def _createRotation(self):
selBonds = selection.currentBonds()
if len(selBonds) == 1:
addRotation(selBonds[0])
return
replyobj.error("Exactly one bond must be selected "
"in graphics window\n")
def unselBonds(): from chimera.selection import currentBonds selBonds = currentBonds(asDict=True) unsel = [] for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): unsel.extend(filter(lambda b: b not in selBonds, m.bonds)) return unsel
def unselBonds():
from chimera.selection import currentBonds
selBonds = currentBonds(asDict=True)
unsel = []
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
unsel.extend(filter(lambda b: b not in selBonds, m.bonds))
return unsel
def selected_links(self):
links = []
bonds = selection.currentBonds()
for b in bonds:
if self.bond_to_link.has_key(b):
links.append(self.bond_to_link[b])
return links
def selected_links(self):
links = []
from chimera.selection import currentBonds
bonds = currentBonds()
for b in bonds:
if self.bond_to_link.has_key(b):
links.append(self.bond_to_link[b])
return links
def print_path_length():
from chimera import selection
bonds = selection.currentBonds()
msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def print_path_length(): from chimera import selection bonds = selection.currentBonds() msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds)) from chimera import replyobj replyobj.status(msg) # Show on status line replyobj.message(msg) # Record in reply log
def select_connected():
'Select atoms and bonds connected to currently selected atoms and bnods'
from chimera import selection, Atom
atoms_and_bonds = selection.currentAtoms() + selection.currentBonds()
reached = set(atoms_and_bonds)
i = 0
while i < len(atoms_and_bonds):
ab = atoms_and_bonds[i]
if isinstance(ab, Atom):
n = ([b for b in ab.bonds if not b in reached] +
[a for a in ab.neighbors if not a in reached])
else:
n = [a for a in ab.atoms if not a in reached]
atoms_and_bonds.extend(n)
reached.update(set(n))
i += 1
selection.setCurrent(atoms_and_bonds)
def print_model_path_lengths():
from chimera import selection
bonds = selection.currentBonds()
mbonds = {}
for b in bonds:
m = b.molecule
if m in mbonds:
mbonds[m].append(b)
else:
mbonds[m] = [b]
for m, bonds in mbonds.items():
msg = ('%s: %d bonds with total length %g\n' %
(m.name, len(bonds), path_length(bonds)))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def print_model_path_lengths():
from chimera import selection
bonds = selection.currentBonds()
mbonds = {}
for b in bonds:
m = b.molecule
if m in mbonds:
mbonds[m].append(b)
else:
mbonds[m] = [b]
for m, bonds in mbonds.items():
msg = ('%s: %d bonds with total length %g\n'
% (m.name, len(bonds), path_length(bonds)))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def zone_cb(self, event=None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from SurfaceZone import path_points, surface_zone
points = path_points(atoms, bonds, surface.openState.xform.inverse())
if len(points) > 0:
surface_zone(surface, points, radius, auto_update=True)
else:
self.message('No atoms are selected')
def zone_cb(self, event = None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from SurfaceZone import path_points, surface_zone
points = path_points(atoms, bonds, surface.openState.xform.inverse())
if len(points) > 0:
surface_zone(surface, points, radius, auto_update = True)
else:
self.message('No atoms are selected')
def color_zone_cb(self, event = None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
xform_to_surface = surface.openState.xform.inverse()
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from ColorZone import points_and_colors, color_zone
points, colors = points_and_colors(atoms, bonds, xform_to_surface)
if len(points) > 0:
color_zone(surface, points, colors, radius, auto_update = True)
else:
self.message('No atoms are selected')
def _any_selected(self):
from chimera import selection, Molecule, MSMSModel, PseudoBondGroup
text = ""
numAtoms = len(selection.currentAtoms())
if numAtoms:
text = "%d atom" % numAtoms
if numAtoms > 1:
text += "s"
numBonds = len(selection.currentBonds())
if numBonds:
if text:
text += ", "
text += "%d bond" % numBonds
if numBonds > 1:
text += "s"
numEdges = len(selection.currentEdges())
if numEdges != numBonds:
if text:
text += ", "
numPBonds = numEdges - numBonds
text += "%d pbond" % numPBonds
if numPBonds > 1:
text += "s"
graphs = selection.currentGraphs()
numSurfs = numObjs = 0
for g in graphs:
if isinstance(g, (Molecule, PseudoBondGroup)):
continue
if isinstance(g,
MSMSModel) or "surf" in g.__class__.__name__.lower():
numSurfs += 1
else:
numObjs += 1
if numSurfs:
if text:
text += ", "
text += "%d surf" % numSurfs
if numSurfs > 1:
text += "s"
if numObjs:
if text:
text += ", "
text += "%d obj" % numObjs
if numObjs > 1:
text += "s"
import help
if not text:
help.register(self.selections_button, balloon="no selection")
show_message("selection cleared", blankAfter=5)
return False
else:
help.register(self.selections_button, balloon=text)
if self.first_selection:
self.first_selection = False
show_message(text,
followWith="up-arrow to increase selection "
"(atoms->residues->chains etc.)")
else:
show_message(text)
return True
def selBonds(noneReturnsAll=True, implied=False, create=False):
bonds = selection.currentBonds()
extendSelection(bonds, 'bonds', noneReturnsAll, implied, create)
return bonds
def _any_selected(self):
from chimera import selection, Molecule, MSMSModel, PseudoBondGroup
text = ""
numAtoms = len(selection.currentAtoms())
if numAtoms:
text = "%d atom" % numAtoms
if numAtoms > 1:
text += "s"
numBonds = len(selection.currentBonds())
if numBonds:
if text:
text += ", "
text += "%d bond" % numBonds
if numBonds > 1:
text += "s"
numEdges = len(selection.currentEdges())
if numEdges != numBonds:
if text:
text += ", "
numPBonds = numEdges - numBonds
text += "%d pbond" % numPBonds
if numPBonds > 1:
text += "s"
graphs = selection.currentGraphs()
numSurfs = numObjs = 0
for g in graphs:
if isinstance(g, (Molecule, PseudoBondGroup)):
continue
if isinstance(g, MSMSModel) or "surf" in g.__class__.__name__.lower():
numSurfs += 1
else:
numObjs += 1
if numSurfs:
if text:
text += ", "
text += "%d surf" % numSurfs
if numSurfs > 1:
text += "s"
if numObjs:
if text:
text += ", "
text += "%d obj" % numObjs
if numObjs > 1:
text += "s"
import help
if not text:
help.register(self.selections_button, balloon="no selection")
show_message("selection cleared", blankAfter=5)
return False
else:
help.register(self.selections_button, balloon=text)
if self.first_selection:
self.first_selection = False
show_message(text, followWith="up-arrow to increase selection "
"(atoms->residues->chains etc.)")
else:
show_message(text)
return True
def selBonds(noneReturnsAll=True, implied=False, create=False): bonds = selection.currentBonds() extendSelection(bonds, 'bonds', noneReturnsAll, implied, create) return bonds