def align_molecule():
# TODO: Not ported.
from chimera import selection
atoms = selection.currentAtoms(ordered=True)
mols = set([a.molecule for a in atoms])
if len(mols) != 1:
return
mol = mols.pop()
molxf = mol.openState.xform
from Molecule import atom_positions
axyz = atom_positions(atoms, molxf)
from numpy import roll, float32, float64
from Matrix import xform_matrix, xform_points
from chimera.match import matchPositions
xflist = []
for mset in cage_marker_sets():
for p in polygons(mset):
if p.n == len(atoms):
c = p.center()
vxyz = [p.vertex_xyz(m) for m in p.vertices]
exyz = (0.5 * (vxyz + roll(vxyz, 1, axis=0))).astype(float32)
xform_points(exyz, mset.transform(), molxf)
xf, rms = matchPositions(exyz.astype(float64),
axyz.astype(float64))
xflist.append(xf)
molxf.multiply(xflist[0])
mol.openState.xform = molxf
import MultiScale
mm = MultiScale.multiscale_manager()
tflist = [xform_matrix(xf) for xf in xflist]
mm.molecule_multimer(mol, tflist)
def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c],
serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(
serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c], serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def interpolate(mol, molXform, segments, equivAtoms, method, rMethod,
frames, cartesian, cb):
# mol molecule where new coordinate sets are added
# should already have first frame in place
# molXform transform to convert atoms from their own
# local coordinate system into "mol" local coordinates
# (usually [inverse transform of trajectory model] x
# [transform of target model])
# segments list of 2-tuples of matching residue lists
# equivAtoms dictionary of equivalent atoms
# key is atom from first frame
# value is 2-tuple of atoms from last frame and "mol"
# method interpolation method name
# rMethod rate profile, e.g., "linear"
# frames number of frames to generate in trajectory
# cartesian use cartesian coordinate interpolation?
# cb function called for every frame generated
import InterpResidue
from util import getAtomList, findBestMatch
import chimera
from chimera import match
method = findBestMatch(method, InterpolationMap.iterkeys())
interpolateFunction = InterpolationMap[method]
rMethod = findBestMatch(rMethod, RateMap.iterkeys())
rateFunction = RateMap[rMethod]
if cartesian:
planFunction = InterpResidue.planCartesian
else:
planFunction = InterpResidue.planInternal
rate = rateFunction(frames)
numFrames = len(rate) + 1
activeCS = mol.activeCoordSet
csSize = len(mol.activeCoordSet.coords())
baseCS = max(mol.coordSets.keys()) + 1
segMap = {}
plan = {}
for seg in segments:
rList0, rList1 = seg
aList0 = getAtomList(rList0)
aList1 = [ equivAtoms[a0] for a0 in aList0 ]
c1 = chimera.Point([ a.coord() for a in aList1 ])
segMap[seg] = (aList0, aList1, molXform.apply(c1))
for r in rList0:
plan[r] = planFunction(r)
import numpy
def coordsToPosition(atoms):
return numpy.array([a.coord().data() for a in atoms])
def xformCoordsToPosition(atoms):
return numpy.array([molXform.apply(a.coord()).data()
for a in atoms])
lo = 0.0
interval = 1.0
for i in range(len(rate)):
f = (rate[i] - lo) / interval
lo = rate[i]
interval = 1.0 - lo
cs = mol.newCoordSet(baseCS + i, csSize)
for seg in segments:
aList0, aList1, c1 = segMap[seg]
c = chimera.Point([ a.coord() for a in aList0 ])
cList0 = coordsToPosition(aList0)
cList1 = xformCoordsToPosition(aList1)
xform, rmsd = match.matchPositions(cList1, cList0)
xf, xf1 = interpolateFunction(xform, c, c1, f)
xf1.multiply(molXform)
rList0, rList1 = seg
for r in rList0:
InterpResidue.applyPlan(plan[r], r, cs, f,
equivAtoms, xf, xf1)
mol.activeCoordSet = cs
if cb:
cb(mol)
cs = mol.newCoordSet(baseCS + len(rate), csSize)
for a0, a1 in equivAtoms.iteritems():
a0.setCoord(molXform.apply(a1.coord()), cs)
