def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Gromacs', {})
self.topologyOption = InputFileOption(parent,
1,
"Run input (.tpr)",
inputPrefs.get('Topology', True),
None,
filters=[("Topology", ["*.tpr"])
],
title="Choose .tpr File",
entryWidth=20,
historyID="GromacsTop")
self.trajectoryOption = InputFileOption(
parent,
2,
"Trajectory (.trr)",
inputPrefs.get('Trajectory', True),
None,
entryWidth=20,
title="Choose Trajectory File",
filters=[("Portable trajectory", ["*.trr"])],
defaultFilter=0,
historyID="GromacsTrajectory")
parent.columnconfigure(1, weight=1)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES, PDB_STYLE
inputPrefs = prefs[INPUT_FILES].setdefault(formatName, {})
class PdbStyleOption(EnumOption):
values = ["single file", "multiple files"]
self.style = PdbStyleOption(parent, 0,
"PDB frames contained in", prefs[PDB_STYLE],
self._styleChangeCB)
self.options = {}
globs = []
for ext in chimera.fileInfo.extensions("PDB"):
globs.append("*" + ext)
filters = [("PDB", globs)]
self.singleFrame = Tkinter.Frame(parent)
self.singleFrame.columnconfigure(1, weight=1)
self.options[self.single] = InputFileOption(self.singleFrame,
0, self.single, inputPrefs.get(self.single, True), None,
filters=filters, title="Choose Multi-model PDB File",
defaultFilter="PDB", historyID="PDB traj multi-model")
self.multiFrame = Tkinter.Frame(parent)
self.multiFrame.columnconfigure(1, weight=1)
self.options[self.multiStart] = InputFileOption(
self.multiFrame, 0, self.multiStart,
inputPrefs.get(self.multiStart, True), None,
title="Choose First PDB File", defaultFilter="PDB",
filters=filters, historyID="PDB traj multi start")
self.options[self.multiEnd] = InputFileOption(self.multiFrame,
1, self.multiEnd, inputPrefs.get(self.multiEnd, True),
None, title="Choose Last PDB File", defaultFilter="PDB",
filters=filters, historyID="PDB traj multi end")
parent.columnconfigure(1, weight=1)
self._styleChangeCB(self.style)
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption, EnumOption
import itertools
info = Tk.Label(parent, justify=Tk.LEFT, wraplength=300, text=
"Model alternate conformations of loops using "
"Modeller from <http://salilab.org/>.\n"
"First select the loops you wish to model."
" Then choose the number of models "
"you wish to generate.")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options,
text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Restrict selections to turns", True, None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
self.waters = BooleanOption(options, row.next(),
"Include waters", False, None)
self.waters.disable()
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
self.count = IntOption(options, row.next(), "Number of models",
10, None, min=1, sticky=Tk.W)
#self.start = IntOption(options, row.next(),
# "Starting model number", 1, None, min=0)
class Refinement(EnumOption):
values = ('very fast', 'fast', 'slow', 'very slow',
'slow large', 'none')
self.refine = Refinement(options, row.next(), "Refinement",
'fast', None)
button = Tk.Button(options, text="Prune selection",
command=self.prune)
button.grid(row=row.next(), column=0, columnspan=2, pady=2)
self.start = 1
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod9v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES, GROMOS_SCALING
inputPrefs = prefs[INPUT_FILES].setdefault('Gromos', {})
self.options = []
for i in range(len(self.labels)):
label = self.labels[i]
self.options.append(
InputFileOption(parent,
i,
label,
inputPrefs.get(label, True),
None,
title="Choose %s File" % label,
historyID="Gromos %s" % label))
self.scalingOption = FloatOption(
parent,
len(self.labels),
"Angstrom conversion",
prefs[GROMOS_SCALING],
None,
balloon="scale factor to convert trajectory\n"
"coordinates to angstroms",
width=4,
sticky='w')
parent.columnconfigure(1, weight=1)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault(self.formatName, {})
self.options = []
for i in range(len(self.labels)):
label = self.labels[i]
self.options.append(
InputFileOption(parent,
i,
label,
inputPrefs.get(label, True),
None,
title="Choose %s File" % label,
historyID="%s %s" % (self.formatName, label)))
parent.columnconfigure(1, weight=1)
f = Tkinter.Frame(parent)
f.grid(row=len(self.labels), column=0, columnspan=2)
Tkinter.Label(f, text="PSF/DCD support courtesy of").grid(row=0,
column=0,
sticky='e')
from chimera import help
Tkinter.Button(f,
text="MDTools",
padx=0,
pady=0,
command=lambda: help.display(
"http://www.ks.uiuc.edu/~jim/mdtools/")).grid(
row=0, column=1, sticky='w')
class ParamGUI:
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Gromacs', {})
self.topologyOption = InputFileOption(parent,
1,
"Run input (.tpr)",
inputPrefs.get('Topology', True),
None,
filters=[("Topology", ["*.tpr"])
],
title="Choose .tpr File",
entryWidth=20,
historyID="GromacsTop")
self.trajectoryOption = InputFileOption(
parent,
2,
"Trajectory (.trr)",
inputPrefs.get('Trajectory', True),
None,
entryWidth=20,
title="Choose Trajectory File",
filters=[("Portable trajectory", ["*.trr"])],
defaultFilter=0,
historyID="GromacsTrajectory")
parent.columnconfigure(1, weight=1)
def loadEnsemble(self, startFrame, endFrame, callback):
topology = self.topologyOption.get()
trajectory = self.trajectoryOption.get()
if not os.path.exists(topology):
raise ValueError("Topology file does not exist!")
