)
# Get list of clashing asymmetric units.
asu_list = contacting_asymmetric_units(clist, crystal,
include_000_unit_cell = True)
# Place markers representing each asym unit.
marker_set = contact_marker_model(molecule, crystal, clist, asu_list)
cmodels = [marker_set.marker_model()]
if make_copies:
# Make molecule copies.
cm = make_asu_copies(molecule, contacting_asu(clist), crystal)
cmodels.extend(cm)
# Zoom to show all asym units.
zoom_to_fit(padding = 0.05)
# Remember contact models so they can be replaced if recalculated.
if replace and hasattr(molecule, 'crystal_contact_models'):
from chimera import openModels
openModels.close(molecule.crystal_contact_models)
molecule.crystal_contact_models = cmodels
return cmodels
def close_model(self):
v = self.volume
if v:
from chimera import openModels
openModels.close([v])
if refMol == None:
refMol = mols[:1]
if len(refMol) == 0:
raise MidasError("No reference molecule specified")
elif len(refMol) > 1:
raise MidasError("Multiple reference molecules specified")
refMol = refMol[0]
if modelId is not None and type(modelId) != int:
try:
modelId = int(modelId[1:])
except:
raise MidasError("modelId value must be integer")
from chimera import suppressNewMoleculeProcessing, \
restoreNewMoleculeProcessing
suppressNewMoleculeProcessing()
try:
m = combine(mols, refMol, newChainIDs=newChainIDs, log=log)
except CombineError, v:
restoreNewMoleculeProcessing()
raise MidasError(v)
from chimera import openModels
m.name = name
kw = {'shareXform': False}
if modelId != None:
kw['baseId'] = modelId
openModels.add([m], **kw)
m.openState.xform = refMol.openState.xform
restoreNewMoleculeProcessing()
if close:
openModels.close(mols)
if refMol == None:
refMol = mols[:1]
if len(refMol) == 0:
raise MidasError("No reference molecule specified")
elif len(refMol) > 1:
raise MidasError("Multiple reference molecules specified")
refMol = refMol[0]
if modelId is not None and type(modelId) != int:
try:
modelId = int(modelId[1:])
except:
raise MidasError("modelId value must be integer")
from chimera import suppressNewMoleculeProcessing, \
restoreNewMoleculeProcessing
suppressNewMoleculeProcessing()
try:
m = combine(mols, refMol, newChainIDs=newChainIDs, log=log)
except CombineError, v:
restoreNewMoleculeProcessing()
raise MidasError(v)
from chimera import openModels
m.name = name
kw = {'shareXform': False}
if modelId != None:
kw['baseId'] = modelId
openModels.add([m], **kw)
m.openState.xform = refMol.openState.xform
restoreNewMoleculeProcessing()
if close:
openModels.close(mols)
def make_orthoslice_images(
rlist, # Segmentation regions.
volume, # Volume model.
trace_spacing=None, # Physical units.
trace_tip_length=None, # Physical units.
unbend_size=1.5, # Factor multipied by region diameter.
unbend_yaxis=(0, 0, 1),
unbend_grid_spacing=1, # Factor multiplied by minimum voxel size.
slice_spacing=None, # 3-tuple, physical units.
xy_trim=0.3, # Factor multipled by unbent grid width/height.
panel_aspect=0.5, # Minimum aspect ratio for tiled layout.
image_spacing=20, # Pixels between 3 sets of slices.