mol.activeCoordSet = cs
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
# load needed coord sets...
frameNums = range(self.startFrame, self.endFrame+1, self.stride)
for frameNum in frameNums:
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum,
makeCurrent=False)
# compute RMSDs
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel,
self.ignoreBulk, self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
numFrames = len(frameNums)
self.status("Fetching %d coordinate arrays" % numFrames)
numpyArrays = {}
from time import time
t0 = time()
for i, fn in enumerate(frameNums):
numpyArrays[fn] = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(fn))
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
if i == numFrames - 1:
self.status("Fetched %d coordinate arrays"
% (i+1))
else:
elapsed = time() - t0
perSec = elapsed / (i+1)
remaining = perSec * (numFrames - (i+1))
self.status("Fetched %d of %d coordinate arrays"
"\nAbout %.1f minutes remaining" %
(i+1, numFrames, remaining / 60.0))
t0 = time()
totalRMSDs = numFrames * (numFrames - 1) / 2
self.status("Computing %d RMSDs" % totalRMSDs)
from EnsembleMatch.distmat import DistanceMatrix
fullDM = DistanceMatrix(numFrames)
sameAs = {}
for i, frame1 in enumerate(frameNums):
na1 = numpyArrays[frame1]
for j, frame2 in enumerate(frameNums[i+1:]):
na2 = numpyArrays[frame2]
rmsd = matchPositions(na1, na2)[1]
fullDM.set(i, i+j+1, rmsd)
if rmsd == 0.0:
sameAs[frame2] = frame1
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
numComputed = totalRMSDs - ((numFrames - (i+1)) *
(numFrames - (i+2))) / 2
if numComputed == totalRMSDs:
self.status("Computed %d RMSDs" % totalRMSDs)
else:
elapsed = time() - t0
perSec = elapsed / numComputed
remaining = perSec * (totalRMSDs - numComputed)
if remaining < 50:
timeEst = "%d seconds" % int(
remaining + 0.5)
else:
timeEst = "%.1f minutes" % (
remaining / 60.0)
self.status("Computed %d of %d RMSDs\n"
"About %s remaining" % (numComputed,
totalRMSDs, timeEst))
self.status("Generating clusters")
self.buttonWidgets['Close'].configure(text="Close")
if not sameAs:
dm = fullDM
reducedFrameNums = frameNums
indexMap = range(len(frameNums))
elif len(sameAs) == numFrames - 1:
raise UserError("All frames to cluster are identical!")
self.Close()
else:
dm = DistanceMatrix(numFrames - len(sameAs))
reducedFrameNums = []
indexMap = []
for i, fn in enumerate(frameNums):
if fn in sameAs:
continue
reducedFrameNums.append(fn)
indexMap.append(i)
for i in range(len(reducedFrameNums)):
mapi = indexMap[i]
for j in range(i+1, len(reducedFrameNums)):
mapj = indexMap[j]
dm.set(i, j, fulldm.get(mapi, mapj))
from EnsembleMatch.nmrclust import NMRClust
clustering = NMRClust(dm)
self.clusterMap = {}
self.representatives = []
self.clusters = []
unsortedClusters = [(c, clustering.representative(c))
for c in clustering.clusters]
# sort the clusters so that the coloring is reproducible
# while trying to avoid using adjacent colors for
# adjacent clusters
clusters = [unsortedClusters.pop()]
while unsortedClusters:
bestCluster = bestVal = None
for uc in unsortedClusters:
val = abs(uc[-1] - clusters[-1][-1])
if len(clusters) > 1:
val += 0.5 * abs(uc[-1]
- clusters[-2][-1])
if len(clusters) > 2:
val += 0.25 * abs(uc[-1]
- clusters[-3][-1])
if bestVal == None or val > bestVal:
bestCluster = uc
bestVal = val
unsortedClusters.remove(bestCluster)
clusters.append(bestCluster)
colors = colorRange(len(clusters))
for c, rep in clusters:
cluster = Cluster()
cluster.color = colors.pop()
self.clusters.append(cluster)
cluster.representative = reducedFrameNums[rep]
cluster.members = []
for m in c.members():
f = reducedFrameNums[m]
self.clusterMap[f] = cluster
cluster.members.append(f)
for dup, base in sameAs.items():
c = self.clusterMap[base]
self.clusterMap[dup] = c
c.members.append(dup)
self.status("%d clusters" % len(self.clusters))
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.addColumn("Color", "color", format=(False, False),
titleDisplay=False)
membersCol = self.table.addColumn("Members",
"lambda c: len(c.members)", format="%d")
self.table.addColumn("Representative Frame", "representative",
format="%d")
self.table.setData(self.clusters)
self.table.launch(browseCmd=self.showRep)
self.table.sortBy(membersCol)
self.table.sortBy(membersCol) # to get descending order
self.table.grid(sticky="nsew")
self.timeLine = Pmw.ScrolledCanvas(parent, canvas_height="0.5i")
self.timeLine.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
self.zoom = 2.0
self.drawTimeLine()
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
top = parent.winfo_toplevel()
menuBar = Tkinter.Menu(top)
top.config(menu=menuBar)
self.dependentDialogs = []
rmsdMenu = Tkinter.Menu(menuBar)
menuBar.add_cascade(label="RMSD", menu=rmsdMenu)
rmsdMenu.add_command(label="Change thresholds...",
command=self.launchRmsdBoundsDialog)
numFrames = self.endFrame - self.startFrame + 1
scale1size = numFrames / self.stride
if scale1size < 200:
scale = int(1 + 200 / scale1size)
else:
scale = 1
# load needed coord sets...
for frameNum in range(self.startFrame, self.endFrame + 1, self.stride):
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum, makeCurrent=False)
self.widgets = []
width = max(len(str(self.endFrame)), 6)
for i in range(2):
entryFrame = Tkinter.Frame(parent)
entryFrame.grid(row=1, column=i)
entry = Pmw.EntryField(entryFrame,
labelpos='w',
entry_width=width,
label_text="Frame",
validate='numeric')
entry.configure(command=lambda ent=entry: self.entryCB(ent))
entry.grid(row=0, column=0)
self.widgets.append(entry)
goBut = Tkinter.Button(entryFrame,
text="Go",
padx=0,
pady=0,
command=lambda ent=entry: self.entryCB(ent))
goBut.grid(row=0, column=1)
self.widgets.append(goBut)
self.widgets[0].insert(0, "Click")
self.widgets[2].insert(0, "on map")
for widget in self.widgets:
if isinstance(widget, Pmw.EntryField):
widget = widget.component('entry')
widget.config(state='disabled')
size = scale1size * scale
self.scrCanvas = Pmw.ScrolledCanvas(parent,
canvas_bg="blue",
canvas_width=size,
canvas_height=size,
borderframe=True)
self.scrCanvas.grid(row=0, column=0, columnspan=2, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
# compute RMSD/image canvas
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel, self.ignoreBulk,
self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
self.rects = {}
numpyArrays = {}
if self.recolor:
rmsds = []
minRmsd = maxRmsd = None
for step1, frame1 in enumerate(
range(self.startFrame, self.endFrame + 1, self.stride)):
self.status("compute/show RMSDs for frame %d" % frame1)
try:
na1 = numpyArrays[frame1]
except KeyError:
na1 = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(frame1))
numpyArrays[frame1] = na1
canvas = self.scrCanvas.component('canvas')
for step2, frame2 in enumerate(
range(frame1, self.endFrame + 1, self.stride)):
try:
na2 = numpyArrays[frame2]
except KeyError:
na2 = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(frame2))
numpyArrays[frame2] = na2
rmsd = matchPositions(na1, na2)[1]
if self.recolor:
rmsds.append(rmsd)
color = self.tkRmsdColor(rmsd)
rect1 = canvas.create_rectangle(step1 * scale,
(step1 + step2) * scale,
(step1 + 1) * scale,
(step1 + step2 + 1) * scale,
fill=color,
outline="")
self.rects[rect1] = (frame1, frame2, rmsd)
rect2 = canvas.create_rectangle((step1 + step2) * scale,
step1 * scale,
(step1 + step2 + 1) * scale,
(step1 + 1) * scale,
fill=color,
outline="")
self.rects[rect2] = (frame2, frame1, rmsd)
if frame1 != frame2:
if minRmsd is None:
minRmsd = maxRmsd = rmsd
elif rmsd < minRmsd:
minRmsd = rmsd
elif rmsd > maxRmsd:
maxRmsd = rmsd
if step1 == 0:
self.scrCanvas.resizescrollregion()
self._computing = True
self._abort = False
canvas.update() # show each line and allow quit
self._computing = False
if self._abort:
canvas.after_idle(self.Close)
return
self.buttonWidgets['Close'].configure(text="Close")
if self.recolor:
self.status("Calculating recoloring thresholds\n")
rmsds.sort()
newMin = float("%.1f" % rmsds[int(len(rmsds) / 3)])
newMax = float("%.1f" % rmsds[int(2 * len(rmsds) / 3)])
if newMin == newMax:
if newMin > 0:
newMin -= 0.1
else:
newMax += 0.1
self.newMinMax(newMin, newMax)
canvas.bind("<Motion>", self.mouseOverCB)
canvas.bind("<Button-1>", self.mouseClickCB)
self.status("Calculated RMSD varies from %.3f to %.3f\n" %
(minRmsd, maxRmsd),
log=True)
def getRotamers(res,
phi=None,
psi=None,
cisTrans="trans",
resType=None,
lib="Dunbrack",
log=False):
"""Takes a Residue instance and optionally phi/psi angles
(if different from the Residue), residue type (e.g. "TYR"), and/or
rotamer library name. Returns a boolean and a list of Molecule
instances. The boolean indicates whether the rotamers are backbone
dependent. The Molecules are each a single residue (a rotamer) and
are in descending probability order. Each has an attribute
"rotamerProb" for the probability and "chis" for the chi angles.
"""
# find n/c/ca early to identify swapping non-amino acid before
# the NoResidueRotamersError gets raised, which will attempt
# a swap for ALA/GLY (and result in a traceback)
resAtomsMap = res.atomsMap
try:
n = resAtomsMap["N"][0]
ca = resAtomsMap["CA"][0]
c = resAtomsMap["C"][0]
except KeyError:
raise LimitationError("N, CA, or C missing from %s:"
" needed to position CB" % res)
resType = resType or res.type
if not phi and not psi:
ignore, phi, psi, cisTrans = extractResInfo(res)
if log:
def _info(ang):
if ang is None:
return "none"
return "%.1f" % ang
replyobj.info("%s: phi %s, psi %s" % (res, _info(phi), _info(psi)))
if cisTrans:
replyobj.info(" " + cisTrans)
replyobj.info("\n")
replyobj.status("Retrieving rotamers from %s library\n" %
getattr(lib, "displayName", lib))
bbdep, params = getRotamerParams(resType,
phi=phi,
psi=psi,
cisTrans=cisTrans,
lib=lib)
replyobj.status("Rotamers retrieved from %s library\n" %
getattr(lib, "displayName", lib))