if not os.path.exists(trajectory):
raise ValueError("Trajectory file does not exist!")
from Trajectory.prefs import prefs, INPUT_FILES
# need to change a _copy_ of the dictionary, otherwise
# when we try to save the "original" dictionary will also
# have our changes and no save will occur
from copy import deepcopy
inputPrefs = deepcopy(prefs[INPUT_FILES])
inputPrefs['Gromacs']['Topology'] = topology
inputPrefs['Gromacs']['Trajectory'] = trajectory
prefs[INPUT_FILES] = inputPrefs
loadEnsemble((topology, trajectory), startFrame, endFrame, callback)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Gromacs', {})
self.topologyOption = InputFileOption(parent, 1,
"Run input (.tpr)",
inputPrefs.get('Topology', True),
None, filters=[("Topology", ["*.tpr"])],
title="Choose .tpr File",
entryWidth=20, historyID="GromacsTop")
self.trajectoryOption = InputFileOption(parent, 2,
"Trajectory (.trr)",
inputPrefs.get('Trajectory', True), None,
entryWidth=20, title="Choose Trajectory File",
filters=[("Portable trajectory", ["*.trr"])],
defaultFilter=0, historyID="GromacsTrajectory")
parent.columnconfigure(1, weight=1)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Amber', {})
self.prmtopOption = InputFileOption(parent, 0, "Prmtop",
inputPrefs.get('Prmtop', True),
None, filters=[("Prmtop", ["*.top"])],
title="Choose Prmtop File",
entryWidth=20, historyID="AmberPrmtop")
defaultTrajs = inputPrefs.get('Trajectories', None)
if defaultTrajs is None and 'Trajectory' in inputPrefs:
defaultTrajs = [inputPrefs['Trajectory']]
from Amber import Amber
self.trajectoriesOption = OrderedFileListOption(parent, 1,
"Trajectory", defaultTrajs,
None, addKw=Amber.AddTrajKw)
parent.columnconfigure(1, weight=1)
parent.rowconfigure(1, weight=1)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault(formatName, {})
self.options = {}
globs = []
for ext in chimera.fileInfo.extensions("XYZ"):
globs.append("*" + ext)
filters = [("XYZ", globs)]
self.multiFrame = Tkinter.Frame(parent)
self.multiFrame.columnconfigure(1, weight=1)
self.options[self.multiStart] = InputFileOption(
self.multiFrame, 0, self.multiStart,
inputPrefs.get(self.multiStart, True), None,
title="Choose First XYZ File", defaultFilter="XYZ",
filters=filters, historyID="XYZ traj multi start")
self.options[self.multiEnd] = InputFileOption(self.multiFrame,
1, self.multiEnd, inputPrefs.get(self.multiEnd, True),
None, title="Choose Last XYZ File", defaultFilter="XYZ",
filters=filters, historyID="XYZ traj multi end")
parent.columnconfigure(1, weight=1)
self.multiFrame.grid(row=1, columnspan=2, sticky="ew")
class ParamGUI:
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Gromacs', {})
self.topologyOption = InputFileOption(parent, 1,
"Run input (.tpr)",
inputPrefs.get('Topology', True),
None, filters=[("Topology", ["*.tpr"])],
title="Choose .tpr File",
entryWidth=20, historyID="GromacsTop")
self.trajectoryOption = InputFileOption(parent, 2,
"Trajectory (.trr)",
inputPrefs.get('Trajectory', True), None,
entryWidth=20, title="Choose Trajectory File",
filters=[("Portable trajectory", ["*.trr"])],
defaultFilter=0, historyID="GromacsTrajectory")
parent.columnconfigure(1, weight=1)
def loadEnsemble(self, startFrame, endFrame, callback):
topology = self.topologyOption.get()
trajectory = self.trajectoryOption.get()
if not os.path.exists(topology):
raise ValueError("Topology file does not exist!")
