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 fillInUI(self, parent): Tkinter.Label(parent, text="Collect positions of selected" " atoms over trajectory", relief="ridge", bd=4).grid( row=0, column=0, columnspan=2, sticky="ew") startFrame = self.movie.startFrame endFrame = self.movie.endFrame from chimera.tkoptions import IntOption, BooleanOption, \ FloatOption, StringOption self.startFrame = IntOption(parent, 1, "Starting frame", startFrame, None, min=startFrame, max=endFrame, width=6) numFrames = endFrame - startFrame + 1 defStride = 1 + int(numFrames/300) self.stride = IntOption(parent, 2, "Step size", defStride, None, min=1, max=numFrames, width=3) self.endFrame = IntOption(parent, 3, "Ending frame", endFrame, None, min=startFrame, max=endFrame, width=6) self.doCutoff = BooleanOption(parent, 4, 'Limit data collection' ' to within cutoff distance of any "held steady" atoms', True, None) self.cutoff = FloatOption(parent, 5, "Cutoff distance", prefs[VOLUME_CUTOFF], None, width=4) self.resolution = FloatOption(parent, 6, "Volume grid spacing", prefs[VOLUME_RESOLUTION], None, min=0.0001, width=4) self.volumeName = StringOption(parent, 7, "Volume data name", self.movie.ensemble.name, None, width=20) self.byAtomType = BooleanOption(parent, 8, "Collect data" " separately for each atom type in selection", True, None, balloon="Create a volume data set for" " each type of atom type\n(sp2 oxygen, aromatic carbon," " etc.) in current selection")
def fillInUI(self, parent): from chimera.tkoptions import IntOption, BooleanOption, \ FloatOption Tkinter.Label(parent, text="Create RMSD map of trajectory " "against itself", relief="ridge", bd=4).grid(row=0, column=0, columnspan=2, sticky="ew") startFrame = self.movie.startFrame endFrame = self.movie.endFrame self.startFrame = IntOption(parent, 1, "Starting frame", startFrame, None, min=startFrame, max=endFrame, width=6) numFrames = endFrame - startFrame + 1 defStride = 1 + int(numFrames/300) self.stride = IntOption(parent, 2, "Step size", defStride, None, min=1, max=numFrames, width=3) self.endFrame = IntOption(parent, 3, "Ending frame", endFrame, None, min=startFrame, max=endFrame, width=6) self.minRmsd = FloatOption(parent, 4, "Lower RMSD threshold" " (white)", prefs[RMSD_MIN], None, width=6) self.maxRmsd = FloatOption(parent, 5, "Upper RMSD threshold" " (black)", prefs[RMSD_MAX], None, width=6) self.useSel = BooleanOption(parent, 6, "Restrict map to " "current selection, if any", True, None) self.ignoreBulk = BooleanOption(parent, 7, "Ignore solvent/" "ions", True, None) self.ignoreHyds = BooleanOption(parent, 8, "Ignore hydrogens", True, None) self.recolor = BooleanOption(parent, 9, "Auto-recolor for" " contrast", prefs[RMSD_AUTOCOLOR], None)
class SelectClusterMode(ModalDialog):
buttons = ('Frames', 'Density')
def __init__(self, movie):
self.movie = movie
self.volgridspacing = None
ModalDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter
from chimera.tkoptions import IntOption, BooleanOption, FloatOption
Tkinter.Label(parent, text="Please select visualization mode",
relief="ridge", bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
minspacing = 1
maxspacing = 15
defaultspacing=10
self.volgridspacing = FloatOption(parent, 1, "Volume grid Spacing", defaultspacing, None, min=minspacing, max=maxspacing, width=6)
def Frames(self):
volgridspacing = self.volgridspacing.get()
ModalDialog.Cancel(self, value=(volgridspacing, "Frames"))
def Density(self):
volgridspacing = self.volgridspacing.get()
ModalDialog.Cancel(self, value=(volgridspacing, "Density"))
def destroy(self):
self.movie = None
ModelessDialog.destroy(self)
def fillInUI(self, parent):
from chimera.tkoptions import FloatOption
self.newMin = FloatOption(parent, 0,
"New lower RMSD threshold (white)",
prefs[RMSD_MIN], None)
self.newMax = FloatOption(parent, 1,
"New upper RMSD threshold (black)",
prefs[RMSD_MAX], None)
def __init__(self, parent):
from chimera.tkoptions import IntOption, FloatOption
Tkinter.Frame.__init__(self, parent)
self.nsteps = IntOption(self, 0, "Steps", 100, None)
self.stepsize = FloatOption(self,
1,
"Step size (A)",
0.02,
None,
min=0.0001,
max=1.0)
self.interval = IntOption(self, 2, "Update interval", 10, None)
self.freeze = FreezeOption(self, 3, "Fixed atoms", base.FreezeNone,
None)
def __init__(self, parent): from chimera.tkoptions import IntOption, FloatOption Tkinter.Frame.__init__(self, parent) self.nsteps = IntOption(self, 0, "Steps", 100, None) self.stepsize = FloatOption(self, 1, "Step size (A)", 0.02, None, min=0.0001, max=1.0) self.interval = IntOption(self, 2, "Update interval", 10, None) self.freeze = FreezeOption(self, 3, "Fixed atoms", base.FreezeNone, None)
def fillInUI(self, parent):
import Tkinter
from chimera.tkoptions import IntOption, BooleanOption, FloatOption
Tkinter.Label(parent, text="Please select visualization mode",
relief="ridge", bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
minspacing = 1
maxspacing = 15
defaultspacing=10
self.volgridspacing = FloatOption(parent, 1, "Volume grid Spacing", defaultspacing, None, min=minspacing, max=maxspacing, width=6)
def fillInUI(self, parent): import Pmw, Tkinter row = 0 Tkinter.Label(parent, text="Create plane for selected atoms...").grid( row=row, columnspan=2) row += 1 from chimera.tkoptions import StringOption, BooleanOption self.nameOpt = StringOption(parent, row, "Plane name", "plane", None) row += 1 self.replaceExistingOpt = BooleanOption(parent, row, "Replace existing planes", False, None) row += 1 from chimera.tkoptions import ColorOption, FloatOption self.colorOpt = ColorOption(parent, row, "Color", None, None, balloon="Plane color. If No Color, then the plane" " will be colored to match the structure") row += 1 self.autoRadiusOpt = BooleanOption(parent, row, "Set disk size to enclose atom projections", True, self._radCB) row += 1 self.radRow = row self.radOffsetOpt = FloatOption(parent, row, "Extra radius" " (padding)", 0.0, None) self.radiusOpt = FloatOption(parent, row, "Fixed radius", 10.0, None) self.radiusOpt.forget() row += 1 self.thicknessOpt = FloatOption(parent, row, "Disk thickness", prefs[PLANE_THICKNESS], None)
class ParamGUI:
labels = ["Topology", "Coordinates", "PROMD"]
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 loadEnsemble(self, startFrame, endFrame, callback):
args = []
from Trajectory.prefs import prefs, INPUT_FILES, GROMOS_SCALING
# 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])
for i in range(len(self.labels)):
path = self.options[i].get()
label = self.labels[i]
if not os.path.exists(path):
raise ValueError, \
"%s file '%s' does not exist!" % (
label, path)
inputPrefs['Gromos'][label] = path
args.append(path)
prefs[INPUT_FILES] = inputPrefs
scale = self.scalingOption.get()
prefs[GROMOS_SCALING] = scale
args.append(scale)
loadEnsemble(args, startFrame, endFrame, callback)
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)
class ParamGUI:
labels = ["Topology", "Coordinates", "PROMD"]
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 loadEnsemble(self, startFrame, endFrame, callback):
args = []
from Trajectory.prefs import prefs, INPUT_FILES, GROMOS_SCALING
# 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])
for i in range(len(self.labels)):
path = self.options[i].get()
label = self.labels[i]
if not os.path.exists(path):
raise ValueError, \
"%s file '%s' does not exist!" % (
label, path)
inputPrefs['Gromos'][label] = path
args.append(path)
prefs[INPUT_FILES] = inputPrefs
scale = self.scalingOption.get()
prefs[GROMOS_SCALING] = scale
args.append(scale)
loadEnsemble(args, startFrame, endFrame, callback)
def fillInUI(self, parent):
row = 0
parent.columnconfigure(0, weight=1)
parent.rowconfigure(row, weight=1)
self.chainList = MoleculeChainScrolledListBox(parent,
selectioncommand=self._updateIterRef,
listbox_selectmode='multiple')
self.chainList.grid(row=row, column=0, sticky='nsew')
row += 1
mols = {}
for chain in self.chainList.get():
mol = chain.molecule
if mol in mols:
continue
mols[mol] = chain
self.chainList.setvalue(mols.values())
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.distCutoff = FloatOption(f, 0,
"Residue-residue distance cutoff (angstroms)",
prefs[DIST_CUTOFF], None, balloon="""\
residues whose principal atoms are further apart
than this distance will not be aligned in the
generated sequence alignment""")
self.distCutoff.min = 0.0
