# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
import os
import math
import Tkinter
import chimera
from chimera import selection
from chimera import chimage
from chimera import tkgui
from chimera import match
from chimera import preferences
from chimera.baseDialog import ModelessDialog
import Midas
prefs = preferences.addCategory("EnsembleCluster", preferences.HiddenCategory)
class EnsembleMatch(ModelessDialog):
"""Display a table for manipulating one ensemble relative to another.
The two ensembles should consist of conformers of the same model.
Table rows correspond to conformers in the reference ensemble.
Table columns correspond to conformers in the alternative ensemble.
A conformer in the alternative ensemble will be matched onto
a conformer in the reference ensemble when a table entry is
clicked. The table entry label is the RMSD between the two
conformers."""
title = "Ensemble Match"
help = "ContributedSoftware/ensemblematch/ensemblematch.html"
buttons = ("Save...", "Hide", "Quit")
def __init__(self, refModels, altModels, subSelection, *args, **kw):
#
# Save the subselection (part of model to match)
# as well as the model lists (ordered by subid)
#
self.subSelection = subSelection
l = [ (m.subid, m) for m in refModels ]
l.sort()
self.refModels = [ t[1] for t in l ]
l = [ (m.subid, m) for m in altModels ]
l.sort()
self.altModels = [ t[1] for t in l ]
#
# Grab the atomic coordinates that will be used
# to compute RMSDs and check for errors
#
self.atomDict = {}
counts = []
for ml in self.refModels, self.altModels:
for m in ml:
osl = '%s%s' % (m.oslIdent(), self.subSelection)
try:
s = selection.OSLSelection(osl)
except SyntaxError:
from chimera import UserError
raise UserError("Atom specifier for ensemble match is mangled")
atoms = s.atoms()
self.atomDict[m] = match._coordArray(atoms)
counts.append(len(atoms))
if min(counts) != max(counts):
raise chimera.UserError("Unequal number of atoms "
"found in models")
if counts[0] == 0:
raise chimera.UserError("No atoms match atom specifier")
#
# Add handler to monitor change in display or active
# status changes
#
self.trigger = chimera.triggers.addHandler('check for changes',
self._statusCheck, None)
#
# No save dialog yet
#
self.saveDialog = None
#
# Initialize dialog
#
ModelessDialog.__init__(self, *args, **kw)
#
# Register with extension manager
#
chimera.extension.manager.registerInstance(self)
def fillInUI(self, parent):
#
# Construct user interface
#
self.modelVars = {}
# Find images
top = parent.winfo_toplevel()
dir = os.path.dirname(__file__)
icon = os.path.join(dir, 'move.tiff')
self.moveIcon = chimage.get(icon, top)
icon = os.path.join(dir, 'zoom.tiff')
self.zoomIcon = chimage.get(icon, top)
icon = os.path.join(dir, 'reset.tiff')
self.resetIcon = chimage.get(icon, top)
# Label rows
for n in range(len(self.refModels)):
parent.rowconfigure(n + 1, weight=1)
m = self.refModels[n]
lf = Tkinter.Frame(parent, relief=Tkinter.GROOVE, bd=2)
lf.grid(row=n + 1, column=0, sticky='nsew')
self._addRefConformer(lf, m)
# Label columns
for n in range(len(self.altModels)):
parent.columnconfigure(n + 1, weight=1)
m = self.altModels[n]
lf = Tkinter.Frame(parent, relief=Tkinter.GROOVE, bd=2)
lf.grid(row=0, column=n + 1, sticky='nsew')
self._addAltConformer(lf, m)