if not os.path.exists(trajectory):
raise ValueError("Trajectory file does not exist!")
from Trajectory.prefs import prefs, INPUT_FILES
# need to change a _copy_ of the dictionary, otherwise
# when we try to save the "original" dictionary will also
# have our changes and no save will occur
from copy import deepcopy
inputPrefs = deepcopy(prefs[INPUT_FILES])
inputPrefs['Gromacs']['Topology'] = topology
inputPrefs['Gromacs']['Trajectory'] = trajectory
prefs[INPUT_FILES] = inputPrefs
loadEnsemble((topology, trajectory),
startFrame, endFrame, callback)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('MMTK', {})
self.options = []
for i in range(len(self.labels)):
label = self.labels[i]
self.options.append(
InputFileOption(parent,
i,
label,
inputPrefs.get(label, True),
None,
title="Choose %s File" % label,
historyID="MMTK %s" % label))
parent.columnconfigure(1, weight=1)
class ParamGUI:
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault('Amber', {})
self.prmtopOption = InputFileOption(parent, 0, "Prmtop",
inputPrefs.get('Prmtop', True),
None, filters=[("Prmtop", ["*.top"])],
title="Choose Prmtop File",
entryWidth=20, historyID="AmberPrmtop")
defaultTrajs = inputPrefs.get('Trajectories', None)
if defaultTrajs is None and 'Trajectory' in inputPrefs:
defaultTrajs = [inputPrefs['Trajectory']]
from Amber import Amber
self.trajectoriesOption = OrderedFileListOption(parent, 1,
"Trajectory", defaultTrajs,
None, addKw=Amber.AddTrajKw)
parent.columnconfigure(1, weight=1)
parent.rowconfigure(1, weight=1)
def loadEnsemble(self, startFrame, endFrame, callback):
prmtop = self.prmtopOption.get()
trajectories = self.trajectoriesOption.get()
from chimera import UserError
if not os.path.exists(prmtop):
raise UserError("Parmtop file does not exist!")
if not trajectories:
raise UserError("No trajectory files specified")
for traj in trajectories:
if not os.path.exists(traj):
raise UserError("Trajectory coordinate file"
" (%s) does not exist!" % traj)
from Trajectory.prefs import prefs, INPUT_FILES
# need to change a _copy_ of the dictionary, otherwise
# when we try to save the "original" dictionary will also
# have our changes and no save will occur
from copy import deepcopy
inputPrefs = deepcopy(prefs[INPUT_FILES])
inputPrefs['Amber']['Prmtop'] = prmtop
inputPrefs['Amber']['Trajectories'] = trajectories
prefs[INPUT_FILES] = inputPrefs
loadEnsemble([prmtop] + trajectories, startFrame, endFrame,
callback)
def __init__(self, parent):
from Trajectory.prefs import prefs, INPUT_FILES
inputPrefs = prefs[INPUT_FILES].setdefault(formatName, {})
self.options = []
globs = ["*.ptrj"]
for ext in chimera.fileInfo.extensions("NetCDF generic array"):
globs.append("*" + ext)
filters = [("Particle trajectory", globs)]
for i, label in enumerate(self.labels):
self.options.append(
InputFileOption(parent,
i,
label,
inputPrefs.get(label, True),
None,
title="Choose %s File" % label,
filters=filters,
historyID="Particle %s" % label))
parent.columnconfigure(1, weight=1)
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption
import itertools
info = Tk.Label(parent,
justify=Tk.LEFT,
wraplength=300,
text="Select a molecule with gaps")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options, text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options,
command=self.updateMolecule)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Skip gaps at ends of chains", False,
None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
#self.waters = BooleanOption(options, row.next(),
# "Include waters", False, None)
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod8v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
class Interface(ModelessDialog):
title = "Model Loops with Modeller"
buttons = ("OK", "Cancel")
help = "ContributedSoftware/model/model.html"
def __init__(self, *args, **kw):
ModelessDialog.__init__(self, *args, **kw)
# TODO: initialize instance variables
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption, EnumOption
import itertools
info = Tk.Label(parent, justify=Tk.LEFT, wraplength=300, text=
"Model alternate conformations of loops using "
"Modeller from <http://salilab.org/>.\n"
"First select the loops you wish to model."