show_image=True,
task=None,
):
from math import ceil
from Measure.spine import trace_spine, measure_diameter
from VolumeFilter.unbend import atom_path, unbend_volume
from VolumeFilter.tile import tile_planes
from chimera import openModels
ubgs = unbend_grid_spacing * min(volume.data.step)
axes = ('x', 'y', 'z')
pstep = (10, 10, 10) if slice_spacing is None else [
int(ceil(s / ubgs)) for s in slice_spacing
]
orders = ('ulh', 'urv', 'ulhr')
for ri, r in enumerate(rlist):
if task:
task.updateStatus('region %d (%d of %d)' %
(r.rid, ri + 1, len(rlist)))
# Trace center-line.
mset = trace_spine(r, trace_spacing, trace_tip_length)
# Unbend volume.
p = atom_path([m.atom for m in mset.markers()])
dmax, dmin = measure_diameter(r, mset)
if dmax is None:
print 'Region %d has no diameter' % r.rid
mset.close()
continue
xsize = ysize = unbend_size * dmax
ubv = unbend_volume(volume,
p,
unbend_yaxis,
xsize,
ysize,
ubgs,
open=False)
# ubv.set_representation('solid')
# ubv.set_parameters(show_outline_box = True)
# Create tiled cross-section volumes along 3 axes.
etrim = (xy_trim * ubv.data.size[0], xy_trim * ubv.data.size[1], 0)
etrim = [int(ceil(t)) for t in etrim]
rowcol = rows_and_columns(ubv.data.size, pstep, etrim, panel_aspect)
tparams = zip(axes, pstep, etrim, rowcol, orders)
tv = [
tile_planes(ubv, axis, step, trim, rows, cols, order, open=False)
for axis, step, trim, (rows, cols), order in tparams
]
if [v for v in tv if v is None]:
print 'Region %d has no sections for some axes' % r.rid
mset.close()
openModels.close([v for v in tv if v] + [ubv])
continue
# Make images for each set of slices and combine them side-by-side.
images = (volume_image(tv[0]), volume_image(tv[1], xflip=True),
volume_image(tv[2]))
image = montage_image(images, pad=image_spacing)
image.title = 'Region %d' % r.rid
if show_image:
from Segger.imageviewer import showImage
showImage(image, title=image.title, fit_to_window=True)
# Set image region attribute
r.set_attribute('slices', image)
# Close center line.
mset.close()
def close_model(self):
v = self.volume
if v:
from chimera import openModels
openModels.close([v])
def onPick(self, event):
if self.selection_mode == 'Cell': # Select unique cells
if event.mouseevent.button == 3 or self.ctrl_pressed:
self.keep_selection = True
else:
self.keep_selection = False
if not self.keep_selection:
self.close_current_models()
else:
if len(self.selected_neurons) == 1:
if self.i is not None and self.j is not None:
self.add_model(name='%d,%d' % (self.i, self.j))
if event.mouseevent.button == 1 or event.mouseevent.button == 3:
x, y = event.mouseevent.xdata, event.mouseevent.ydata
self.j, self.i = int(x), int(y)
if (self.i, self.j) not in self.selected_neurons.keys():
frame_id = self.rep_map[self.i, self.j] + 1
if not numpy.isnan(frame_id):
frame_id = int(frame_id)
if self.keep_selection:
self.colors.append('g')
else:
self.colors.append('r')
self.display_frame(frame_id)
if self.keep_selection:
self.add_model(name='%d,%d' % (self.i, self.j))
self.selected_neurons[(self.i, self.j)] = openModels.list()[-1]
self.update_model_color()
else:
model_to_del = self.selected_neurons[(self.i, self.j)]
if model_to_del not in self.init_models:
openModels.close([model_to_del])
del self.selected_neurons[(self.i, self.j)]
self.get_basin(None) # to display the basin around the selected cell
#self._displayData() # commented as it's already done by self.get_basin(None) above
elif self.selection_mode == 'Cluster' and event.mouseevent.button == 1:
self.close_current_models()
if self.highlighted_cluster is not None:
self.highlighted_cluster[numpy.isnan(self.highlighted_cluster)] = False