# Add table entries
# Each column comprises a set of radio buttons.
# This design is selected because each conformer
# in the alternative ensemble can only be matched
# to a single conformer in the reference ensemble.
self.matchVars = {}
self.matchRMSD = {}
for a in range(len(self.altModels)):
alt = self.altModels[a]
var = Tkinter.IntVar(parent)
var.set(-1)
self.matchVars[alt] = var
for r in range(len(self.refModels)):
ref = self.refModels[r]
try:
rmsd = self.matchRMSD[(ref, alt)]
except KeyError:
m = chimera.match.Match(
self.atomDict[ref],
self.atomDict[alt])
rmsd = m.rms
self.matchRMSD[(alt, ref)] = rmsd
b = Tkinter.Radiobutton(parent,
relief=Tkinter.SUNKEN,
text='%.3f' % rmsd,
value=r,
variable=var,
command=lambda s=self, m=alt:
s.matchModel(m))
b.grid(column=a + 1, row=r + 1, sticky='nsew')
def _addRefConformer(self, frame, model):
#
# Add reference conformer label and buttons
# A is for active
# D is for display
#
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
l = Tkinter.Label(frame, text=model.oslIdent())
l.grid(row=0, column=0, sticky='nsew')
va = Tkinter.IntVar(frame)
va.set(model.openState.active and 1 or 0)
ba = Tkinter.Checkbutton(frame,
text='A',
indicatoron=Tkinter.FALSE,
variable=va,
command=lambda v=va, s=self, m=model:
s.activateModel(m, v.get()))
ba.grid(row=0, column=1, sticky='nsew')
vd = Tkinter.IntVar(frame)
vd.set(model.display and 1 or 0)
bd = Tkinter.Checkbutton(frame,
text='D',
indicatoron=Tkinter.FALSE,
variable=vd,
command=lambda v=vd, s=self, m=model:
s.displayModel(m, v.get()))
bd.grid(row=0, column=2, sticky='nsew')
self.modelVars[model] = (va, vd)
br = Tkinter.Button(frame,
image=self.moveIcon,
command=lambda s=self, m=model:
s.manipulateModel(m))
br.grid(row=0, column=3, sticky='nsew')
br = Tkinter.Button(frame,
image=self.zoomIcon,
command=lambda s=self, m=model:
s.zoomModel(m))
br.grid(row=0, column=4, sticky='nsew')
def _addAltConformer(self, frame, model):
#
# Add alternative conformer label and buttons
# A is for active
# D is for display
# R is for reset
#
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
l = Tkinter.Label(frame, text=model.oslIdent())
l.grid(row=0, column=0, columnspan=3, sticky='nsew')
va = Tkinter.IntVar(frame)
va.set(model.openState.active and 1 or 0)
ba = Tkinter.Checkbutton(frame,
text='A',
indicatoron=Tkinter.FALSE,
variable=va,
command=lambda v=va, s=self, m=model:
s.activateModel(m, v.get()))
ba.grid(row=1, column=0, sticky='nsew')
vd = Tkinter.IntVar(frame)
vd.set(model.display and 1 or 0)
bd = Tkinter.Checkbutton(frame,
text='D',
indicatoron=Tkinter.FALSE,
variable=vd,
command=lambda v=vd, s=self, m=model:
s.displayModel(m, v.get()))
bd.grid(row=1, column=1, sticky='nsew')
self.modelVars[model] = (va, vd)
br = Tkinter.Button(frame,
relief=Tkinter.FLAT,
image=self.resetIcon,
command=lambda s=self, m=model:
s.resetModel(m))
br.grid(row=1, column=2, sticky='nsew')
def activateModel(self, model, on):
model.openState.active = on
def displayModel(self, model, on):
model.display = on
def resetModel(self, model):
self.matchVars[model].set(-1)
va, vd = self.modelVars[model]
va.set(0)
vd.set(0)
self.activateModel(model, 0)
self.displayModel(model, 0)
def matchModel(self, model):
n = self.matchVars[model].get()
va, vd = self.modelVars[model]
if n < 0:
va.set(0)
vd.set(0)
self.activateModel(model, 0)
self.displayModel(model, 0)
return
altOSL = '%s%s' % (model.oslIdent(), self.subSelection)
ref = self.refModels[n]
refOSL = '%s%s' % (ref.oslIdent(), self.subSelection)
try:
Midas.match(altOSL, refOSL)
except Midas.MidasError, e:
raise chimera.UserError(str(e))
va.set(1)
vd.set(1)
self.activateModel(model, 1)
self.displayModel(model, 1)
va, vd = self.modelVars[ref]
va.set(1)
vd.set(1)