" Then choose the number of models "
"you wish to generate.")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options,
text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Restrict selections to turns", True, None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
self.waters = BooleanOption(options, row.next(),
"Include waters", False, None)
self.waters.disable()
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
self.count = IntOption(options, row.next(), "Number of models",
10, None, min=1, sticky=Tk.W)
#self.start = IntOption(options, row.next(),
# "Starting model number", 1, None, min=0)
class Refinement(EnumOption):
values = ('very fast', 'fast', 'slow', 'very slow',
'slow large', 'none')
self.refine = Refinement(options, row.next(), "Refinement",
'fast', None)
button = Tk.Button(options, text="Prune selection",
command=self.prune)
button.grid(row=row.next(), column=0, columnspan=2, pady=2)
self.start = 1
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod9v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def prune(self):
from chimera import selection
molecule = self.molecules.getvalue()
import ModUtil
pairs, residues = ModUtil.convertSelection(
selection._currentSelection,
minLen=4, molecule=molecule,
keepHet=self.hetatms.get(),
keepNA=self.nucleic.get(),
turnsOnly=self.turnsOnly.get())
sel = selection.ItemizedSelection()
sel.add(residues)
sel.addImplied()
selection.mergeCurrent(selection.INTERSECT, sel)
return pairs, residues
def Apply(self):
pairs, residues = self.prune()
if not pairs:
from chimera import replyobj
replyobj.status("no residues meet loop modelling criteria")
return
# create a temporary directory to work in
import tempfile
tempdir = tempfile.mkdtemp(prefix="modeller")
print 'Modeller temporary directory:', tempdir
# write PDB file with original coordinates
import os
fname = os.path.join(tempdir, 'original.pdb')
molecule = self.molecules.getvalue()
xform = molecule.openState.xform
xform.invert() # want original coordinates
chimera.viewer.pdbWrite([molecule], xform, fname)
# write out Modeller input file
count = self.count.get()
refine = self.refine.get()
fname = os.path.join(tempdir, "loopopt.py")
f = file(fname, 'w')
writeModeller(f, 'original.pdb', 'loop', pairs, count, refine)
f.close()
# run Modeller -- put up progress dialog
import ModUtil
def cb(process, dirname=tempdir, count=count):
return loopFileCount(dirname, count)
try:
prog = self.modeller.get()
p = ModUtil.run([prog, "loopopt.py"], cb, cwd=tempdir)
except OSError, e:
from chimera import replyobj
replyobj.error("Unable to run modeller: %s\n" % e)
return
# Do concurrent work here
# find atoms that are connected to the residues we will model
atoms = set()
for r in residues:
for a in r.atoms:
atoms.add(a)
outsideAtoms = set()
for a in atoms:
for b in a.bonds:
oa = b.otherAtom(a)
if oa.residue not in residues:
outsideAtoms.add(oa)
outsideAtoms = [(a.residue.id, a.name) for a in outsideAtoms]
residueIds = set([r.id for r in residues])
# TODO: use triggers to monitor process
# and then startup dock interface
# For now, we just wait
returncode = p.wait()
if returncode != 0:
from chimera import replyobj
replyobj.error("Modeller failed\n")
return
# create ViewDock input file from output files
path = makedock(tempdir, residueIds, outsideAtoms)
if not path:
from chimera import replyobj
replyobj.error("No models were generated\n")
return
# undisplay selected residues
for r in residues:
for a in r.atoms:
a.display = False
# startup dock
import ViewDock
v = ViewDock.ViewDock(path, 'Modeller')
# remove long bonds since makedock can't put TERs
# from both the model and the "longbond" PseudoBondGroup
models = [c.chimeraModel for c in v.results.compoundList]
length = 3
sqLen = length * length
for m in models:
for b in m.bonds:
if b.sqlength() >= sqLen:
# get rid of longbond PseudoBonds
a0, a1 = b.atoms
pbs = a0.associations(
chimera.LONGBOND_PBG_NAME, a1)
for pb in pbs:
pb.pseudoBondGroup.deletePseudoBond(pb)
# get rid of bond
m.deleteBond(b)