template = chimera.restmplFindResidue(resType, False, False)
tmplMap = template.atomsMap
tmplN = tmplMap["N"]
tmplCA = tmplMap["CA"]
tmplC = tmplMap["C"]
tmplCB = tmplMap["CB"]
from chimera.molEdit import addAtom, addDihedralAtom, addBond
from chimera.match import matchPositions, _coordArray
xform, rmsd = matchPositions(_coordArray([n, ca, c]),
_coordArray([tmplN, tmplCA, tmplC]))
ncoord = xform.apply(tmplN.coord())
cacoord = xform.apply(tmplCA.coord())
cbcoord = xform.apply(tmplCB.coord())
from data import chiInfo
info = chiInfo[resType]
bondCache = {}
angleCache = {}
torsionCache = {}
from chimera.bondGeom import bondPositions
mols = []
middles = {}
ends = {}
for i, rp in enumerate(params):
m = chimera.Molecule()
mols.append(m)
m.name = "rotamer %d of %s" % (i + 1, res)
r = m.newResidue(resType, ' ', 1, ' ')
# can't use a local variable for r.atomsMap since we receive
# only an unchanging copy of the map
m.rotamerProb = rp.p
m.chis = rp.chis
rotN = addAtom("N", tmplN.element, r, ncoord)
rotCA = addAtom("CA", tmplCA.element, r, cacoord, bondedTo=rotN)
rotCB = addAtom("CB", tmplCB.element, r, cbcoord, bondedTo=rotCA)
todo = []
for i, chi in enumerate(rp.chis):
n3, n2, n1, new = info[i]
blen, angle = _lenAngle(new, n1, n2, tmplMap, bondCache,
angleCache)
n3 = r.atomsMap[n3][0]
n2 = r.atomsMap[n2][0]
n1 = r.atomsMap[n1][0]
new = tmplMap[new]
a = addDihedralAtom(new.name,
new.element,
n1,
n2,
n3,
blen,
angle,
chi,
bonded=True)
todo.append(a)
middles[n1] = [a, n1, n2]
ends[a] = [a, n1, n2]
# if there are any heavy non-backbone atoms bonded to template
# N and they haven't been added by the above (which is the
# case for Richardson proline parameters) place them now
for tnnb in tmplN.bondsMap.keys():
if tnnb.name in r.atomsMap or tnnb.element.number == 1:
continue
tnnbcoord = xform.apply(tnnb.coord())
addAtom(tnnb.name, tnnb.element, r, tnnbcoord, bondedTo=rotN)
# fill out bonds and remaining heavy atoms
from chimera.idatm import typeInfo
from chimera import distance
done = set([rotN, rotCA])
while todo:
a = todo.pop(0)
if a in done:
continue
tmplA = tmplMap[a.name]
for bonded, bond in tmplA.bondsMap.items():
if bonded.element.number == 1:
continue
try:
rbonded = r.atomsMap[bonded.name][0]
except KeyError:
# use middles if possible...
try:
p1, p2, p3 = middles[a]
conn = p3
except KeyError:
p1, p2, p3 = ends[a]
conn = p2
t1 = tmplMap[p1.name]
t2 = tmplMap[p2.name]
t3 = tmplMap[p3.name]
xform, rmsd = matchPositions(_coordArray([p1, p2, p3]),
_coordArray([t1, t2, t3]))
pos = xform.apply(tmplMap[bonded.name].coord())
rbonded = addAtom(bonded.name,
bonded.element,
r,
pos,
bondedTo=a)
middles[a] = [rbonded, a, conn]
ends[rbonded] = [rbonded, a, conn]
if a not in rbonded.bondsMap:
addBond(a, rbonded)
if rbonded not in done:
todo.append(rbonded)
done.add(a)
return bbdep, mols
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
top = parent.winfo_toplevel()
menuBar = Tkinter.Menu(top)
top.config(menu=menuBar)
self.dependentDialogs = []
rmsdMenu = Tkinter.Menu(menuBar)
menuBar.add_cascade(label="RMSD", menu=rmsdMenu)
rmsdMenu.add_command(label="Change thresholds...",
command=self.launchRmsdBoundsDialog)
numFrames = self.endFrame - self.startFrame + 1
scale1size = numFrames / self.stride
if scale1size < 200:
scale = int(1 + 200 / scale1size)
else:
scale = 1
# load needed coord sets...
for frameNum in range(self.startFrame, self.endFrame+1,
self.stride):
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum,
makeCurrent=False)
self.widgets = []
width = max(len(str(self.endFrame)), 6)
for i in range(2):
entryFrame = Tkinter.Frame(parent)
entryFrame.grid(row=1, column=i)
entry = Pmw.EntryField(entryFrame, labelpos='w',
entry_width=width, label_text="Frame",
validate='numeric')
entry.configure(command=lambda ent=entry:
self.entryCB(ent))
entry.grid(row=0, column=0)
self.widgets.append(entry)
goBut = Tkinter.Button(entryFrame, text="Go",
padx=0, pady=0,
command=lambda ent=entry: self.entryCB(ent))
goBut.grid(row=0, column=1)
self.widgets.append(goBut)
self.widgets[0].insert(0, "Click")
self.widgets[2].insert(0, "on map")
for widget in self.widgets:
if isinstance(widget, Pmw.EntryField):
widget = widget.component('entry')
widget.config(state='disabled')
size = scale1size * scale
self.scrCanvas = Pmw.ScrolledCanvas(parent, canvas_bg="blue",
canvas_width=size, canvas_height=size, borderframe=True)
self.scrCanvas.grid(row=0, column=0, columnspan=2,
sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
# compute RMSD/image canvas
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel,
self.ignoreBulk, self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
self.rects = {}
numpyArrays = {}
if self.recolor:
rmsds = []
minRmsd = maxRmsd = None
for step1, frame1 in enumerate(range(self.startFrame,
self.endFrame+1, self.stride)):
self.status("compute/show RMSDs for frame %d" % frame1)
try:
na1 = numpyArrays[frame1]
except KeyError:
na1 = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(frame1))
numpyArrays[frame1] = na1
canvas = self.scrCanvas.component('canvas')
for step2, frame2 in enumerate(range(frame1,
self.endFrame+1, self.stride)):
try:
na2 = numpyArrays[frame2]
except KeyError:
na2 = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(frame2))
numpyArrays[frame2] = na2
rmsd = matchPositions(na1, na2)[1]
if self.recolor:
rmsds.append(rmsd)
color = self.tkRmsdColor(rmsd)
rect1 = canvas.create_rectangle(step1*scale,
(step1+step2)*scale, (step1+1)*scale,
(step1+step2+1)*scale, fill=color,
outline="")
self.rects[rect1] = (frame1, frame2, rmsd)
rect2 = canvas.create_rectangle(
(step1+step2)*scale, step1*scale,
(step1+step2+1)*scale, (step1+1)*scale,
fill=color, outline="")
self.rects[rect2] = (frame2, frame1, rmsd)
if frame1 != frame2:
if minRmsd is None:
minRmsd = maxRmsd = rmsd
elif rmsd < minRmsd:
minRmsd = rmsd
elif rmsd > maxRmsd:
maxRmsd = rmsd
if step1 == 0:
self.scrCanvas.resizescrollregion()
self._computing = True
self._abort = False
canvas.update() # show each line and allow quit
self._computing = False
if self._abort:
canvas.after_idle(self.Close)
return
self.buttonWidgets['Close'].configure(text="Close")
if self.recolor:
self.status("Calculating recoloring thresholds\n")
rmsds.sort()
newMin = float("%.1f" % rmsds[int(len(rmsds)/3)])
newMax = float("%.1f" % rmsds[int(2*len(rmsds)/3)])
if newMin == newMax:
if newMin > 0:
newMin -= 0.1
else:
newMax += 0.1
self.newMinMax(newMin, newMax)
canvas.bind("<Motion>", self.mouseOverCB)
canvas.bind("<Button-1>", self.mouseClickCB)
self.status("Calculated RMSD varies from %.3f to %.3f\n"
% (minRmsd, maxRmsd), log=True)