self.activateModel(ref, 1)
self.displayModel(ref, 1)
def manipulateModel(self, model):
for m in self.refModels:
state = m == model and 1 or 0
va, vd = self.modelVars[m]
va.set(state)
self.activateModel(m, state)
for m in self.altModels:
if m == model:
# In case we're matching the ensemble to itself
continue
n = self.matchVars[m].get()
if n < 0:
state = 0
else:
state = self.refModels[n] == model and 1 or 0
va, vd = self.modelVars[m]
va.set(state)
self.activateModel(m, state)
def zoomModel(self, model):
self.manipulateModel(model)
sel = selection.ItemizedSelection()
for m in self.refModels:
if m.openState.active:
sel.add(m.atoms)
for m in self.altModels:
if m.openState.active:
sel.add(m.atoms)
Midas.window(sel)
def _statusCheck(self, name, closure, triggerData):
try:
for ml in self.refModels, self.altModels:
for m in ml:
va, vd = self.modelVars[m]
if va.get() != m.openState.active:
va.set(m.openState.active)
if vd.get() != m.display:
vd.set(m.display)
except:
self.emQuit()
def Save(self):
if self.saveDialog is None:
self.saveDialog = EnsembleMatchSaveDialog()
files = self.saveDialog.run(self.uiMaster())
if not files:
return
filename = files[0][0]
inclHeaders = self.saveDialog.inclHeaders.get()
f = open(filename, "w")
if inclHeaders:
l = [ m.oslIdent() for m in self.refModels ]
l.insert(0, "")
print >> f, '\t'.join(l)
for alt in self.altModels:
l = [ "%.3f" % self.matchRMSD[(alt, ref)]
for ref in self.refModels ]
if inclHeaders:
l.insert(0, alt.oslIdent())
print >> f, '\t'.join(l)
f.close()
print "RMSD matrix saved in", filename
def Hide(self):
self.emHide()
def Quit(self):
self.emQuit()
#
# Extension manager callback routines
#
def emName(self):
return self.title
def emRaise(self):
self.enter()
def emHide(self):
self.Close()
def emQuit(self):
if self.trigger:
chimera.triggers.deleteHandler('check for changes',
self.trigger)
self.trigger = None
self.destroy()
chimera.extension.manager.deregisterInstance(self)
from OpenSave import SaveModal
class EnsembleMatchSaveDialog(SaveModal):
title = "Save RMSD Matrix"
def __init__(self, **kw):
SaveModal.__init__(self, clientPos="s", clientSticky="w", **kw)
def fillInUI(self, master):
SaveModal.fillInUI(self, master)
self.inclHeaders = Tkinter.IntVar(master)
self.inclHeaders.set(0)
b = Tkinter.Checkbutton(
self.clientArea, variable=self.inclHeaders,
text="Include row/column headers")
b.pack()
def tile(modelList, scale=1.1, columns = None, viewAll = True):
"Arrange the models in the given list in regular rows and columns"
if not modelList:
return
# Make table of openState objects (share same transform)
osModels = {}
for m in modelList:
o = m.openState
if o in osModels:
osModels[o].append(m)
else:
osModels[o] = [m]
sortList = [ (min([(m.id, m.subid) for m in mlist]), o)
for o,mlist in osModels.items() ]
sortList.sort()
oStates = [ t[1] for t in sortList ]
#
# Find the bounding sphere of each model. We first display the
# model so that the bounding boxes get computed
# correctly, and reset the display status afterwards.
#
displayed = {}
for m in modelList:
displayed[m] = m.display
m.display = True
bSpheres = {}
for o,mlist in osModels.items():
for m in mlist:
has_bounds, s = m.bsphere()
if has_bounds:
s.xform(o.xform)
if o in bSpheres:
bSpheres[o].merge(s)
else:
bSpheres[o] = s
if not bSpheres:
return
oStates = [o for o in oStates if o in bSpheres]
radius = max([s.radius for s in bSpheres.values()]) * scale
for m, disp in displayed.iteritems():
m.display = disp
#
# Find the number of rows and columns that best match the
# viewer aspect ratio
#
nPos = len(bSpheres)
if columns is None:
rows, cols = rowAndColumnSize(nPos)
else:
cols = columns
rows = (nPos + cols - 1) / cols
#
# Update transformation of models to place them in proper
# row and column
#
diameter = radius * 2