self.highlighted_cluster = numpy.bool_(self.highlighted_cluster)
frame_ids = self.rep_map[self.highlighted_cluster] + 1
frame_ids = frame_ids[~numpy.isnan(frame_ids)]
n = len(frame_ids)
if self.clustermode[1] == "Frames":
if n > 10:
frame_ids = frame_ids[::n/10] # take only ten representatives
for frame_id in frame_ids:
frame_id = int(frame_id)
self.display_frame(frame_id)
self.add_model(name='cluster')
elif self.clustermode[1] == 'Density':
if n > 100:
frame_ids = frame_ids[::n/100] # take only 100 representatives
trajMol = self.movie.model._mol
if chimera.selection.currentEmpty():
#something to select all atoms
runCommand("select #%d" % self.movie_id)
atoms = [a for a in chimera.selection.currentAtoms() if a.molecule == trajMol]
name="ClusterDensityMap"
self.computeVolume(atoms, frame_ids=frame_ids,volumeName=name, spacing=self.clustermode[0])
model_id=openModels.listIds()[-1][0]
#Midas.color('aquamarine,s', '#%d' %model_id)
runCommand("volume #%d level 50. color aquamarine style surface" %model_id)
class CombineDialog(ModelessDialog):
title = "Copy/Combine Molecular Models"
help = "UsersGuide/modelpanel.html#combine"
def __init__(self, models=None):
self.initModels = models
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(parent,
listbox_selectmode='extended', labelpos='w',
label_text="Molecules to combine/copy:")
if self.initModels:
self.molListBox.setvalue(self.initModels)
self.molListBox.grid(row=0, column=0, columnspan=2,
sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
from chimera.tkoptions import StringOption, IntOption
self.molNameEntry = StringOption(parent, 1, "New model's"
" name", "combination", None)
curIDs = set([i1 for i1, i2 in openModels.listIds()])
mid = 0
while mid in curIDs:
mid += 1
self.modelID = IntOption(parent, 2, "New model's ID", mid, None)
from chimera.widgets import MoleculeOptionMenu
self.refMolMenu = MoleculeOptionMenu(parent, labelpos='w',
label_text="Coordinate system of:",
initialitem=self.initModels[0])
self.refMolMenu.grid(row=3, column=0, columnspan=2, sticky='w')
import Pmw
chb = self.chainHandlingButtons = Pmw.RadioSelect(parent,
buttontype="radiobutton", labelpos='w',
label_text="If original molecules have duplicate\n"
"single-letter chain IDs, then:", orient="vertical")
self.buttonTexts = ["rename them uniquely",
"retain them (residues may be renumbered)"]
for bt in self.buttonTexts:
chb.add(bt)
chb.setvalue(self.buttonTexts[0])
chb.grid(row=4, column=0, columnspan=2)
import Tkinter
self.closeModelsVar = Tkinter.IntVar(parent)
self.closeModelsVar.set(False)
Tkinter.Checkbutton(parent, text="Close source models",
variable=self.closeModelsVar).grid(
row=5, column=0, columnspan=2)
def Apply(self):
mols = self.molListBox.getvalue()
from chimera import UserError
if not mols:
self.enter()
raise UserError("Must specify at least one molecular"
" model to combine/copy")
from chimera import suppressNewMoleculeProcessing, \
restoreNewMoleculeProcessing
suppressNewMoleculeProcessing()
newChainIDs = (self.chainHandlingButtons.getvalue()
== self.buttonTexts[0])
refMol = self.refMolMenu.getvalue()
from Combine import combine, CombineError
try:
m = combine(mols, refMol,
newChainIDs=newChainIDs, log=True)
except CombineError, v:
restoreNewMoleculeProcessing()
self.enter()
raise UserError(v)
m.name = self.molNameEntry.get()
openModels.add([m], baseId=self.modelID.get(), shareXform=False)
m.openState.xform = refMol.openState.xform
restoreNewMoleculeProcessing()
if self.closeModelsVar.get():
openModels.close(mols)
def unshow_curve(self):
if self.curve_model:
from chimera import openModels
openModels.close([self.curve_model])
self.curve_model = None