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
# load needed coord sets...
frameNums = range(self.startFrame, self.endFrame + 1, self.stride)
for frameNum in frameNums:
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum, makeCurrent=False)
# compute RMSDs
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel, self.ignoreBulk,
self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
numFrames = len(frameNums)
self.status("Fetching %d coordinate arrays" % numFrames)
numpyArrays = {}
from time import time
t0 = time()
for i, fn in enumerate(frameNums):
numpyArrays[fn] = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(fn))
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
if i == numFrames - 1:
self.status("Fetched %d coordinate arrays" % (i + 1))
else:
elapsed = time() - t0
perSec = elapsed / (i + 1)
remaining = perSec * (numFrames - (i + 1))
self.status("Fetched %d of %d coordinate arrays"
"\nAbout %.1f minutes remaining" %
(i + 1, numFrames, remaining / 60.0))
t0 = time()
totalRMSDs = numFrames * (numFrames - 1) / 2
self.status("Computing %d RMSDs" % totalRMSDs)
from EnsembleMatch.distmat import DistanceMatrix
fullDM = DistanceMatrix(numFrames)
sameAs = {}
for i, frame1 in enumerate(frameNums):
na1 = numpyArrays[frame1]
for j, frame2 in enumerate(frameNums[i + 1:]):
na2 = numpyArrays[frame2]
rmsd = matchPositions(na1, na2)[1]
fullDM.set(i, i + j + 1, rmsd)
if rmsd == 0.0:
sameAs[frame2] = frame1
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
numComputed = totalRMSDs - ((numFrames - (i + 1)) * (numFrames -
(i + 2))) / 2
if numComputed == totalRMSDs:
self.status("Computed %d RMSDs" % totalRMSDs)
else:
elapsed = time() - t0
perSec = elapsed / numComputed
remaining = perSec * (totalRMSDs - numComputed)
if remaining < 50:
timeEst = "%d seconds" % int(remaining + 0.5)
else:
timeEst = "%.1f minutes" % (remaining / 60.0)
self.status("Computed %d of %d RMSDs\n"
"About %s remaining" %
(numComputed, totalRMSDs, timeEst))
self.status("Generating clusters")
self.buttonWidgets['Close'].configure(text="Close")
if not sameAs:
dm = fullDM
reducedFrameNums = frameNums
indexMap = range(len(frameNums))
elif len(sameAs) == numFrames - 1:
raise UserError("All frames to cluster are identical!")
self.Close()
else:
dm = DistanceMatrix(numFrames - len(sameAs))
reducedFrameNums = []
indexMap = []
for i, fn in enumerate(frameNums):
if fn in sameAs:
continue
reducedFrameNums.append(fn)
indexMap.append(i)
for i in range(len(reducedFrameNums)):
mapi = indexMap[i]
for j in range(i + 1, len(reducedFrameNums)):
mapj = indexMap[j]
dm.set(i, j, fulldm.get(mapi, mapj))
from EnsembleMatch.nmrclust import NMRClust
clustering = NMRClust(dm)
self.clusterMap = {}
self.representatives = []
self.clusters = []
unsortedClusters = [(c, clustering.representative(c))
for c in clustering.clusters]
# sort the clusters so that the coloring is reproducible
# while trying to avoid using adjacent colors for
# adjacent clusters
clusters = [unsortedClusters.pop()]
while unsortedClusters:
bestCluster = bestVal = None
for uc in unsortedClusters:
val = abs(uc[-1] - clusters[-1][-1])
if len(clusters) > 1:
val += 0.5 * abs(uc[-1] - clusters[-2][-1])
if len(clusters) > 2:
val += 0.25 * abs(uc[-1] - clusters[-3][-1])
if bestVal == None or val > bestVal:
bestCluster = uc
bestVal = val
unsortedClusters.remove(bestCluster)
clusters.append(bestCluster)
colors = colorRange(len(clusters))
for c, rep in clusters:
cluster = Cluster()
cluster.color = colors.pop()
self.clusters.append(cluster)
cluster.representative = reducedFrameNums[rep]
cluster.members = []
for m in c.members():
f = reducedFrameNums[m]
self.clusterMap[f] = cluster
cluster.members.append(f)
for dup, base in sameAs.items():
c = self.clusterMap[base]
self.clusterMap[dup] = c
c.members.append(dup)
self.status("%d clusters" % len(self.clusters))
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.addColumn("Color",
"color",
format=(False, False),
titleDisplay=False)
membersCol = self.table.addColumn("Members",
"lambda c: len(c.members)",
format="%d")
self.table.addColumn("Representative Frame",
"representative",
format="%d")
self.table.setData(self.clusters)
self.table.launch(browseCmd=self.showRep)
self.table.sortBy(membersCol)
self.table.sortBy(membersCol) # to get descending order
self.table.grid(sticky="nsew")
self.timeLine = Pmw.ScrolledCanvas(parent, canvas_height="0.5i")
self.timeLine.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
self.zoom = 2.0
self.drawTimeLine()