r = 0
c = 0
ref = bSpheres[oStates[0]].center
xforms = {}
for o in oStates:
s = bSpheres[o]
cx,cy,cz = s.center.data()
dx = ref.x - cx + c * diameter
dy = ref.y - cy - r * diameter
dz = ref.z - cz
xf = chimera.Xform.translation(dx, dy, dz)
xforms[m] = xf
o.globalXform(xf)
c = c + 1
if c == cols:
r = r + 1
c = 0
#
# Update viewing parameters so all models appear in viewer
#
if viewAll:
chimera.viewer.viewAll(resetCofrMethod=False)
def rowAndColumnSize(nPos):
vWidth, vHeight = chimera.viewer.windowSize
vRatio = vWidth / float(vHeight)
for rows in range(1, nPos + 1):
cols = int((nPos + rows - 1) / rows)
ratio = cols / float(rows)
if ratio < vRatio:
score = ratio / vRatio
else:
score = vRatio / ratio
try:
if score > bestScore:
best = (rows, cols)
bestScore = score
except NameError:
best = (rows, cols)
bestScore = score
return best
def bboxSize(m):
for a in m.atoms:
c = a.coord()
try:
if c.x < minX:
minX = c.x
elif c.x > maxX:
maxX = c.x
if c.y < minY:
minY = c.y
elif c.y > maxY:
maxY = c.y
if c.z < minZ:
minZ = c.z
elif c.z > maxZ:
maxZ = c.z
except NameError:
minX = maxX = c.x
minY = maxY = c.y
minZ = maxZ = c.z
return minX, maxX, minY, maxY, minZ, maxZ
def boundingSphere(m):
"Compute the bounding sphere with center at average atomic coordinates"
sumX = 0
sumY = 0
sumZ = 0
atoms = m.atoms
for a in atoms:
c = a.coord()
sumX = sumX + c.x
sumY = sumY + c.y
sumZ = sumZ + c.z
center = chimera.Coord()
center.x = sumX / len(atoms)
center.y = sumY / len(atoms)
center.z = sumZ / len(atoms)
rsq = 0
for a in atoms:
nrsq = center.sqdistance(a.coord())
if nrsq > rsq:
rsq = nrsq
return center.x, center.y, center.z, math.sqrt(rsq)
def cluster(modelList, subSelection):
"Assign a cluster id to each model in the list"
if not modelList:
import chimera
raise chimera.UserError("No ensemble selected")
d = EnsembleCluster(modelList, subSelection)
class EnsembleCluster(ModelessDialog):
"""Display a table for manipulating clusters."""
title = "Ensemble Cluster"
help = "ContributedSoftware/ensemblematch/ensemblecluster.html"
buttons = ("Save", "Hide", "Quit")
def __init__(self, modelList, subSelection, *args, **kw):
from chimera import preferences
self._removeHandler = None
for m in modelList:
m.preclusterColor = m.color
self.subSelection = subSelection
self._cluster(modelList)
ModelessDialog.__init__(self, *args, **kw)
chimera.extension.manager.registerInstance(self)
self._removeHandler = chimera.openModels.addRemoveHandler(
self._modelsChanged, None)
def __del__(self):
if self._removeHandler:
chimera.openModels.deleteRemoveHandler(self._removeHandler)
def _cluster(self, modelList):
from chimera import replyobj
from distmat import DistanceMatrix
replyobj.status("Computing distance matrix")
modelList = [ m for m in modelList if len(m.atoms) > 0 ]
fulldm = DistanceMatrix(len(modelList))
sameAs = {}
atoms = [ match._coordArray(self._getAtoms(m))
for m in modelList ]
for i in range(len(modelList)):
mi = modelList[i]
if mi in sameAs:
continue
ai = atoms[i]
for j in range(i + 1, len(modelList)):
aj = atoms[j]
if len(ai) != len(aj):
mj = modelList[j]
print ("%s (%d atoms) and "
"%s (%d atoms) not matched" %
(mi.oslIdent(),
len(ai),
mj.oslIdent(),
len(aj)))
fulldm.set(i, j, float("inf"))
continue
m = chimera.match.Match(ai, aj)
if m.rms <= 0:
mj = modelList[j]
sameAs[mj] = mi
print ("Zero RMSD between %s and %s" %
(mi.oslIdent(), mj.oslIdent()))
fulldm.set(i, j, m.rms)
print "RMSD/Distance matrix"
print fulldm
if not sameAs:
dm = fulldm
models = modelList
else:
dm = DistanceMatrix(len(modelList) - len(sameAs))
models = []
indexMap = []
for i, mi in enumerate(modelList):
if mi in sameAs:
continue
models.append(mi)
indexMap.append(i)
