def Apply(self):
startFrame = self.startFrame.get()
stride = self.stride.get()
if (len(self.movie.ensemble) - (startFrame-1)) / stride > 1000:
dlg = AskYesNoDialog("RMSD map will be %d pixels wide"
" and tall. Okay?")
if dlg.run(self.uiMaster()) == "no":
self.enter()
return
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less"
" than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside"
" of trajectory")
prefs[RMSD_MIN] = self.minRmsd.get()
prefs[RMSD_MAX] = self.maxRmsd.get()
prefs[RMSD_AUTOCOLOR] = self.recolor.get()
RmsdMapDialog(self.movie, startFrame, self.stride.get(),
endFrame, self.useSel.get(), prefs[RMSD_MIN],
prefs[RMSD_MAX], self.ignoreBulk.get(),
self.ignoreHyds.get(), prefs[RMSD_AUTOCOLOR])
def LoadStructure(self):
sel = self.blastTable.selected()
if not sel:
sel = self.parser.matches
sel = [ m for m in sel if m.pdb ]
if len(sel) > 5:
from chimera.baseDialog import AskYesNoDialog
from chimera import tkgui
d = AskYesNoDialog("This will load %d models."
" Proceed?" % len(sel),
default="Yes")
if d.run(self.uiMaster().winfo_toplevel()) != "yes":
return
mList = []
for m in sel:
if not m.pdb:
continue
parts = m.pdb.split('_')
pdb = parts[0]
mol = chimera.openModels.open(pdb, type="PDBID")[0]
mList.append((m, mol))
if self.reference is None:
# Make the first model loaded the reference model
# so others align to it.
m, mol = mList[0]
self._setReference(m, mol)
for m, mol in mList:
if mol is self.molecule:
continue
resList = self._getMatchResidues(m, mol)
if resList:
self._match(mol, m, resList)
def _readonlyCB(self, opt):
prefFile = preferences.filename()
if not prefFile:
# If no file name, changes make no difference.
return
newState = opt.get()
if ((newState and preferences.isReadonly())
or (not newState and not preferences.isReadonly())):
# No change in state
return
if newState:
# Make readonly. This is always okay.
preferences.setReadonly(True)
else:
# Make not readonly. See if the file is
# writable. If not, ask the user if he wants
# to change permission.
if not _canWrite(prefFile):
from chimera.baseDialog import AskYesNoDialog
d = AskYesNoDialog("File is not writable."
" Try changing permissions?")
answer = d.run(self._ui)
if answer == "no":
opt.ui().set(1)
return
try:
sbuf = os.stat(prefFile)
import stat
mode = sbuf.st_mode | stat.S_IWRITE
os.chmod(prefFile, mode)
except os.error, s:
opt.ui().set(1)
raise chimera.UserError("cannot make %s "
"writable: %s" % (prefFile, s))
preferences.setReadonly(False)
def runDemo(script, demo_name):
global _currentDemo
if _currentDemo:
import tkMessageBox
## get some info about the demo user wants to open
import ChimeraDemo
try:
d = ChimeraDemo.ChimeraDemo(script, demo_name)
except DemoError:
demo_title = ' '.join(demo_name.split("_"))
else:
demo_title = d.getTitle()
del d
if _currentDemo.demo.getSrcText() == script:
dlg_msg = "You are already running the demo '%s'.\n\n " \
"Would you like close this demo, and all " \
"associated models, and start over?" \
% _currentDemo.getTitle()
else:
dlg_msg = "You already have a demo in progress ('%s').\n\n" \
"Would you like to close this demo, and " \
"all associated models, and open up the " \
"'%s' demo?" \
% ( _currentDemo.getTitle(), demo_title)
dlg = AskYesNoDialog(dlg_msg,
title="Demo in progress",
help="ContributedSoftware/demos/demos.html")
res = dlg.run(chimera.tkgui.app)
#res = tkMessageBox.askquestion(master=chimera.tkgui.app,
# title="Demo in progress",
# message=dlg_msg
# )
if res == 'yes':
## a demo *is* currently running, and user wants to start
## this new demo...
_currentDemo.Cancel()
d = createDemoFromScript(script, title=demo_name)
if d:
_currentDemo = d
return True
else:
return False
elif res == 'no':
## a demo *is* currently running, and user doesn't want
## to start this new demo
return False
else:
d = createDemoFromScript(script, title=demo_name)
if d:
## no demo is currently running, start this new one...
_currentDemo = d
return True
else:
return False
def runDemo(script, demo_name):
global _currentDemo
if _currentDemo:
import tkMessageBox
## get some info about the demo user wants to open
import ChimeraDemo
try:
d = ChimeraDemo.ChimeraDemo(script, demo_name)
except DemoError:
demo_title = ' '.join( demo_name.split("_"))
else:
demo_title = d.getTitle()
del d
if _currentDemo.demo.getSrcText() == script:
dlg_msg = "You are already running the demo '%s'.\n\n " \
"Would you like close this demo, and all " \
"associated models, and start over?" \
% _currentDemo.getTitle()
else:
dlg_msg = "You already have a demo in progress ('%s').\n\n" \
"Would you like to close this demo, and " \
"all associated models, and open up the " \
"'%s' demo?" \
% ( _currentDemo.getTitle(), demo_title)
dlg = AskYesNoDialog(dlg_msg, title="Demo in progress",
help="ContributedSoftware/demos/demos.html")
res = dlg.run(chimera.tkgui.app)
#res = tkMessageBox.askquestion(master=chimera.tkgui.app,
# title="Demo in progress",
# message=dlg_msg
# )
if res == 'yes':
## a demo *is* currently running, and user wants to start
## this new demo...
_currentDemo.Cancel()
d = createDemoFromScript(script, title=demo_name)
if d:
_currentDemo = d
return True
else:
return False
elif res == 'no':
## a demo *is* currently running, and user doesn't want
## to start this new demo
return False
else:
d = createDemoFromScript(script, title=demo_name)
if d:
## no demo is currently running, start this new one...
_currentDemo = d
return True
else:
return False
def __init__(self):
AskYesNoDialog.__init__(
self,
"Please include your email address so we can notify\n"
"you when the bug is fixed or ask for additional\n"
"information. Otherwise, please describe what you\n"
"where doing when the bug occurred.",
justify='left')
def Save(self):
from chimera.tkgui import GENERAL, CONFIRM_OVERWRITE
from chimera.preferences import preferences
if preferences.get(GENERAL, CONFIRM_OVERWRITE):
for path in self.millerBrowser.getPaths():
import os
if (os.path.exists(path) and not os.path.isdir(path)):
dlg = AskYesNoDialog("Overwrite %s?" % path)
if dlg.run(self.uiMaster()) == "no":
self.enter()
return
getattr(self, self.keepEquiv())()
def Save(self):
from chimera.tkgui import GENERAL, CONFIRM_OVERWRITE
from chimera.preferences import preferences
if preferences.get(GENERAL, CONFIRM_OVERWRITE):
for path in self.millerBrowser.getPaths():
import os
if (os.path.exists(path) and
not os.path.isdir(path)):
dlg = AskYesNoDialog("Overwrite %s?"
% path)
if dlg.run(self.uiMaster()) == "no":
self.enter()
return
getattr(self, self.keepEquiv())()
def Apply(self):
selectedResidues = chimera.selection.currentResidues()
if not selectedResidues:
self.enter()
raise UserError("No residues selected")
if len(selectedResidues) > 10:
from chimera.baseDialog import AskYesNoDialog
numSel = len(selectedResidues)
if AskYesNoDialog("You have %d residues selected which"
" could bring up %d rotamer dialogs.\n"
"Continue?" % (numSel, numSel)).run(
chimera.tkgui.app) == "no":
self.enter()
return
resType = self.resType.get()
lib = self.rotLib.get()
from Rotamers import NoResidueRotamersError
try:
for sr in selectedResidues:
RotamerDialog(sr, resType, lib)
except NoResidueRotamersError:
from SwapRes import swap
for sr in selectedResidues:
replyobj.info("Swapping %s to %s\n" % (sr, resType))
swap(sr, resType, bfactor=None)
replyobj.status("Swapped %d residue(s)\n" % len(selectedResidues))
def _readonlyCB(self, opt):
prefFile = preferences.filename()
if not prefFile:
# If no file name, changes make no difference.
return
newState = opt.get()
if ((newState and preferences.isReadonly())
or (not newState and not preferences.isReadonly())):
# No change in state
return
if newState:
# Make readonly. This is always okay.
preferences.setReadonly(True)
else:
# Make not readonly. See if the file is
# writable. If not, ask the user if he wants
# to change permission.
if not _canWrite(prefFile):
from chimera.baseDialog import AskYesNoDialog
d = AskYesNoDialog("File is not writable."