class MatchTypeOption(SymbolicEnumOption):
values = ["any", "all"]
labels = ["at least one other", "all others"]
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.matchType = MatchTypeOption(f, 0,
"Residue aligned in column if within cutoff of",
prefs[ANYALL], None, balloon="""\
whether a residue needs to match the distance cutoff to all other
residues in its column, or just to one residue in the column""")
class GapCharOption(SymbolicEnumOption):
values = [".", "-", "~"]
labels = [". (period)", "- (dash)", "~ (tilde)"]
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.gapChar = GapCharOption(f, 0, "Gap character",
prefs[GAPCHAR], None, balloon="""\
character used to depict gaps in alignment""")
self.circularVar = Tkinter.IntVar(parent)
self.circularVar.set(prefs[CIRCULAR])
Tkinter.Checkbutton(parent, variable=self.circularVar, text=
"Allow for circular permutation").grid(row=row,
column=0, sticky='w')
row += 1
self.iterateVar = Tkinter.IntVar(parent)
self.iterateVar.set(prefs[ITERATE])
Tkinter.Checkbutton(parent, command=self._iterParamsDisplay,
text="Iterate superposition/alignment...",
variable=self.iterateVar).grid(
row=row, column=0, columnspan=2, sticky='w')
row += 1
self.iterParams = Pmw.Group(parent, hull_padx=2,
tag_text="Iteration Parameters")
self.iterParams.grid(row=row, column=0, columnspan=2)
row += 1
inside = self.iterParams.interior()
Tkinter.Label(inside, text="Iterate alignment:").grid(
row=0, column=0, rowspan=2, sticky='e')
self.iterConvergeVar = Tkinter.IntVar(parent)
self.iterConvergeVar.set(prefs[ITER_CONVERGE])
f = Tkinter.Frame(inside)
f.grid(row=0, column=1, sticky='w')
Tkinter.Radiobutton(f, value=False, text="at most",
variable=self.iterConvergeVar).grid(row=0, column=0)
self.iterLimit = Pmw.EntryField(f, labelpos='e',
label_text="times", validate={'min': 1,
'validator': 'numeric'}, value=str(prefs[ITER_AMOUNT]),
entry_width=2, entry_justify="center")
self.iterLimit.grid(row=0, column=1)
Tkinter.Radiobutton(inside, text="until convergence",
value=True, variable=self.iterConvergeVar).grid(
row=1, column=1, sticky='w')
inside.rowconfigure(2, minsize="0.1i")
Tkinter.Label(inside, text="Superimpose full columns:"
).grid(row=3, rowspan=2, column=0, sticky='e')
self.iterAllColsVar = Tkinter.IntVar(parent)
self.iterAllColsVar.set(prefs[ITER_ALL_COLS])
Tkinter.Radiobutton(inside, text="across entire alignment",
value=True, variable=self.iterAllColsVar).grid(
row=3, column=1, sticky='w')
f = Tkinter.Frame(inside)
f.grid(row=4, column=1, sticky='w')
Tkinter.Radiobutton(f, text="in stretches of at least",
variable=self.iterAllColsVar,
value=False).grid(row=0, column=0)
self.stretchLen = Pmw.EntryField(f, labelpos='e',
label_text="consecutive columns",
validate={'min': 2, 'validator': 'numeric'},
value=str(prefs[ITER_CONSECUTIVE_COLS]),
entry_width=1, entry_justify="center")
self.stretchLen.grid(row=0, column=1)
self.referenceMenu = Pmw.OptionMenu(inside, labelpos='w',
items=Pmw.ScrolledListBox.get(self.chainList),
label_text="Reference chain for matching:")
self.referenceMenu.grid(row=5, column=0, columnspan=2)
self._iterParamsDisplay()
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
from chimera import help
b = Tkinter.Button(f, text="Save settings", pady=0,
command=self._saveSettings)
b.grid(row=0, column=0)
help.register(b, balloon="Save current settings")
b = Tkinter.Button(f, text="Reset to defaults", pady=0,
command=self._restoreSettings)
b.grid(row=0, column=1)
help.register(b, balloon="Reset dialog to factory defaults")
f.columnconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
class Match2Align(ModelessDialog):
title = "Create Alignment from Superposition"
oneshot = True
help = "ContributedSoftware/matchalign/matchalign.html"
def fillInUI(self, parent):
row = 0
parent.columnconfigure(0, weight=1)
parent.rowconfigure(row, weight=1)
self.chainList = MoleculeChainScrolledListBox(parent,
selectioncommand=self._updateIterRef,
listbox_selectmode='multiple')
self.chainList.grid(row=row, column=0, sticky='nsew')
row += 1
mols = {}
for chain in self.chainList.get():
mol = chain.molecule
if mol in mols:
continue
mols[mol] = chain
self.chainList.setvalue(mols.values())
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.distCutoff = FloatOption(f, 0,
"Residue-residue distance cutoff (angstroms)",
prefs[DIST_CUTOFF], None, balloon="""\
residues whose principal atoms are further apart
than this distance will not be aligned in the
generated sequence alignment""")
self.distCutoff.min = 0.0
class MatchTypeOption(SymbolicEnumOption):
values = ["any", "all"]
labels = ["at least one other", "all others"]
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.matchType = MatchTypeOption(f, 0,
"Residue aligned in column if within cutoff of",
prefs[ANYALL], None, balloon="""\
whether a residue needs to match the distance cutoff to all other
residues in its column, or just to one residue in the column""")
class GapCharOption(SymbolicEnumOption):
values = [".", "-", "~"]
labels = [". (period)", "- (dash)", "~ (tilde)"]
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
row += 1
self.gapChar = GapCharOption(f, 0, "Gap character",
prefs[GAPCHAR], None, balloon="""\
character used to depict gaps in alignment""")
self.circularVar = Tkinter.IntVar(parent)
self.circularVar.set(prefs[CIRCULAR])
Tkinter.Checkbutton(parent, variable=self.circularVar, text=
"Allow for circular permutation").grid(row=row,
column=0, sticky='w')
row += 1
self.iterateVar = Tkinter.IntVar(parent)
self.iterateVar.set(prefs[ITERATE])
Tkinter.Checkbutton(parent, command=self._iterParamsDisplay,
text="Iterate superposition/alignment...",
variable=self.iterateVar).grid(
row=row, column=0, columnspan=2, sticky='w')
row += 1
self.iterParams = Pmw.Group(parent, hull_padx=2,
tag_text="Iteration Parameters")
self.iterParams.grid(row=row, column=0, columnspan=2)
row += 1
inside = self.iterParams.interior()
Tkinter.Label(inside, text="Iterate alignment:").grid(
row=0, column=0, rowspan=2, sticky='e')
self.iterConvergeVar = Tkinter.IntVar(parent)
self.iterConvergeVar.set(prefs[ITER_CONVERGE])
f = Tkinter.Frame(inside)
f.grid(row=0, column=1, sticky='w')
Tkinter.Radiobutton(f, value=False, text="at most",
variable=self.iterConvergeVar).grid(row=0, column=0)
self.iterLimit = Pmw.EntryField(f, labelpos='e',
label_text="times", validate={'min': 1,
'validator': 'numeric'}, value=str(prefs[ITER_AMOUNT]),
entry_width=2, entry_justify="center")
self.iterLimit.grid(row=0, column=1)
Tkinter.Radiobutton(inside, text="until convergence",
value=True, variable=self.iterConvergeVar).grid(
row=1, column=1, sticky='w')
inside.rowconfigure(2, minsize="0.1i")
Tkinter.Label(inside, text="Superimpose full columns:"
).grid(row=3, rowspan=2, column=0, sticky='e')
self.iterAllColsVar = Tkinter.IntVar(parent)
self.iterAllColsVar.set(prefs[ITER_ALL_COLS])
Tkinter.Radiobutton(inside, text="across entire alignment",
value=True, variable=self.iterAllColsVar).grid(
row=3, column=1, sticky='w')
f = Tkinter.Frame(inside)
f.grid(row=4, column=1, sticky='w')
Tkinter.Radiobutton(f, text="in stretches of at least",
variable=self.iterAllColsVar,
value=False).grid(row=0, column=0)
self.stretchLen = Pmw.EntryField(f, labelpos='e',
label_text="consecutive columns",
validate={'min': 2, 'validator': 'numeric'},
value=str(prefs[ITER_CONSECUTIVE_COLS]),
entry_width=1, entry_justify="center")
self.stretchLen.grid(row=0, column=1)
self.referenceMenu = Pmw.OptionMenu(inside, labelpos='w',
items=Pmw.ScrolledListBox.get(self.chainList),
label_text="Reference chain for matching:")
self.referenceMenu.grid(row=5, column=0, columnspan=2)
self._iterParamsDisplay()
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
from chimera import help
b = Tkinter.Button(f, text="Save settings", pady=0,
command=self._saveSettings)
b.grid(row=0, column=0)
help.register(b, balloon="Save current settings")
b = Tkinter.Button(f, text="Reset to defaults", pady=0,
command=self._restoreSettings)
b.grid(row=0, column=1)
help.register(b, balloon="Reset dialog to factory defaults")
f.columnconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
def Apply(self):
chains = self.chainList.getvalue()
if len(chains) < 2:
replyobj.error("Must choose at least two chains\n")
self.enter()
return
mols = {}
for chain in chains:
if chain.molecule in mols:
replyobj.error(
"Please choose only one chain per model\n")
