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 activate_only():
'Activate only selected models'
from chimera import selection, Model
osactive = set([
m.openState for m in selection.currentGraphs() if isinstance(m, Model)
])
osall = set([m.openState for m in chimera.openModels.list()])
for os in osall:
os.active = (os in osactive)
def mark_zero():
from VolumePath import place_marker, show_volume_path_dialog
from chimera import selection as s, Point
mlist = s.currentGraphs()
if len(mlist) == 0:
place_marker((0, 0, 0))
else:
for m in mlist:
m0 = m.openState.xform.apply(Point(0, 0, 0)).data()
place_marker(m0)
show_volume_path_dialog()
def test(spacing=200.0, tip_length=50):
from Segger.regions import Segmentation
from chimera import selection
segs = [
m for m in selection.currentGraphs() if isinstance(m, Segmentation)
]
for seg in segs:
for r in seg.selected_regions():
mset = trace_spine(r, spacing, tip_length, r.color)
mset.region = r
def mark_zero():
from VolumePath import place_marker, show_volume_path_dialog
from chimera import selection as s, Point
mlist = s.currentGraphs()
if len(mlist) == 0:
place_marker((0,0,0))
else:
for m in mlist:
m0 = m.openState.xform.apply(Point(0,0,0)).data()
place_marker(m0)
show_volume_path_dialog()
def _selChangeCB(self, *args): selGraphs = set(selection.currentGraphs()) itemModels = set([item.model for item in geomManager.items]) selItems = selGraphs & itemModels chosenItems = set([item.model for item in self.table.selected()]) if chosenItems != selItems: items = [item for item in geomManager.items if item.model in selItems] self.table.select(items) if self.geomSelAtomsVar.get(): self._itemsSelectAtoms(items, add=True) self.feedback(items)
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box=not shown)
v.show()
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box = not shown)
v.show()
def clip_adjust():
'Toggle mouse modes to move per-model clip plane of selected model'
from chimera import selection, openModels, tkgui
mlist = [
m for m in selection.currentGraphs() if m.useClipPlane and m.display
]
if len(mlist) == 0:
mlist = [m for m in openModels.list() if m.useClipPlane and m.display]
if clip_adjust_enabled():
if len(mlist) == 0 or tkgui.getClipModel() in mlist:
enable_clip_adjust(False)
else:
tkgui.setClipModel(mlist[0])
elif mlist:
enable_clip_adjust(mlist[0])
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 unselModels(): from chimera.selection import currentGraphs selModels = currentGraphs(asDict=True) return filter(lambda m: m not in selModels, chimera.openModels.list())
rc("open " + fn)
#Add Gasteiger charges
initiateAddCharges(method='gasteiger', nogui=True)
rc('surface vertexDensity 2') # Add surface to molecule
rc('coulombic -10 red 0 white 10 blue'
) # Colr surface by coulombic charge
rc(
'select'
) # Select the molecule from the model panel, also selects the surface for processing
#------------------------------------------------------------------
# Surface processing
#------------------------------------------------------------------
#Surface processing section
slist = [m for m in selection.currentGraphs() if isinstance(m, MSMSModel)
] # initiates selected surface to object
vertices = [] # empty list to populate with vertices
s = slist[0] # takes the surface from the surface object
p = s.surfacePieces[0] # Function of MSMSModel
va, ta = p.geometry #Extract the list of vertices and triangles
rgba = p.vertexColors
'''
coords = []
for i, v in enumerate(va):
x, y, z = v #Get cartesian coordinates of vertex
point = (x, y, z) #Convert coords to tuple.....durh, probably could have just used the v vertex object here
coords.append(point) #Add the distance to the coords list
'''
def unselModels():
from chimera.selection import currentGraphs
selModels = currentGraphs(asDict=True)
return filter(lambda m: m not in selModels, chimera.openModels.list())
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