for i in range(len(models)):
im = indexMap[i]
for j in range(i + 1, len(models)):
jm = indexMap[j]
dm.set(i, j, fulldm.get(im, jm))
replyobj.status("Using %d of %d models for clustering" %
(dm.size, fulldm.size))
from nmrclust import NMRClust
nmrc = NMRClust(dm)
id = 0
cList = []
for c in nmrc.clusters:
members = c.members()
cList.append((len(members), c, members))
cList.sort()
cList.reverse()
clusterInfo = []
for i, (size, c, members) in enumerate(cList):
mList = []
for member in members:
m = models[member]
m.clusterId = id
m.clusterRep = 0
mList.append(m)
rep = nmrc.representative(c)
m = models[rep]
m.clusterRep = size
clusterInfo.append((m, mList))
id += 1
for mj, mi in sameAs.iteritems():
mj.clusterId = mi.clusterId
mj.clusterRep = 0
clusterInfo[mj.clusterId][1].append(mj)
replyobj.status("Generated %d clusters" % id)
self.nmrc = nmrc
self.modelList = modelList
self.clusterInfo = clusterInfo
def _getAtoms(self, m):
if not self.subSelection:
atoms = m.atoms
else:
osl = '%s%s' % (m.oslIdent(), self.subSelection)
s = selection.OSLSelection(osl)
wanted = s.vertices(asDict=True)
atoms = [ a for a in m.atoms if a in wanted ]
return atoms
def _modelsChanged(self, triggerName, closure, mols):
self.modelList = [ m for m in self.modelList if m not in mols ]
for i, (rep, mList) in enumerate(self.clusterInfo):
newList = [ m for m in mList if m not in mols ]
if not newList:
# All members of cluster deleted
self.clusterInfo[i] = (None, [])
continue
if rep in mols:
newRep = mList[0]
newRep.clusterRep = rep.clusterRep
else:
newRep = rep
if newRep is not rep or len(newList) != len(mList):
self.clusterInfo[i] = (newRep, newList)
def fillInUI(self, parent):
import Pmw, Tkinter
from chimera import chimage
self.parent = parent
d = prefs.get("treatment", {})
self.treatmentShow = d.get("show", 0)
self.treatmentSelAtom = d.get("selectAtoms", 0)
self.treatmentSelAtomOf = d.get("selectAtomsOf", "all members")
self.treatmentSelModel = d.get("selectModels", 1)
self.treatmentSelModelOf = d.get("selectModelsOf", "all members")
self.treatmentColorModel = d.get("colorModels", 1)
self.treatmentColorModelOf = d.get("colorModelsOf", "all members")
self.rightArrow = chimage.get("rightarrow.png", parent)
self.downArrow = chimage.get("downarrow.png", parent)
if self.treatmentShow:
relief = "sunken"
image = self.downArrow
else:
relief = "flat"
image = self.rightArrow
self.treatmentGroup = Pmw.Group(parent,
collapsedsize=0,
tagindent=0,
ring_relief=relief,
tag_pyclass=Tkinter.Button,
tag_text=" Treatment of Chosen Clusters",
tag_relief="flat",
tag_compound="left",
tag_image=image,
tag_command=self._treatmentCB)
if not self.treatmentShow:
self.treatmentGroup.collapse()
self.treatmentGroup.pack(side="top", fill="x", padx=3)
self.treatmentSelAtomVar = Tkinter.IntVar(parent)
if self.treatmentSelAtom:
self.treatmentSelAtomVar.set(1)
else:
self.treatmentSelAtomVar.set(0)
f = Tkinter.Frame(self.treatmentGroup.interior())
f.pack(side="top", fill="x")
self.treatmentSelAtomButton = Tkinter.Checkbutton(f,
text=" Select atoms of",
onvalue=1, offvalue=0,
variable=self.treatmentSelAtomVar,
command=self._treatmentSelAtomCB)
self.treatmentSelAtomButton.pack(side="left")
self.treatmentSelAtomMenu = Pmw.OptionMenu(f,
items = ( "representatives",
"all members" ),
initialitem=self.treatmentSelAtomOf,
menubutton_pady=0,
command=self._treatmentSelAtomCB)
self.treatmentSelAtomMenu.pack(side="left")
self.treatmentColorModelVar = Tkinter.IntVar(parent)
if self.treatmentColorModel:
self.treatmentColorModelVar.set(1)
else:
self.treatmentColorModelVar.set(0)
f = Tkinter.Frame(self.treatmentGroup.interior())
f.pack(side="top", fill="x")
self.treatmentColorModelButton = Tkinter.Checkbutton(f,
text=" Color",
onvalue=1, offvalue=0,