self.enter()
return
mols[chain.molecule] = 1
cutoff = float(self.distCutoff.get())
matchType = self.matchType.get()
gapChar = self.gapChar.get()
circular = self.circularVar.get()
from align import match2align
from Midas import match, rmsd
seqs = match2align(chains, cutoff, matchType, gapChar, circular)
cols = alignedCols(seqs)
replyobj.info("%d fully populated columns\n" % (len(cols)))
if self.iterateVar.get():
best = None
iteration = 1
refChain = self.chainList.itemMap[
self.referenceMenu.getvalue()]
if self.iterConvergeVar.get():
iterLimit = None
else:
self.iterLimit.invoke()
iterLimit = int(self.iterLimit.getvalue())
if self.iterAllColsVar.get():
stretchLen = 1
else:
self.stretchLen.invoke()
stretchLen = int(self.stretchLen.getvalue())
while True:
refSeq = [s for s in seqs
if s.molecule == refChain.molecule][0]
# cull columns based on stretch len criteria
stretch = []
culled = []
for col in cols:
if not stretch or stretch[-1]+1 == col:
stretch.append(col)
continue
if len(stretch) >= stretchLen:
culled.extend(stretch)
stretch = [col]
if len(stretch) >= stretchLen:
culled.extend(stretch)
if stretchLen > 1:
replyobj.info("%d fully populated"
" columns in at least %d"
" column stretches\n" % (
len(culled), stretchLen))
if not culled:
break
# match
refAtoms = columnAtoms(refSeq, culled)
for seq in seqs:
if seq.molecule == refSeq.molecule:
continue
seqAtoms = columnAtoms(seq, culled)
replyobj.info("Matching %s onto %s\n"
% (seq.name, refSeq.name))
match(seqAtoms, refAtoms)
seqs = match2align(chains, cutoff, matchType,
gapChar, circular, statusPrefix=
"Iteration %d: " % iteration)
cols = alignedCols(seqs)
replyobj.info("Iteration %d: %d fully populated"
" columns\n" % (iteration, len(cols)))
if best == None or len(cols) > len(best):
best = cols
else:
break
if iterLimit and iteration >= iterLimit:
break
iteration += 1
if len(seqs) == 2:
mav = showAlignment(seqs, "Match of %s and %s" %
(seqs[0].name, seqs[1].name))
else:
mav = showAlignment(seqs, "Match -> Align (%d models)"
% len(seqs))
from MultAlignViewer.MAViewer import MATCHED_REGION_INFO
name, fill, outline = MATCHED_REGION_INFO
mav.newRegion(name="Fully populated columns", columns=cols,
fill=fill, outline=outline)
if cols:
# show pairwise RMSD matrix in fully populated columns
matchAtoms = {}
for seq in seqs:
matchAtoms[seq] = columnAtoms(seq, cols)
replyobj.info("\nEvaluating superpositions across all %d fully"
" populated columns in the final alignment:\n"
% len(cols))
dsqSum = 0
for i, s1 in enumerate(seqs):
for s2 in seqs[i+1:]:
v = rmsd(matchAtoms[s1], matchAtoms[s2],
log=False)
dsqSum += v * v
replyobj.info("RMSD of %s with %s: %.3f\n" %
(s1.name, s2.name, v))
from math import sqrt
replyobj.info("Overall RMSD: %.3f\n\n" % sqrt(2 * dsqSum /
(len(seqs) * (len(seqs)-1))))
mav.status("RMSDs reported in Reply Log", color="purple")
replyobj.status("RMSDs reported in Reply Log", color="purple")
else:
mav.status("No fully populated columns in alignment", color="blue")
def _iterParamsDisplay(self):
if self.iterateVar.get():
self.iterParams.grid()
else:
self.iterParams.grid_remove()
def _restoreSettings(self):
from prefs import defaults
self.distCutoff.set(defaults[DIST_CUTOFF])
self.matchType.set(defaults[ANYALL])
self.gapChar.set(defaults[GAPCHAR])
self.circularVar.set(defaults[CIRCULAR])
self.iterateVar.set(defaults[ITERATE])
self._iterParamsDisplay()
self.iterConvergeVar.set(defaults[ITER_CONVERGE])
self.iterLimit.setvalue(str(defaults[ITER_AMOUNT]))
self.iterAllColsVar.set(defaults[ITER_ALL_COLS])
self.stretchLen.setvalue(str(defaults[ITER_CONSECUTIVE_COLS]))
def _saveSettings(self):
prefs[DIST_CUTOFF] = float(self.distCutoff.get())
prefs[ANYALL] = self.matchType.get()
prefs[GAPCHAR] = self.gapChar.get()
prefs[CIRCULAR] = self.circularVar.get()
prefs[ITERATE] = self.iterateVar.get()
prefs[ITER_CONVERGE] = self.iterConvergeVar.get()
self.iterLimit.invoke()
prefs[ITER_AMOUNT] = int(self.iterLimit.getvalue())
prefs[ITER_ALL_COLS] = self.iterAllColsVar.get()
self.stretchLen.invoke()
prefs[ITER_CONSECUTIVE_COLS] = int(self.stretchLen.getvalue())
def _updateIterRef(self, *args):
self.referenceMenu.setitems([self.chainList.valueMap[chain]
for chain in self.chainList.getvalue()])
def fillInUI(self, parent):
Tkinter.Label(parent,
text="Collect positions of selected"
" atoms over trajectory",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.doCutoff = BooleanOption(
parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms', True,
None)
self.cutoff = FloatOption(parent,
5,
"Cutoff distance",
prefs[VOLUME_CUTOFF],
None,
width=4)
self.resolution = FloatOption(parent,
6,
"Volume grid spacing",
prefs[VOLUME_RESOLUTION],
None,
min=0.0001,
width=4)
self.volumeName = StringOption(parent,
7,
"Volume data name",
self.movie.ensemble.name,
None,
width=20)
self.byAtomType = BooleanOption(
parent,
8, "Collect data"
" separately for each atom type in selection",
True,
None,
balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
class CreatePlaneDialog(ModelessDialog):
title = "Define Plane"
help = "ContributedSoftware/structuremeas/structuremeas.html#define-plane"
provideStatus = True
statusPosition = "above"
def fillInUI(self, parent):
import Pmw, Tkinter
row = 0
Tkinter.Label(parent, text="Create plane for selected atoms...").grid(
row=row, columnspan=2)
row += 1
from chimera.tkoptions import StringOption, BooleanOption
self.nameOpt = StringOption(parent, row, "Plane name", "plane", None)
row += 1
self.replaceExistingOpt = BooleanOption(parent, row,
"Replace existing planes", False, None)
row += 1
from chimera.tkoptions import ColorOption, FloatOption
self.colorOpt = ColorOption(parent, row, "Color", None, None,
balloon="Plane color. If No Color, then the plane"
" will be colored to match the structure")
row += 1
self.autoRadiusOpt = BooleanOption(parent, row,
"Set disk size to enclose atom projections", True, self._radCB)
row += 1
self.radRow = row
self.radOffsetOpt = FloatOption(parent, row, "Extra radius"
" (padding)", 0.0, None)
self.radiusOpt = FloatOption(parent, row, "Fixed radius", 10.0, None)
self.radiusOpt.forget()
row += 1
self.thicknessOpt = FloatOption(parent, row, "Disk thickness",
prefs[PLANE_THICKNESS], None)
def Apply(self):
from chimera import UserError
if self.replaceExistingOpt.get():
planeManager.removePlanes(planeManager.planes)
kw = {
'color': self.colorOpt.get(),
'thickness': self.thicknessOpt.get()
}
prefs[PLANE_THICKNESS] = kw['thickness']
if self.autoRadiusOpt.get():
kw['radiusOffset'] = self.radOffsetOpt.get()
else:
kw['radius'] = self.radiusOpt.get()
replyobj.info("Creating plane\n")
selAtoms = selection.currentAtoms()
if len(selAtoms) < 3:
self.enter()
raise UserError("Need to select at least three"
" atoms to define a plane")
planeManager.createPlane(self.nameOpt.get().strip(), selAtoms, **kw)
def _radCB(self, opt):
if opt.get():
self.radiusOpt.forget()
self.radOffsetOpt.manage()
else:
self.radOffsetOpt.forget()
self.radiusOpt.manage()
class RmsdStarter(ModelessDialog):
title = "Get RMSD Map Parameters"
help = "ContributedSoftware/movie/movie.html#rmsd"
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption
Tkinter.Label(parent,
text="Create RMSD map of trajectory "
"against itself",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.minRmsd = FloatOption(parent,
4, "Lower RMSD threshold"
" (white)",
prefs[RMSD_MIN],
None,
width=6)
self.maxRmsd = FloatOption(parent,
5, "Upper RMSD threshold"
" (black)",
prefs[RMSD_MAX],
None,
width=6)
self.useSel = BooleanOption(
parent, 6, "Restrict map to "
"current selection, if any", True, None)
self.ignoreBulk = BooleanOption(parent, 7, "Ignore solvent/"
"ions", True, None)
self.ignoreHyds = BooleanOption(parent, 8, "Ignore hydrogens", True,
None)
self.recolor = BooleanOption(parent, 9, "Auto-recolor for"
" contrast", prefs[RMSD_AUTOCOLOR], None)
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])
class VolumeDialog(ModelessDialog):
title = "Calculate Atomic Occupancy"
help = "ContributedSoftware/movie/movie.html#occupancy"
provideStatus = True
statusPosition = "left"
buttons = ('OK', 'Close')
default= 'OK'
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def map(self, e=None):
if not self.movie.holdingSteady:
self.status("No atoms being held steady -- see Help",
color="red")
def fillInUI(self, parent):
Tkinter.Label(parent, text="Collect positions of selected"