" Try changing permissions?")
answer = d.run(self._ui)
if answer == "no":
opt.ui().set(1)
return
try:
sbuf = os.stat(prefFile)
import stat
mode = sbuf.st_mode | stat.S_IWRITE
os.chmod(prefFile, mode)
except os.error, s:
opt.ui().set(1)
raise chimera.UserError(
"cannot make %s "
"writable: %s" %
(prefFile, s))
preferences.setReadonly(False)
def Apply(self):
startFrame = self.startFrame.get()
stride = self.stride.get()
if (len(self.movie.ensemble) - (startFrame - 1)) / stride > 1000:
dlg = AskYesNoDialog("RMSD map will be %d pixels wide"
" and tall. Okay?")
if dlg.run(self.uiMaster()) == "no":
self.enter()
return
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less" " than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside" " of trajectory")
prefs[RMSD_MIN] = self.minRmsd.get()
prefs[RMSD_MAX] = self.maxRmsd.get()
prefs[RMSD_AUTOCOLOR] = self.recolor.get()
RmsdMapDialog(self.movie, startFrame, self.stride.get(), endFrame,
self.useSel.get(), prefs[RMSD_MIN], prefs[RMSD_MAX],
self.ignoreBulk.get(), self.ignoreHyds.get(),
prefs[RMSD_AUTOCOLOR])
def _surfaceCheck(self):
if getattr(self, "_surfaceOkayed", False):
return True
mol = self.model.Molecule()
assocSurfs = chimera.openModels.list(mol.id,
mol.subid,
modelTypes=[chimera.MSMSModel])
if not assocSurfs:
return True
from chimera.baseDialog import AskYesNoDialog
answer = AskYesNoDialog(
"A surface model exists for this"
" trajectory.\nThe surface will be recalculated for each frame"
" which will slow playback significantly.\nYou may want to close"
" the surface before playing the trajectory.\nContinue anyway?"
).run(self.uiMaster())
self._surfaceOkayed = answer == "yes"
return self._surfaceOkayed
def __init__(self): AskYesNoDialog.__init__(self, "Please include your email address so we can notify\n" "you when the bug is fixed or ask for additional\n" "information. Otherwise, please describe what you\n" "where doing when the bug occurred.", justify='left')
def writePrmtop(m, topfile, parmset, unchargedAtoms=None):
import os
import chimera
from chimera import replyobj
from WriteMol2 import writeMol2
from tempfile import mkdtemp
status = replyobj.status
if unchargedAtoms and parmset.lower().endswith("ua"):
# united atom
replyobj.warning("Some uncharged/untyped protons expected due"
" to use of united-atom force field.\n")
unchargedHeavy = []
skip = []
for uncharged in unchargedAtoms.values():
for uc in uncharged:
if uc.element.number == 1:
skip.append(uc)
else:
unchargedHeavy.append(uc)
unchargedAtoms = unchargedHeavy
else:
skip = []
if unchargedAtoms:
if chimera.nogui:
raise ValueError("Some atoms don't have charges/types")
from chimera.baseDialog import AskYesNoDialog
d = AskYesNoDialog("Some atoms don't have charges/types"
" assigned. Write prmtop anyway?")
if d.run(chimera.tkgui.app) == "no":
return
tempDir = mkdtemp()
def _clean():
for fn in os.listdir(tempDir):
os.unlink(os.path.join(tempDir, fn))
os.rmdir(tempDir)
sleapIn = os.path.join(tempDir, "sleap.in.mol2")
writeMol2([m], sleapIn, status=status, gaffType=True, skip=skip)
leaprc = os.path.join(tempDir, "solvate.cmd")
writeLeaprc(tempDir, topfile, parmset, leaprc)
chimeraRoot = os.environ["CHIMERA"]
amberHome = os.path.join(chimeraRoot, "bin", "amber10")
acHome = os.path.join(chimeraRoot, "bin", "antechamber")
command = [os.path.join(amberHome, "exe", "sleap"), "-f", leaprc]
print 'command: ', command
if status:
status("Running sleap" )
from subprocess import Popen, STDOUT, PIPE
# For some reason on Windows, if shell==False then antechamber
# cannot run bondtype via system().
import sys
if sys.platform == "win32":
shell = True
else:
shell = False
replyobj.info("Running sleap command: %s\n" % " ".join(command))
import os
os.environ["AMBERHOME"]=amberHome
os.environ["ACHOME"]=acHome
sleapMessages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=tempDir, shell=shell, bufsize=1).stdout
while True:
line = sleapMessages.readline()
if not line:
break
replyobj.status("(writeprmtop) %s" % line, log=True)
if not os.path.exists(topfile):
_clean()
from chimera import NonChimeraError
raise NonChimeraError("Failure running sleap \n"
"Check reply log for details\n")
else:
replyobj.status("Wrote parmtop file %s\n" % topfile, log=True)
def interpolate(self, m, xform, **kw):
"""Interpolate to new conformation 'm'."""
