def createPlane(self, name, atoms, number=None, radius=None,
radiusOffset=0.0, color=None, sourceModel=None,
thickness=defaults[PLANE_THICKNESS]):
if len(atoms) < 3:
raise ValueError("Need at least 3 atoms to define plane")
numbers = dict([(pl.number, pl) for pl in self.planes])
if number == None:
if numbers:
number = max(numbers.keys()) + 1
else:
number = 1
elif number in numbers:
self.removePlanes([numbers[number]])
if color == None:
from StructMeasure import matchStructureColor
color = matchStructureColor(atoms)
if sourceModel == None:
sourceModel = self._getSourceModel(atoms)
import StructMeasure
if radius == None:
plane, proj, radius = StructMeasure.plane(
chimera.numpyArrayFromAtoms(atoms), findBounds=True)
radius += radiusOffset
else:
plane = StructMeasure.plane(
chimera.numpyArrayFromAtoms(atoms), findBounds=False)
replyobj.info("%s has radius %g\n" % (name, radius))
self.planeOrdinal += 1
return self._instantiatePlane(number, name, self.planeOrdinal, color,
radius, thickness, sourceModel, atoms, plane)
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 createAxis(self,
name,
atoms,
number=None,
radius=None,
color=None,
sourceModel=None,
helicalCorrection=True,
massWeighting=False):
if len(atoms) < 3:
raise ValueError("Need at least 3 atoms to define axis")
numbers = dict([(a.number, a) for a in self.axes])
if number == None:
if numbers:
number = max(numbers.keys()) + 1
else:
number = 1
elif number in numbers:
self.removeAxes([numbers[number]])
if color == None:
from StructMeasure import matchStructureColor
color = matchStructureColor(atoms)
if sourceModel == None:
sourceModel = self._getSourceModel(atoms)
axisKw = {}
if massWeighting:
from numpy import array
axisKw['weights'] = array([a.element.mass for a in atoms])
import StructMeasure
if radius == None:
pt, vec, b1, b2, radius = StructMeasure.axis(
chimera.numpyArrayFromAtoms(atoms),
findBounds=True,
findRadius=True,
iterate=helicalCorrection,
**axisKw)
else:
pt, vec, b1, b2 = StructMeasure.axis(
chimera.numpyArrayFromAtoms(atoms),
findBounds=True,
findRadius=False,
iterate=helicalCorrection,
**axisKw)
replyobj.info("%s has radius %g\n" % (name, radius))
return self._instantiateAxis(number, name, color, radius, sourceModel,
atoms, pt, vec, (b1, b2))
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))
[writer.writerow(r) for r in table]
# gather the names of .pdb files in the folder
file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]
# loop through the files, opening, processing, and closing each in turn
for fn in file_names:
replyobj.status("Processing " + fn) # show what file we're working on
rc("open " + fn)
rc("delete markers")
#make receptor plane #select the top of each transmembrane# measure the center of the pocket (#1)#make a plane that mimics the mebrane (p1)
rc("select #0:32,87,100,166,188,260,277")
rc("measure center sel mark true radius .3")
rc("define plane sel")
atoms = selection.currentAtoms()
numpyCorrds = numpyArrayFromAtoms(atoms)
plane = StructMeasure.plane(numpyCorrds)
#
#select chemokine #measure axis of mass for the chemokine (a1)#measure center of mass for the chemokine (#2)#centriod for chemokine (c1)
rc("select :.b")
rc("define axis color red radius 2 sel")
rc("measure center sel mark true radius .3")
rc("define centroid mass true color blue radius 10 sel")
#
#
z_distance = Midas.distance(
'#1:1'
'#2:1'
) #distance center of mass of chemokine to center of pocket at membrane
z_short = Midas.distance(
'#1',
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [
{
'tr3d': Xform.xform(-0.50000042, 0.86602516, 0.00000116, -103.53997515,
-0.86602516, -0.50000042, 0.00000058, 179.33655802,
0.00000108, -0.00000072, 1.00000000, 0.00005125, orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}
]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))] for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j-i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [{
'tr3d':
Xform.xform(-0.50000042,
0.86602516,
0.00000116,
-103.53997515,
-0.86602516,
-0.50000042,
0.00000058,
179.33655802,
0.00000108,
-0.00000072,
1.00000000,
0.00005125,
orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))]
for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j - i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def matchAtoms(fixedAtoms, movableAtoms, fCoordSet=None, mCoordSet=None):
mArray = chimera.numpyArrayFromAtoms(movableAtoms, mCoordSet)
fArray = chimera.numpyArrayFromAtoms(fixedAtoms, fCoordSet)
return matchPositions(fArray, mArray)
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 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 matchAtoms(fixedAtoms, movableAtoms, fCoordSet=None, mCoordSet=None): mArray = chimera.numpyArrayFromAtoms(movableAtoms, mCoordSet) fArray = chimera.numpyArrayFromAtoms(fixedAtoms, fCoordSet) return matchPositions(fArray, mArray)
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()