" atoms over trajectory", relief="ridge", bd=4).grid(
row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent, 1, "Starting frame",
startFrame, None, min=startFrame, max=endFrame, width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames/300)
self.stride = IntOption(parent, 2, "Step size", defStride,
None, min=1, max=numFrames, width=3)
self.endFrame = IntOption(parent, 3, "Ending frame", endFrame,
None, min=startFrame, max=endFrame, width=6)
self.doCutoff = BooleanOption(parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms',
True, None)
self.cutoff = FloatOption(parent, 5, "Cutoff distance",
prefs[VOLUME_CUTOFF], None, width=4)
self.resolution = FloatOption(parent, 6, "Volume grid spacing",
prefs[VOLUME_RESOLUTION], None, min=0.0001, width=4)
self.volumeName = StringOption(parent, 7, "Volume data name",
self.movie.ensemble.name, None, width=20)
self.byAtomType = BooleanOption(parent, 8, "Collect data"
" separately for each atom type in selection",
True, None, balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
def Apply(self):
from chimera import UserError
atoms = chimera.selection.currentAtoms()
if not atoms:
self.enter()
raise UserError("No atoms selected")
startFrame = self.startFrame.get()
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")
if self.doCutoff.get():
bound = prefs[VOLUME_CUTOFF] = self.cutoff.get()
else:
bound = None
prefs[VOLUME_RESOLUTION] = self.resolution.get()
step = self.stride.get()
spacing = self.resolution.get()
name = self.volumeName.get()
atomTypes = {}
if self.byAtomType.get():
for a in atoms:
atomTypes.setdefault(a.idatmType, []).append(a)
if len(atomTypes) > 1:
for atomType, atAtoms in atomTypes.items():
self.movie.computeVolume(atAtoms,
startFrame=startFrame,
endFrame=endFrame, step=step,
bound=bound, spacing=spacing,
volumeName=name+" ["+atomType+"]")
else:
self.movie.computeVolume(atoms, startFrame=startFrame,
endFrame=endFrame, step=step, bound=bound,
spacing=spacing, volumeName=name)
class Interface(ModelessDialog):
title = 'Nucleotides'
help = "ContributedSoftware/nucleotides/nucleotides.html"
buttons = ("NDB Colors",) + ModelessDialog.buttons
provideStatus = True
def __init__(self, *args, **kw):
self.currentStyle = self.saveui_defaultItem()
ModelessDialog.__init__(self, *args, **kw)
self.__firstcanvas = True
def fillInUI(self, parent):
parent.columnconfigure(0, pad=2)
parent.columnconfigure(1, pad=2)
import itertools
row = itertools.count()
self.showBackbone = BackboneOption(parent, row.next(),
'Show backbone as', 'ribbon', None)
self.showSide = SideOption(parent, row.next(),
'Show side (sugar/base) as', 'fill/slab',
self._showSideCB)
self.showOrientation = BooleanOption(parent, row.next(),
'Show base orientation', default.ORIENT, None)
import Tix
self.nb = Tix.NoteBook(parent)
self.nb.grid(row=row.next(), column=0, columnspan=2, sticky=Tk.EW, padx=2)
# ladder page
self.nb.add("ladder", label="Ladder Options")
f = self.nb.page("ladder")
if Tk.TkVersion >= 8.5:
parent.tk.call('grid', 'anchor', f._w, Tk.N)
prow = itertools.count()
self.skipNonBase = BooleanOption(f, prow.next(),
'Ignore non-base H-bonds', default.IGNORE, None)
self.showStubs = BooleanOption(f, prow.next(),
'Show stubs', default.STUBS, None)
self.rungRadius = FloatOption(f, prow.next(), 'Rung radius',
default.RADIUS, None)
self.rungRadius.min = 0.0
self.useExisting = BooleanOption(f, prow.next(),
'Using existing H-bonds', default.USE_EXISTING,
self._useExistingCB)
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(f, None, colorOptions=False)
#self.relaxParams.relaxConstraints = False
self.relaxParams.grid(row=prow.next(), columnspan=2,
sticky='nsew', padx=2)
# slab page
self.nb.add("slab", label="Slab Options")
f = self.nb.page("slab")
if Tk.TkVersion >= 8.5:
parent.tk.call('grid', 'anchor', f._w, Tk.N)
prow = itertools.count()
self.thickness = FloatOption(f, prow.next(), 'Thickness',
default.THICKNESS, None)
self.thickness.min = 0.01
self.shape = ShapeOption(f, prow.next(), 'Slab object',
default.SHAPE, None)
self.hideBases = BooleanOption(f, prow.next(),
'Hide base atoms', default.HIDE, None)
self.showGlycosidic = BooleanOption(f, prow.next(),
'Separate glycosidic bond', default.GLYCOSIDIC,
None)
self.nb.add("style", label="Slab Style", raisecmd=self.map)
# style page
f = self.nb.page("style")
if Tk.TkVersion >= 8.5:
f.tk.call('grid', 'anchor', f._w, Tk.N)
info = NA.findStyle(self.currentStyle)
from chimera.preferences import saveui
f2 = Tk.Frame(f)
self.saveui = saveui.SaveUI(f2, self)
f2.grid(row=prow.next(), column=0, columnspan=2, sticky=Tk.EW,
padx=2, pady=2)
self.anchor = AnchorOption(f, prow.next(), 'Anchor',
info[NA.ANCHOR], self._drawStyle)
f2 = Pmw.Group(f, tag_text=NA.PURINE.title())
f2.grid(row=prow.next(), column=0, columnspan=2, sticky=Tk.EW,
padx=2)
f2 = f2.interior()
f2.columnconfigure(0, weight=1, pad=2, uniform='a')
f2.columnconfigure(1, weight=1, uniform='a')
f2.columnconfigure(2, weight=1)
self.purine_canvas = Tk.Canvas(f2, width=1, height=1) #,
#borderwidth=2, relief=Tk.RIDGE)
r = prow.next()
self.purine_canvas.grid(row=r, column=0, rowspan=3,
sticky=Tk.NSEW, padx=2, pady=2)
corners = info[NA.PURINE]
self.puLL = Float2Option(f2, prow.next(), 'Lower left',
corners[0], self._drawStyle, startCol=1)
self.puUR = Float2Option(f2, prow.next(), 'Upper right',
corners[1], self._drawStyle, startCol=1)
f3 = Pmw.Group(f, tag_text="%s, %s" % (NA.PYRIMIDINE.title(),
NA.PSEUDO_PYRIMIDINE.title()))
r = prow.next()
f3.grid(row=r, column=0, columnspan=2, sticky=Tk.EW, padx=2)
f3 = f3.interior()
f3.columnconfigure(0, weight=1, pad=2, uniform='a')
f3.columnconfigure(1, weight=1, uniform='a')
f3.columnconfigure(2, weight=1)
self.pyrimidine_canvas = Tk.Canvas(f3, width=1, height=1) #,
#borderwidth=2, relief=Tk.RIDGE)
r = prow.next()
self.pyrimidine_canvas.grid(row=r, column=0, rowspan=3,
sticky=Tk.NSEW, padx=2, pady=2)
corners = info[NA.PYRIMIDINE]
self.pyLL = Float2Option(f3, prow.next(), 'Lower left',
corners[0], self._drawStyle, startCol=1)
self.pyUR = Float2Option(f3, prow.next(), 'Upper right',
corners[1], self._drawStyle, startCol=1)
self.restrict = Tk.IntVar(parent)
self.restrict.set(1)
cb = Tk.Checkbutton(parent, variable=self.restrict,
text="Restrict OK/Apply to current selection, if any")
cb.grid(row=row.next(), columnspan=2)
parent.pack(ipady=2)
self._showSideCB()
chimera.triggers.addHandler(NA.TRIGGER_SLAB_STYLES,
self._updateStyles, None)
def map(self, event=None):
# need to update_idletasks so canvases in grid will have a size
page = self.nb.raised()
if page == 'style':
if self.__firstcanvas:
self.uiMaster().update_idletasks()
self._drawStyle()
self.__firstcanvas = False
def _updateStyles(self, trigger, closure, arg):
# pick up programmic changes in list of slab styles
self.saveui.updateComboList()
def saveui_label(self):
return "Slab Style"
def saveui_presetItems(self):
return NA.SystemStyles.keys()
def saveui_userItems(self):
return NA.userStyles.keys()
def saveui_defaultItem(self):
return 'long'
def saveui_select(self, name):
self.currentStyle = name
self._setSlabStyle(name)
def saveui_save(self, name):
info = self._getInfo()
NA.addStyle(name, info)
self.status("Slab style \"%s\" saved" % name)
return True # successful
def saveui_delete(self, name):
NA.removeStyle(name)
self.status("Slab style \"%s\" deleted" % name)
return True # successful
def _showSideCB(self, *args):
side = self.showSide.get()
hasSlab = 'slab' in side
if side.startswith('fill') or hasSlab:
self.showOrientation.enable()
else:
self.showOrientation.disable()
if hasSlab:
self.nb.raise_page('slab')
elif side == 'ladder':
self.nb.raise_page('ladder')
if side == 'tube/slab':
# tube connects to C1' if no slab
# if slab, it goes to the middle of slab
self.showGlycosidic.enable()
return
self.showGlycosidic.disable()
def _useExistingCB(self, *args):
useExisting = self.useExisting.get()
if useExisting:
self.relaxParams.disable()
else:
self.relaxParams.enable()
def Apply(self):
from chimera import selection
if not self.restrict.get() or selection.currentEmpty():
molecules = chimera.openModels.list(
modelTypes=[chimera.Molecule])
residues = []
for mol in molecules:
residues.extend(mol.residues)
else:
residues = selection.currentResidues()
molecules = tuple(set(r.molecule for r in residues))
residues = [r for r in residues
if r.ribbonResidueClass.isNucleic()]
backbone = self.showBackbone.get()