variable=self.treatmentColorModelVar,
command=self._treatmentColorModelCB)
self.treatmentColorModelButton.pack(side="left")
self.treatmentColorModelMenu = Pmw.OptionMenu(f,
items = ( "representatives",
"all members" ),
initialitem=self.treatmentColorModelOf,
menubutton_pady=0,
command=self._treatmentColorModelCB)
self.treatmentColorModelMenu.pack(side="left")
self.treatmentSelModelVar = Tkinter.IntVar(parent)
if self.treatmentSelModel:
self.treatmentSelModelVar.set(1)
else:
self.treatmentSelModelVar.set(0)
f = Tkinter.Frame(self.treatmentGroup.interior())
f.pack(side="top", fill="x")
self.treatmentSelModelButton = Tkinter.Checkbutton(f,
text=" Choose",
onvalue=1, offvalue=0,
variable=self.treatmentSelModelVar,
command=self._treatmentSelModelCB)
self.treatmentSelModelButton.pack(side="left")
self.treatmentSelModelMenu = Pmw.OptionMenu(f,
items = ( "representatives",
"all members" ),
initialitem=self.treatmentSelModelOf,
menubutton_pady=0,
labelpos="e",
label_text=" in Model Panel",
command=self._treatmentSelModelCB)
self.treatmentSelModelMenu.pack(side="left")
height = min(len(self.nmrc.clusters), 10)
values = []
maxLength = 0
for id in range(len(self.nmrc.clusters)):
m = self.clusterInfo[id][0]
n = len(self.clusterInfo[id][1])
v = "%d (%d models, rep: %s)" % (id, n, m.oslIdent())
values.append(v)
if len(v) > maxLength:
maxLength = len(v)
self.listbox = Pmw.ScrolledListBox(self.parent,
listbox_selectmode="extended",
listbox_width=maxLength,
listbox_height=height,
selectioncommand=self._listboxSelect)
self.listbox.pack(fill="both", expand=True)
self.listbox.setlist(values)
def _treatmentCB(self):
self.treatmentShow = not self.treatmentShow
if self.treatmentShow:
self.treatmentGroup.configure(ring_relief="groove",
tag_image=self.downArrow)
self.treatmentGroup.expand()
else:
self.treatmentGroup.configure(ring_relief="flat",
tag_image=self.rightArrow)
self.treatmentGroup.collapse()
self._savePrefs()
def _savePrefs(self):
prefs["treatment"] = {
"show": self.treatmentShow,
"selectAtoms": self.treatmentSelAtom,
"selectAtomsOf": self.treatmentSelAtomOf,
"selectModels": self.treatmentSelModel,
"selectModelsOf": self.treatmentSelModelOf,
"colorModels": self.treatmentColorModel,
"colorModelsOf": self.treatmentColorModelOf,
}
prefs.save()
def _treatmentSelAtomCB(self, ignore=None):
selAtom = self.treatmentSelAtomVar.get()
selAtomOf = self.treatmentSelAtomMenu.getvalue()
if (selAtom == self.treatmentSelAtom
and selAtomOf == self.treatmentSelAtomOf):
return
self.treatmentSelAtom = selAtom
self.treatmentSelAtomOf = selAtomOf
self._selectionCB()
self._savePrefs()
def _treatmentColorModelCB(self, ignore=None):
colorModel = self.treatmentColorModelVar.get()
colorModelOf = self.treatmentColorModelMenu.getvalue()
if (colorModel == self.treatmentColorModel
and colorModelOf == self.treatmentColorModelOf):
return
self.treatmentColorModel = colorModel
self.treatmentColorModelOf = colorModelOf
self._colorCB()
self._savePrefs()
def _treatmentSelModelCB(self, ignore=None):
selModel = self.treatmentSelModelVar.get()
selModelOf = self.treatmentSelModelMenu.getvalue()
if (selModel == self.treatmentSelModel
and selModelOf == self.treatmentSelModelOf):
return
self.treatmentSelModel = selModel
self.treatmentSelModelOf = selModelOf
self._modelPanelCB()
self._savePrefs()
def _listboxSelect(self):
self._selectionCB()
self._colorCB()
self._modelPanelCB()
def _getSelected(self):
cursel = self.listbox.getcurselection()
if not cursel:
idList = range(len(self.clusterInfo))
else:
idList = [ int(v.split(None, 1)[0]) for v in cursel ]
return idList
def _modelPanelCB(self):
if not self.treatmentSelModel:
return
if self.treatmentSelModelOf == "representatives":