#
# Get all the options
#
if kw.has_key("method"):
self.method = kw["method"]
if kw.has_key("rate"):
self.rate = kw["rate"]
if kw.has_key("frames"):
self.frames = kw["frames"]
if kw.has_key("cartesian"):
self.cartesian = kw["cartesian"]
if kw.has_key("minimize"):
self.minimize = kw["minimize"]
if kw.has_key("steps"):
self.steps = kw["steps"]
if self.minimize:
self.callback = self.minimizeCallback
else:
self.callback = self.interpolateCallback
#
# Find matching set of residues. First try for
# one-to-one residue match, and, if that fails,
# then finding a common set of residues.
#
import Segment
sm = self.mol
try:
results = Segment.segmentHingeExact(sm, m)
except ValueError:
results = Segment.segmentHingeApproximate(sm, m)
segments, atomMap, unusedResidues, unusedAtoms = results
for r in unusedResidues:
sm.deleteResidue(r)
for a in unusedAtoms:
sm.deleteAtom(a)
if unusedResidues or unusedAtoms:
from chimera import Sequence
Sequence.invalidate(sm)
if self.minimize:
from chimera.baseDialog import AskYesNoDialog
from chimera.tkgui import app
d = AskYesNoDialog(
"Cannot minimize with non-identical models.\n"
"Continue without minimization?",
default="Yes")
if d.run(app) != "yes":
raise ValueError("terminated at user request")
self.minimize = False
self.callback = self.interpolateCallback
#
# Interpolate between last conformation in trajectory
# and new conformations
#
sm.activeCoordSet = sm.coordSets[max(sm.coordSets.keys())]
from Interpolate import interpolate
import chimera
combinedXform = chimera.Xform(self.inverseXform)
combinedXform.multiply(xform)
interpolate(sm, combinedXform,
segments, atomMap, self.method,
self.rate, self.frames,
self.cartesian, self.callback)
def interpolate(self, m, xform, **kw):
"""Interpolate to new conformation 'm'."""
#
# Get all the options
#
if kw.has_key("method"):
self.method = kw["method"]
if kw.has_key("rate"):
self.rate = kw["rate"]
if kw.has_key("frames"):
self.frames = kw["frames"]
if kw.has_key("cartesian"):
self.cartesian = kw["cartesian"]
if kw.has_key("minimize"):
self.minimize = kw["minimize"]
if kw.has_key("steps"):
self.steps = kw["steps"]
if self.minimize:
self.callback = self.minimizeCallback
else:
self.callback = self.interpolateCallback
#
# Find matching set of residues. First try for
# one-to-one residue match, and, if that fails,
# then finding a common set of residues.
#
import Segment
sm = self.mol
try:
results = Segment.segmentHingeExact(sm, m)
except ValueError:
results = Segment.segmentHingeApproximate(sm, m)
segments, atomMap, unusedResidues, unusedAtoms = results
for r in unusedResidues:
sm.deleteResidue(r)
for a in unusedAtoms:
sm.deleteAtom(a)
if unusedResidues or unusedAtoms:
from chimera import Sequence
Sequence.invalidate(sm)
if self.minimize:
from chimera.baseDialog import AskYesNoDialog
from chimera.tkgui import app
d = AskYesNoDialog(
"Cannot minimize with non-identical models.\n"
"Continue without minimization?",
default="Yes")
if d.run(app) != "yes":
raise ValueError("terminated at user request")
self.minimize = False
self.callback = self.interpolateCallback
#
# Interpolate between last conformation in trajectory
# and new conformations
#
sm.activeCoordSet = sm.coordSets[max(sm.coordSets.keys())]
from Interpolate import interpolate
import chimera
combinedXform = chimera.Xform(self.inverseXform)
combinedXform.multiply(xform)
interpolate(sm, combinedXform, segments, atomMap, self.method,
self.rate, self.frames, self.cartesian, self.callback)