display = backbone != 'atoms & bonds'
for r in residues:
r.ribbonDisplay = display
side = self.showSide.get()
if side == 'ladder':
distSlop = 0.0
angleSlop = 0.0
relax = self.relaxParams.relaxConstraints
if relax:
distSlop = self.relaxParams.relaxDist
angleSlop = self.relaxParams.relaxAngle
NA.set_ladder(molecules, residues,
rungRadius=self.rungRadius.get(),
showStubs=self.showStubs.get(),
skipNonBaseHBonds=self.skipNonBase.get(),
useExisting=self.useExisting.get(),
distSlop=distSlop, angleSlop=angleSlop)
return
if side.endswith('slab'):
if self.currentStyle is None:
info = self._getInfo()
NA.addStyle(None, info)
showGly = self.anchor.get() != NA.SUGAR
if showGly and side.startswith('tube'):
showGly = self.showGlycosidic.get()
NA.set_slab(side, molecules, residues,
style=self.currentStyle,
thickness=self.thickness.get(),
orient=self.showOrientation.get(),
shape=self.shape.get(), showGly=showGly,
hide=self.hideBases.get())
if side.startswith('fill'):
for r in residues:
r.fillDisplay = True
else:
for r in residues:
r.fillDisplay = False
if side.endswith('fill'):
if self.showOrientation.get():
NA.set_orient(molecules, residues)
else:
NA.set_normal(molecules, residues)
elif side.startswith('atoms'):
NA.set_normal(molecules, residues)
return
def _showBase(self, type, info, canvas):
# assume height is greater than width
# keep in mind, canvases are "left-handed", so y is inverted
# get unique bases of given type
unique_bases = {}
for b in NA.standard_bases.values():
if b['type'] == type:
unique_bases[id(b)] = b
# compute drawing parameters
win_width = canvas.winfo_width()
if win_width == 1:
# no size assigned yet
return
win_height = canvas.winfo_height()
# TODO: figure out how much room we really need for text
if win_width < win_height:
win_scale = .8 * win_width
else:
win_scale = .8 * win_height
x_offset = .1 * win_width + 2 # 2==borderwidth
if type == NA.PURINE:
min = NA.purine_min
max = NA.purine_max
other = NA.pyrimidine_max[0] - NA.pyrimidine_min[0]
elif type == NA.PYRIMIDINE:
min = NA.pyrimidine_min
max = NA.pyrimidine_max
other = NA.purine_max[0] - NA.purine_min[0]
width = max[0] - min[0]
if other > width:
width = other
scale = win_scale / width
# center vertically
height = (max[1] - min[1]) * scale
win_height -= (win_height - height) / 2
# clear canvas
canvas.addtag_all('all')
canvas.delete('all')
def cvt_coords(c):
for i in range(0, len(c), 2):
c[i] = (c[i] - min[0]) * scale + x_offset
c[i + 1] = win_height \
- (c[i + 1] - min[1]) * scale
def draw_line(b, names):
coords = []
for n in names:
c = b[n]
coords += [c[0], c[1]]
if len(names) > 2:
# close line
coords += coords[0:2]
cvt_coords(coords)
kw = {'width':2}
canvas.create_line(*coords, **kw)
c1p_coords = None
for b in unique_bases.values():
rn = b['ring atom names']
draw_line(b, rn)
for o in b['other bonds']:
draw_line(b, o)
if c1p_coords is None:
c1p_coords = list(b["C1'"][0:2])
else:
coords = b["C1'"][0:2]
if coords[0] < c1p_coords[0]:
c1p_coords[0] = coords[0]
if coords[1] > c1p_coords[1]:
c1p_coords[1] = coords[1]
corners = info[type]
anchor = NA.anchor(info[NA.ANCHOR], type)
offset = b[anchor]
coords = [
offset[0] + corners[0][0], offset[1] + corners[0][1],
offset[0] + corners[1][0], offset[1] + corners[1][1]
]
cvt_coords(coords)
kw = {'fill':'gray25', 'stipple':'gray25'}
canvas.create_rectangle(*coords, **kw)
coords = [min[0], max[1]]
cvt_coords(c1p_coords)
kw = {'text':" C1'", 'anchor':'s'}
canvas.create_text(*c1p_coords, **kw)
def _getInfo(self):
info = {
NA.ANCHOR: self.anchor.get(),
NA.PURINE: (self.puLL.get(), self.puUR.get()),
NA.PYRIMIDINE: (self.pyLL.get(), self.pyUR.get()),
NA.PSEUDO_PYRIMIDINE: (self.pyLL.get(), self.pyUR.get())
}
return info
def _drawStyle(self, *args):
if args:
self.saveui.setItemChanged(True)
self.currentStyle = None
# fill in parameters
info = self._getInfo()
# show bases
self._showBase(NA.PURINE, info, self.purine_canvas)
self._showBase(NA.PYRIMIDINE, info, self.pyrimidine_canvas)
def _setSlabStyle(self, name):
# make options reflect current style
info = NA.findStyle(name)
if not info:
return
self.currentStyle = name
self.anchor.set(info[NA.ANCHOR])
corners = info[NA.PURINE]
self.puLL.set(corners[0])
self.puUR.set(corners[1])
corners = info[NA.PYRIMIDINE]
self.pyLL.set(corners[0])
self.pyUR.set(corners[1])
self._drawStyle()
def NDBColors(self):
from chimera import selection
if selection.currentEmpty():
import Midas
residues = Midas._selectedResidues('#')
else:
residues = selection.currentResidues()
NA.NDBColors(residues)
class ImageSaveDialog(ModelessDialog):
name = "Save Image"
buttons = ['Tips', 'Save As', Cancel]
default = 'Save As'
help = 'UsersGuide/print.html'
provideStatus = True
def fillInUI(self, master):
self._ModelTrigger = None
#self._SetupTrigger = None
self._SizeTrigger = None
self.raytrace = None
# Image Size
imageSetup = Tix.LabelFrame(master, label="Image Size")
imageSetup.pack(fill=Tk.X, ipadx=2, ipady=2)
subframe = imageSetup.frame
#subframe = Tk.Frame(imageSetup.frame)
#subframe.pack(fill=Tk.BOTH, expand=1)
# add in conversion factor for pixels and graphics screen
from chimera import tkgui
win = tkgui.app.graphics
res = tkgui.getScreenMMWidth() / win.winfo_screenwidth()
convert['pixels'] = mm2pt(res)
self.matchAspect = Tk.BooleanVar(master)
self.matchAspect.set(1)
self.usePrint = Tk.BooleanVar(master)
self.usePrint.set(preferences.get(IMAGE_SETUP, USE_PRINT_UNITS))
import itertools
row = itertools.count()
self.showUsePrint = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.usePrint, highlightthickness=0,
text=USE_PRINT_UNITS,
command=self._updateUsePrint)
self.showUsePrint.grid(columnspan=2, row=row.next(), sticky=Tk.W)
w, h = chimera.viewer.windowSize
self.units = ImageUnitsOption(subframe, row.next(), UNITS,
'pixels', self.updateImageUnits)
self.iWidth = FloatOption(subframe, row.next(), 'Image width',
w, self.updateImageWidth, min=1e-10)
self.iHeight = FloatOption(subframe, row.next(), 'Image height',
h, self.updateImageHeight, min=1e-10)
matchAspect = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.matchAspect, highlightthickness=0,
text="Maintain current aspect ratio",
command=self.updateMatchAspect)
matchAspect.grid(columnspan=2, row=row.next(), sticky=Tk.W)
self.grow = Tk.Button(imageSetup.frame, text="Grow to Fit",
command=self.Resize, state=Tk.DISABLED)
fitrow = row.next()
self.grow.grid(row=fitrow, column=0, padx=2, pady=2,
sticky=Tk.NSEW)
self.shrink = Tk.Button(imageSetup.frame, text="Shrink to Fit",
command=lambda f=self.Resize: f(False),
state=Tk.DISABLED)
self.shrink.grid(row=fitrow, column=1, padx=2, pady=2,
sticky=Tk.NSEW)
#fetch = Tk.Button(imageSetup.frame, text="Get Pixels",
# command=self.fetchWindowSize)
#fetch.grid(row=row.next(), column=0, padx=2, pady=2, sticky=Tk.NSEW)
#calc = Tk.Button(imageSetup.frame, text="Image Setup",
# command=self.showImageSetupDialog)
#calc.grid(row=row.next(), column=1, padx=2, pady=2, sticky=Tk.NSEW)
self.printRes = FloatOption(subframe, row.next(), DPI,
preferences.get(IMAGE_SETUP, DPI),
self._updatePrint, min=1)
# Image Information
info = Tix.LabelFrame(master, label="Image Information")
info.pack(fill=Tk.X)
d = Tk.Label(info.frame, text="Description:")
d.grid(columnspan=2, row=0, column=0, sticky=Tk.W, padx=2,
pady=1)
self.description = Tk.Entry(info.frame)
info.frame.grid_columnconfigure(0, weight=1)
info.frame.grid_columnconfigure(1, weight=1)
self.description.grid(columnspan=2, row=1, column=0,
sticky=Tk.EW, padx=2, pady=2)
imageCredits = Tk.Button(info.frame,
text="Image Credits",
command=self.showImageCreditsDialog)
imageCredits.grid(row=2, column=0, padx=2, pady=2)
credit = Tk.Button(info.frame, text="Citing Chimera",
command=lambda: help.display("credits.html"))
credit.grid(row=2, column=1, padx=2, pady=2)
# Image camera
self.raytrace = BooleanOption(master, -1,
'Raytrace with POV-Ray', False,
self._updateRaytrace)
self.raytraceOptions = Tk.Button(master, text=POVRAY_SETUP,
command=self.showPOVRayOptions)
self.raytraceOptions.pack()
self.raytraceOptions.pack_forget()
self.supersample = SupersampleOption(master, -1, SUPERSAMPLE,
preferences.get(IMAGE_SETUP, SUPERSAMPLE),
self._updateSS)
self.adjustFOV = AdjustFOVOption(master, -1, ADJUST_FOV,
preferences.get(IMAGE_SETUP, ADJUST_FOV),
self._updateAdjustFOV)
self.printMode = _PrintModeOption(master, -1,
'Image camera mode', _PrintModeOption.SAME,
self._updatePrintMode)