# Choose representative
mList = [ self.clusterInfo[id][0]
for id in self._getSelected() ]
self._getModelPanel().selectionChange(mList)
elif self.treatmentSelModelOf == "all members":
# Choose cluster
mList = []
for id in self._getSelected():
mList.extend(self.clusterInfo[id][1])
self._getModelPanel().selectionChange(mList)
else:
# No action
pass
def _selectionCB(self):
from chimera import selection
if not self.treatmentSelAtom:
return
if self.treatmentSelAtomOf == "representatives":
# Select representative
selection.clearCurrent()
mList = [ self.clusterInfo[id][0]
for id in self._getSelected() ]
selection.addCurrent(mList)
selection.addImpliedCurrent()
elif self.treatmentSelAtomOf == "all members":
# Select cluster
selection.clearCurrent()
mList = []
for id in self._getSelected():
mList.extend(self.clusterInfo[id][1])
selection.addCurrent(mList)
selection.addImpliedCurrent()
else:
# No action
pass
def _getModelPanel(self):
from ModelPanel import ModelPanel
from chimera import dialogs
return dialogs.display(ModelPanel.name)
def _colorCB(self):
if self.treatmentColorModel == 0:
# No action
return
idList = self._getSelected()
from CGLtk.color import colorRange
from chimera import MaterialColor
colorList = [MaterialColor(r, g, b, 1.0)
for r, g, b in colorRange(len(idList))]
lb = self.listbox.component("listbox")
origColor = lb["fg"]
origSelColor = lb["selectforeground"]
for i, color in enumerate(colorList):
id = idList[i]
if self.treatmentColorModelOf == "representatives":
# Color representative
for m in self.clusterInfo[id][1]:
m.color = m.preclusterColor
self._resetColor(m)
self.clusterInfo[id][0].color = color
else:
# Color cluster
for m in self.clusterInfo[id][1]:
m.color = color
self._resetColor(m)
r, g, b, a = color.rgba()
tkColor = "#%02x%02x%02x" % (int(r * 255),
int(g * 255),
int(b * 255))
lb.itemconfigure(id, fg=tkColor,
selectforeground=tkColor)
for id in range(len(self.clusterInfo)):
if id in idList:
continue
for m in self.clusterInfo[id][1]:
m.color = m.preclusterColor
self._resetColor(m)
lb.itemconfigure(id, fg=origColor,
selectforeground=origSelColor)
def _resetColor(self, m):
for a in m.atoms:
a.color = None
a.surfaceColor = None
a.labelColor = None
a.vdwColor = None
for b in m.bonds:
b.color = None
b.labelColor = None
def Hide(self):
self.emHide()
def Quit(self):
self.emQuit()
def Save(self):
if not hasattr(self, '_saveDialog'):
self._saveDialog = _SaveClusteringInfo(self,
title="Save Clusting Information")
self._saveDialog.enter()
def destroy(self):
if hasattr(self, '_saveDialog'):
self._saveDialog.destroy()
delattr(self, '_saveDialog')
# calling ModelessDialog.Close causes recursion
ModelessDialog.destroy(self)
#
# Extension manager callback routines
#
def emName(self):
return self.title
def emRaise(self):
self.enter()
def emHide(self):
self.Close()
def emQuit(self):
self.destroy()
chimera.extension.manager.deregisterInstance(self)
from OpenSave import SaveModeless
class _SaveClusteringInfo(SaveModeless):
def __init__(self, clusterDialog, **kw):
self.clusterDialog = clusterDialog
SaveModeless.__init__(self, **kw)
def Apply(self):
clusterIDs = self.clusterDialog._getSelected()
clusterInfos = [self.clusterDialog.clusterInfo[id] for id in clusterIDs]
clusterInfos.sort(lambda c1, c2: cmp(len(c2[1]), len(c1[1])) \
or cmp(min(c1[1]), min(c2[1])))
from OpenSave import osOpen
saveFile = osOpen(self.getPaths()[0], 'w')
print>>saveFile, "# one cluster per line; first model on each line is representative"
for clusterInfo in clusterInfos:
print>>saveFile, clusterInfo[0],
for member in sorted(clusterInfo[1]):
if member == clusterInfo[0]:
continue
print>>saveFile, member,
print>>saveFile, ""
saveFile.close()
def destroy(self):
self.clusterDialog = None
SaveModeless.destroy(self)