self.lenticular = IntOption(master, -1,
'Number of lenticular images',
chimera.Camera.lenticularImageCount(),
self._updateLenticular, min=2, width=4)
self.lenticular.forget()
# switch to user's prefered units
self.adjust = convert['pixels']
units = preferences.get(IMAGE_SETUP, UNITS)
self._updateUsePrint()
self.units.set(units)
self.updateImageUnits()
def map(self, event=None):
self._ModelTrigger = chimera.triggers.addHandler('Model',
self._computeMaxLineWidth, None)
#self._SetupTrigger = chimera.triggers.addHandler(IMAGE_SETUP,
# self._computeMaxLineWidth, None)
self._SizeTrigger = chimera.triggers.addHandler(
'graphics window size', self._resetSize, None)
self._computeMaxLineWidth()
def unmap(self, event=None):
if self._ModelTrigger:
chimera.triggers.deleteHandler('Model',
self._ModelTrigger)
self._ModelTrigger = None
#if self._SetupTrigger:
# chimera.triggers.deleteHandler(IMAGE_SETUP,
# self._SetupTrigger)
# self._SetupTrigger = None
def _computeMaxLineWidth(self, *args):
if self.raytrace and self.raytrace.get():
# not relevant if raytracing
self.status('', blankAfter=0)
return
# this should be called models are modified, when the
# image size changes and when image setup parameters
# change (DPI, supersampling)
opengl_max = min(
chimera.opengl_getFloat("max point size"),
chimera.opengl_getFloat("max line width"))
max_lw = max([m.lineWidth
for m in chimera.openModels.list(all=True)
if hasattr(m, 'lineWidth')])
# compute tile scaling factor like C++ code does
width = self.iWidth.get()
height = self.iHeight.get()
horizPixels, vertPixels, supersample = \
imageArgs(self.units.get(), width, height)
width, height = chimera.viewer.windowSize
tileScale = float(horizPixels) / float(width)
tmp = float(vertPixels) / float(height)
if tmp > tileScale:
tileScale = tmp
tileScale *= supersample
opengl_max /= tileScale
if max_lw > opengl_max:
color = 'red'
else:
color = 'black'
self.status('effective maximum line width is %g' % opengl_max,
color=color, blankAfter=0)
#def Print(self):
# self.Cancel()
# image, options = self.getImage()
# filename = tempfile.mktemp()
# image.save(filename, **options)
# cmd = preferences.get(PAGE_SETUP, PRINTER_CMD)
# cmd = re.sub('%s', "'" + filename + "'", cmd)
# os.system(cmd)
# os.unlink(filename)
def SaveAs(self):
# now save the image
self.Cancel()
printMode = self.printMode.get()
raytrace = self.raytrace.get()
if printMode == _PrintModeOption.SAME:
printMode = None
if not chimera.nogui and raytrace and chimera.viewer.clipping:
dialog = ClipWarning()
if not dialog.run(chimera.tkgui.app):
return
saveImage(None, self.iWidth.get(), self.iHeight.get(),
units=self.units.get(), master=self.uiMaster(),
description=self.description.get().strip(),
printMode=printMode, raytrace=raytrace)
def Tips(self):
import help
help.display(self.help + "#tips")
def Resize(self, larger=True):
vw, vh = chimera.viewer.windowSize
iw = self.iWidth.get()
ih = self.iHeight.get()
vaspect = vw / float(vh)
iaspect = iw / float(ih)
from chimera import tkgui
top = tkgui.app.winfo_toplevel()
if larger:
if vaspect < iaspect:
w = int(vw * iaspect / vaspect + 0.5)
if w != vw:
top.wm_geometry('')
tkgui.app.graphics.config(width=w)
elif vaspect > iaspect:
h = int(vh * vaspect / iaspect + 0.5)
if h != vh:
top.wm_geometry('')
tkgui.app.graphics.config(height=h)
else:
if vaspect < iaspect:
h = int(vh * vaspect / iaspect + 0.5)
if h != vh:
top.wm_geometry('')
tkgui.app.graphics.config(height=h)
elif vaspect > iaspect:
w = int(vw * iaspect / vaspect + 0.5)
if w != vw:
top.wm_geometry('')
tkgui.app.graphics.config(width=w)
def fetchWindowSize(self):
w, h = chimera.viewer.windowSize
self.units.set('pixels')
self.updateImageUnits()
self.iWidth.set(w)
self.iHeight.set(h)
def _updateRaytrace(self, option):
raytrace = option.get()
if raytrace:
self.printMode.forget()
self.lenticular.forget()
self.supersample.forget()
self.raytraceOptions.pack()
else:
self.raytraceOptions.pack_forget()
self.printMode.manage()
self.supersample.manage()
self._updatePrintMode(self.printMode)
self._computeMaxLineWidth()
def _updatePrintMode(self, option):
printMode = option.get()
if printMode == 'lenticular':
self.lenticular.manage()
else:
self.lenticular.forget()
def _updateLenticular(self, option):
count = option.get()
chimera.Camera.setLenticularImageCount(count)
def updateMatchAspect(self, *args):
if self.matchAspect.get():
self.grow.config(state=Tk.DISABLED)
self.shrink.config(state=Tk.DISABLED)
self.Resize()
else:
self.grow.config(state=Tk.NORMAL)
self.shrink.config(state=Tk.NORMAL)
def updateImageUnits(self, *args):
units = self.units.get()
if units == 'pixels':
self.printRes.disable()
self.adjustFOV.disable()
else:
self.printRes.enable()
self.adjustFOV.enable()
if units != preferences.get(IMAGE_SETUP, UNITS):
preferences.set(IMAGE_SETUP, UNITS, units)
try:
adjust = convert[units]
except KeyError:
adjust = -1
if adjust == self.adjust:
return
if self.adjust != -1 and adjust != -1:
factor = self.adjust / adjust
w = self.iWidth.get() * factor
self.iWidth.set(w)
h = self.iHeight.get() * factor
self.iHeight.set(h)
if adjust == -1:
# entering pixel mode
w, h = chimera.viewer.windowSize
self.iWidth.set(w)
self.iHeight.set(h)
elif self.adjust == -1:
pass
# leaving pixel mode, sanity check
#w, h = paper_types[preferences.get(PAGE_SETUP, PAPER_TYPE)]
#if self.iWidth.get() > w:
# self.iWidth.set(w)
#if self.iHeight.get() > h:
# self.iHeight.set(h)
self.adjust = adjust
self._computeMaxLineWidth()
def updateImageWidth(self, option):
# adjust height to compensate for new width
if self.matchAspect.get():
iWidth = option.get()
w, h = chimera.viewer.windowSize
self.iHeight.set(iWidth * h / w)
self._computeMaxLineWidth()
def updateImageHeight(self, option):
# adjust width to compensate for new height
if self.matchAspect.get():
iHeight = option.get()
w, h = chimera.viewer.windowSize
self.iWidth.set(iHeight * w / h)
self._computeMaxLineWidth()
def _resetSize(self, triggerName, myData, sizes):
width, height, mmwidth, mmheight = sizes
units = self.units.get()
if units == 'pixels':
self.iWidth.set(width)
self.iHeight.set(height)
else:
adjust = convert['millimeters'] / convert[units]
self.iWidth.set(mmwidth * adjust)
self.iHeight.set(mmheight * adjust)
self._computeMaxLineWidth()
def _updateUsePrint(self):
usePrint = self.usePrint.get()
preferences.set(IMAGE_SETUP, USE_PRINT_UNITS, usePrint)
if not usePrint:
values = ['pixels']
else:
values = convert.keys()
try:
values.remove('pixels')
except ValueError:
pass
values.sort()
self.units.values = values
self.units.remakeMenu()
if usePrint:
self.units.set('inches')
else:
self.units.set('pixels')
self.updateImageUnits()
if not usePrint:
self.fetchWindowSize()
def _updatePrint(self, option):
res = option.get()
preferences.set(IMAGE_SETUP, DPI, res)
def _updateAdjustFOV(self, option):
adjust = option.get()
preferences.set(IMAGE_SETUP, ADJUST_FOV, adjust)
def _updateSS(self, option):
ss = option.get()
preferences.set(IMAGE_SETUP, SUPERSAMPLE, ss)
self._computeMaxLineWidth()
#def showImageSetupDialog(self, *args):
# import dialogs
# d = dialogs.display("preferences")
# d.setCategoryMenu(IMAGE_SETUP)
def showImageCreditsDialog(self, *args):
import dialogs
d = dialogs.display("preferences")
d.setCategoryMenu(IMAGE_CREDITS)
def showPOVRayOptions(self, *args):
import dialogs
d = dialogs.display("preferences")
d.setCategoryMenu(POVRAY_SETUP)
class CreateAxesDialog(ModelessDialog):
title = "Define Axes"
help = "ContributedSoftware/structuremeas/structuremeas.html#define-axes"
provideStatus = True
statusPosition = "above"
MODE_HELICES, MODE_SELECTION = range(2)
def fillInUI(self, parent):
import Pmw, Tkinter
row = 0
Tkinter.Label(parent, text="Create axis for...").grid(row=row,
sticky='w')
row += 1
self.modeVar = Tkinter.IntVar(parent)
self.modeVar.set(self.MODE_HELICES)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='nsew')
row += 1
Tkinter.Radiobutton(f,
text="Each helix in:",
command=self._helixCB,
variable=self.modeVar,
value=self.MODE_HELICES).grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(f,
listbox_selectmode='extended')
self.molList.grid(row=0, column=1, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
f.rowconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='w')
row += 1
Tkinter.Radiobutton(f,
text="Selected atoms (axis name:",
command=self._selCB,
variable=self.modeVar,
value=self.MODE_SELECTION).grid(row=0, column=0)
self.axisNameVar = Tkinter.StringVar(parent)
self.axisNameVar.set("axis")
Tkinter.Entry(f, textvariable=self.axisNameVar,
width=10).grid(row=0, column=1)
Tkinter.Label(f, text=")").grid(row=0, column=2)
paramGroup = Pmw.Group(parent, tag_text="Axis Parameters")
paramGroup.grid(row=row, column=0)
row += 1
paramFrame = paramGroup.interior()
prow = 0
butFrame = Tkinter.Frame(paramFrame)
butFrame.grid(row=prow, column=0, columnspan=3)
prow += 1
self.massWeighting = Tkinter.IntVar(parent)
self.massWeighting.set(False)
self._mwButton = Tkinter.Checkbutton(butFrame,
command=self._mwCB,
text="Mass weighting",
variable=self.massWeighting)
self._mwButton.grid(row=0, column=0, sticky='w')
self._mwButton.grid_remove()
self.helixCorrection = Tkinter.IntVar(parent)
self.helixCorrection.set(True)
Tkinter.Checkbutton(butFrame,
text="Use helical correction",
command=self._hcCB,
variable=self.helixCorrection).grid(row=1,
column=0,
sticky='w')
self.replaceExisting = Tkinter.IntVar(parent)
self.replaceExisting.set(True)
Tkinter.Checkbutton(butFrame,
text="Replace existing axes",
variable=self.replaceExisting).grid(row=2,
column=0,
sticky='w')
f = Tkinter.Frame(paramFrame)
f.grid(row=prow, column=0, columnspan=3)
prow += 1
from chimera.tkoptions import ColorOption, FloatOption
self.colorOpt = ColorOption(
f,
prow,
"Color",
None,
None,
balloon="Axis color. If No Color, then the axis"
" will be colored to match the structure")
Tkinter.Label(paramFrame, text="Radius:").grid(row=prow,
column=0,
rowspan=2)
self.fixedRadiusVar = Tkinter.IntVar(parent)
self.fixedRadiusVar.set(False)
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=False).grid(row=prow, column=1)
Tkinter.Label(paramFrame,
text="average axis-atom distance").grid(row=prow,
column=2,
sticky='w')
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=True).grid(row=prow + 1, column=1)
f = Tkinter.Frame(paramFrame)
f.grid(row=prow + 1, column=2, sticky='w')
self.radiusOpt = FloatOption(f,
0,
"angstroms",
prefs[AXIS_RADIUS],
None,
min=0.01)
def Apply(self):
from chimera import UserError
if self.replaceExisting.get():
axisManager.removeAxes(axisManager.axes)
kw = {}
kw['color'] = self.colorOpt.get()
if self.fixedRadiusVar.get():
kw['radius'] = prefs[AXIS_RADIUS] = self.radiusOpt.get()
kw['massWeighting'] = self.massWeighting.get() \
and self.modeVar.get() == self.MODE_SELECTION
kw['helicalCorrection'] = self.helixCorrection.get() \
and not kw['massWeighting']
if kw['helicalCorrection']:
replyobj.info("Creating axes with helical correction\n")
elif kw['massWeighting']:
replyobj.info("Creating axes with mass weighting\n")
else:
replyobj.info("Creating axes\n")
if self.modeVar.get() == self.MODE_HELICES:
mols = self.molList.getvalue()
if not mols:
self.enter()
raise UserError("No molecules chosen")
created = 0
for m in mols:
createHelices(m, **kw)
else:
selAtoms = selection.currentAtoms()
if len(selAtoms) < 3:
self.enter()
raise UserError("Need to select at least three"
" atoms to define an axis")
axisManager.createAxis(self.axisNameVar.get().strip(), selAtoms,
**kw)
def _helixCB(self):
self._mwButton.grid_remove()
def _hcCB(self):
if self.helixCorrection.get() and self.massWeighting.get():
self.massWeighting.set(False)
def _mwCB(self):
if self.massWeighting.get() and self.helixCorrection.get():
self.helixCorrection.set(False)
def _selCB(self):
self._mwButton.grid()
def fillInUI(self, parent):
parent.columnconfigure(0, pad=2)
parent.columnconfigure(1, pad=2)
import itertools
row = itertools.count()
self.showBackbone = BackboneOption(parent, row.next(),
'Show backbone as', 'ribbon', None)
self.showSide = SideOption(parent, row.next(),
'Show side (sugar/base) as', 'fill/slab',
self._showSideCB)
self.showOrientation = BooleanOption(parent, row.next(),
'Show base orientation', default.ORIENT, None)
import Tix
self.nb = Tix.NoteBook(parent)
self.nb.grid(row=row.next(), column=0, columnspan=2, sticky=Tk.EW, padx=2)
# ladder page
self.nb.add("ladder", label="Ladder Options")
f = self.nb.page("ladder")
if Tk.TkVersion >= 8.5:
parent.tk.call('grid', 'anchor', f._w, Tk.N)
prow = itertools.count()
self.skipNonBase = BooleanOption(f, prow.next(),
'Ignore non-base H-bonds', default.IGNORE, None)
self.showStubs = BooleanOption(f, prow.next(),
'Show stubs', default.STUBS, None)
self.rungRadius = FloatOption(f, prow.next(), 'Rung radius',
default.RADIUS, None)
self.rungRadius.min = 0.0
self.useExisting = BooleanOption(f, prow.next(),
'Using existing H-bonds', default.USE_EXISTING,
self._useExistingCB)
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(f, None, colorOptions=False)
#self.relaxParams.relaxConstraints = False
self.relaxParams.grid(row=prow.next(), columnspan=2,
sticky='nsew', padx=2)
# slab page
self.nb.add("slab", label="Slab Options")
f = self.nb.page("slab")
if Tk.TkVersion >= 8.5:
parent.tk.call('grid', 'anchor', f._w, Tk.N)
prow = itertools.count()
self.thickness = FloatOption(f, prow.next(), 'Thickness',
default.THICKNESS, None)
self.thickness.min = 0.01
self.shape = ShapeOption(f, prow.next(), 'Slab object',
default.SHAPE, None)
self.hideBases = BooleanOption(f, prow.next(),
'Hide base atoms', default.HIDE, None)
self.showGlycosidic = BooleanOption(f, prow.next(),
'Separate glycosidic bond', default.GLYCOSIDIC,
None)
self.nb.add("style", label="Slab Style", raisecmd=self.map)
# style page
f = self.nb.page("style")
if Tk.TkVersion >= 8.5:
f.tk.call('grid', 'anchor', f._w, Tk.N)
info = NA.findStyle(self.currentStyle)
from chimera.preferences import saveui
f2 = Tk.Frame(f)
self.saveui = saveui.SaveUI(f2, self)
f2.grid(row=prow.next(), column=0, columnspan=2, sticky=Tk.EW,
padx=2, pady=2)
self.anchor = AnchorOption(f, prow.next(), 'Anchor',
info[NA.ANCHOR], self._drawStyle)
f2 = Pmw.Group(f, tag_text=NA.PURINE.title())
f2.grid(row=prow.next(), column=0, columnspan=2, sticky=Tk.EW,
padx=2)
f2 = f2.interior()
f2.columnconfigure(0, weight=1, pad=2, uniform='a')
f2.columnconfigure(1, weight=1, uniform='a')
f2.columnconfigure(2, weight=1)
self.purine_canvas = Tk.Canvas(f2, width=1, height=1) #,
#borderwidth=2, relief=Tk.RIDGE)
r = prow.next()
self.purine_canvas.grid(row=r, column=0, rowspan=3,
sticky=Tk.NSEW, padx=2, pady=2)
corners = info[NA.PURINE]
self.puLL = Float2Option(f2, prow.next(), 'Lower left',
corners[0], self._drawStyle, startCol=1)
self.puUR = Float2Option(f2, prow.next(), 'Upper right',
corners[1], self._drawStyle, startCol=1)
f3 = Pmw.Group(f, tag_text="%s, %s" % (NA.PYRIMIDINE.title(),
NA.PSEUDO_PYRIMIDINE.title()))
r = prow.next()
f3.grid(row=r, column=0, columnspan=2, sticky=Tk.EW, padx=2)
f3 = f3.interior()
f3.columnconfigure(0, weight=1, pad=2, uniform='a')
f3.columnconfigure(1, weight=1, uniform='a')
f3.columnconfigure(2, weight=1)
self.pyrimidine_canvas = Tk.Canvas(f3, width=1, height=1) #,
#borderwidth=2, relief=Tk.RIDGE)
r = prow.next()
self.pyrimidine_canvas.grid(row=r, column=0, rowspan=3,
sticky=Tk.NSEW, padx=2, pady=2)
corners = info[NA.PYRIMIDINE]
self.pyLL = Float2Option(f3, prow.next(), 'Lower left',
corners[0], self._drawStyle, startCol=1)
self.pyUR = Float2Option(f3, prow.next(), 'Upper right',
corners[1], self._drawStyle, startCol=1)
self.restrict = Tk.IntVar(parent)
self.restrict.set(1)
cb = Tk.Checkbutton(parent, variable=self.restrict,
text="Restrict OK/Apply to current selection, if any")
cb.grid(row=row.next(), columnspan=2)
parent.pack(ipady=2)
self._showSideCB()
chimera.triggers.addHandler(NA.TRIGGER_SLAB_STYLES,
self._updateStyles, None)
class AnisoDialog(ModelessDialog):
title = "Thermal Ellipsoids"
name = "anisotropic ellipsoids"
buttons = ("Show Ellipsoids", "Hide Ellipsoids", "Close")
help = "ContributedSoftware/thermal/thermal.html"
builtinPresets = [("Simple ellipsoid", {}),
("Principal axes", {
"ellipsoid": False,
"axisFactor": 1.0
}),
("Principal ellipses", {
"ellipsoid": False,
"ellipseFactor": 1.0
}), ("Ellipsoid and principal axes", {
"axisFactor": 1.5
}),
("Octant lines", {
"ellipseFactor": 1.01,
"ellipseColor": (0, 0, 0, 1)
}),
("Snow globe axes", {
"ellipsoidColor": (1, 1, 1, 1),
"transparency": 50.0,
"axisFactor": 0.99
}),
("Snow globe ellipses", {
"ellipsoidColor": (1, 1, 1, 1),
"transparency": 50.0,
"ellipseFactor": 0.99
})]
def fillInUI(self, parent):
import Pmw, Tkinter
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.presetsMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Presets", menu=self.presetsMenu)
presets = self.builtinPresets + prefs[PRESETS]
for label, kw in presets:
self.presetsMenu.add_command(
label=label, command=lambda kw=kw: self.preset(**kw))
self.presetsMenu.add_separator()
self.presetsMenu.add_command(label="Preset from current settings...",
command=self.startDefinePreset)
self.presetsMenu.add_command(label="Delete user preset...",
command=self.startDeletePreset)
from chimera.tkgui import aquaMenuBar
row = aquaMenuBar(menubar, parent, row=0, columnspan=2)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
self._modFromCalc = False
self.scaling = Pmw.EntryField(parent,
labelpos='w',
value='1',
label_text="Scale factor:",
entry_width=5,
validate={
'validator': 'real',
'min': 0.0
},
modifiedcommand=self._scaleTypingCB,
command=self.ShowEllipsoids)
self.scaling.grid(row=row, column=0)
self.smoothing = Pmw.EntryField(parent,
labelpos='w',
label_text="Smoothing level:",
validate={
'validator': 'numeric',
'min': 1,
'max': 100
},
value='3',
entry_width=2,
command=self.ShowEllipsoids)
self.smoothing.grid(row=row, column=1)
row += 1
self.calculator = Pmw.EntryField(
parent,
labelpos='w',
label_text="Set scale factor for probability (%):",
entry_width=4,
command=self._prob2scaling)
self.calculator.grid(row=row, column=0, columnspan=2)
row += 1
from chimera.tkoptions import SymbolicEnumOption, \
FloatOption, RGBAOption
self.showEllipsoidVar = Tkinter.IntVar(parent)
self.showEllipsoidVar.set(True)
ellipsoidGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict ellipsoids",
tag_variable=self.showEllipsoidVar)
ellipsoidGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = ellipsoidGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.ellipsoidColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
class TransparencyOption(SymbolicEnumOption):
values = [
None, 0.0, 10.0, 20.0, 30.0, 40.0, 50.0, 60.0, 70.0, 80.0,
90.0, 100.0
]
labels = [
"same as color", "0%", "10%", "20%", "30%", "40%", "50%",
"60%", "70%", "80%", "90%", "100%"
]
self.transparencyOpt = TransparencyOption(inside, 1, "Transparency",
None, None)
self.showAxesVar = Tkinter.IntVar(parent)
self.showAxesVar.set(False)
axesGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict principal axes",
tag_variable=self.showAxesVar)
axesGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = axesGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.axisColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
self.axisFactorOpt = FloatOption(inside,
1,
"Length factor",
1.5,
self.ShowEllipsoids,
balloon="relative to ellipsoids",
sticky="w")
self.axisThicknessOpt = FloatOption(inside,
2,
"Thickness",
0.01,
self.ShowEllipsoids,
sticky="w")
self.showEllipsesVar = Tkinter.IntVar(parent)
self.showEllipsesVar.set(False)
ellipsesGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict principal ellipses",
tag_variable=self.showEllipsesVar)
ellipsesGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = ellipsesGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.ellipseColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
self.ellipseFactorOpt = FloatOption(inside,
1,
"Size factor",
1.0,
self.ShowEllipsoids,
balloon="relative to ellipsoids",
sticky="w")
self.ellipseThicknessOpt = FloatOption(inside,
2,
"Thickness",
0.02,
self.ShowEllipsoids,
sticky="w")
self.selRestrictVar = Tkinter.IntVar(parent)
self.selRestrictVar.set(False)
Tkinter.Checkbutton(parent,
text="Restrict Show/Hide to current"
" selection, if any",
variable=self.selRestrictVar).grid(row=row,
column=0,
columnspan=2)
row += 1
def ShowEllipsoids(self, *args):
if self.showAxesVar.get():
axisFactor = self.axisFactorOpt.get()
else:
axisFactor = None
if self.showEllipsesVar.get():
ellipseFactor = self.ellipseFactorOpt.get()
else:
ellipseFactor = None
kw = {
'color': self.ellipsoidColorOpt.get(),
'smoothing': int(self.smoothing.getvalue()),
'scale': float(self.scaling.getvalue()),
'showEllipsoid': self.showEllipsoidVar.get(),
'transparency': self.transparencyOpt.get(),
'axisFactor': axisFactor,
'axisColor': self.axisColorOpt.get(),
'axisThickness': self.axisThicknessOpt.get(),
'ellipseFactor': ellipseFactor,
'ellipseColor': self.ellipseColorOpt.get(),
'ellipseThickness': self.ellipseThicknessOpt.get()
}
if self.selRestrictVar.get():
from chimera.selection import currentAtoms
selAtoms = currentAtoms()
if selAtoms:
kw['targets'] = selAtoms
from Aniso import aniso
from Midas import MidasError
try:
aniso(**kw)
except MidasError:
from chimera import UserError
raise UserError("No atoms chosen had anisotropic" " information")
def HideEllipsoids(self):
kw = {}
if self.selRestrictVar.get():
from chimera.selection import currentAtoms
selAtoms = currentAtoms()
if selAtoms:
kw['targets'] = selAtoms
from Aniso import unaniso
unaniso(**kw)
def preset(self,
ellipsoid=True,
ellipsoidColor=None,
transparency=None,
axisFactor=None,
axisColor=None,
axisThickness=0.01,
ellipseFactor=None,
ellipseColor=None,
ellipseThickness=0.02):
self.showEllipsoidVar.set(ellipsoid)
if ellipsoid:
self.ellipsoidColorOpt.set(ellipsoidColor)
self.transparencyOpt.set(transparency)
if axisFactor:
self.showAxesVar.set(True)
self.axisFactorOpt.set(axisFactor)
self.axisColorOpt.set(axisColor)
self.axisThicknessOpt.set(axisThickness)
else:
self.showAxesVar.set(False)
if ellipseFactor:
self.showEllipsesVar.set(True)
self.ellipseFactorOpt.set(ellipseFactor)
self.ellipseColorOpt.set(ellipseColor)
self.ellipseThicknessOpt.set(ellipseThickness)
else:
self.showEllipsesVar.set(False)
self.ShowEllipsoids()
def startDefinePreset(self):
if not hasattr(self, "_presetNameDialog"):
import Pmw
self._presetNameDialog = Pmw.PromptDialog(
self.uiMaster(),
title="Preset Name",
label_text="Preset name:",
entryfield_labelpos='w',
defaultbutton=0,
buttons=('OK', 'Cancel'),
command=self._definePresetCB)
self._presetNameDialog.show()
def startDeletePreset(self):
if not prefs[PRESETS]:
from chimera import UserError
raise UserError("No user presets have been defined")
if not hasattr(self, "_presetDeleteDialog"):
import Pmw
self._presetDeleteDialog = Pmw.SelectionDialog(
self.uiMaster(),
title="Delete Preset",
label_text="Preset name:",
scrolledlist_labelpos='n',
defaultbutton=0,
scrolledlist_items=[ps[0] for ps in prefs[PRESETS]],
buttons=('OK', 'Cancel'),
command=self._deletePresetCB)
self._presetDeleteDialog.show()
def _definePresetCB(self, button):
self._presetNameDialog.withdraw()
if button is None or button == 'Cancel':
return
name = self._presetNameDialog.get().strip()
if not name:
self._presetNameDialog.show()
from chimera import UserError
UserError("Must provide preset name")
if name in [x[0] for x in self.builtinPresets]:
self._presetNameDialog.show()
from chimera import UserError
UserError("Cannot redefine builtin preset")
anisoKw = {}
anisoKw['ellipsoid'] = self.showEllipsoidVar.get()
if anisoKw['ellipsoid']:
anisoKw['ellipsoidColor'] = self.ellipsoidColorOpt.get()
anisoKw['transparency'] = self.transparencyOpt.get()
if self.showAxesVar.get():
anisoKw['axisFactor'] = self.axisFactorOpt.get()
anisoKw['axisColor'] = self.axisColorOpt.get()
anisoKw['axisThickness'] = self.axisThicknessOpt.get()
if self.showEllipsesVar.get():
anisoKw['ellipseFactor'] = self.ellipseFactorOpt.get()
anisoKw['ellipseColor'] = self.ellipseColorOpt.get()
anisoKw['ellipseThickness'] = self.ellipseThicknessOpt.get()
newPreset = (name, anisoKw)
customPresets = prefs[PRESETS][:]
for info in customPresets:
if info[0] == name:
# changing _contents_ of kw dictionary means we don't
# have to redefine the menu command action
info[1].clear()
info[1].update(anisoKw)
break
else:
customPresets.append(newPreset)
self.presetsMenu.insert_command(
len(self.builtinPresets) + len(customPresets),
label=name,
command=lambda kw=anisoKw: self.preset(**kw))
prefs[PRESETS] = customPresets
def _deletePresetCB(self, result):
self._presetDeleteDialog.withdraw()
if result is None or result == 'Cancel':
self._presetDeleteDialog.destroy()
delattr(self, '_presetDeleteDialog')
return
deletions = self._presetDeleteDialog.getvalue()
remaining = [ps for ps in prefs[PRESETS] if ps[0] not in deletions]
prefs[PRESETS] = remaining
for name in deletions:
self.presetsMenu.delete(name)
self._presetDeleteDialog.destroy()
delattr(self, '_presetDeleteDialog')
def _prob2scaling(self):
try:
prob = float(self.calculator.getvalue()) / 100.0
if prob < 0.0 or prob >= 1.0:
raise ValueError("bad prob")
except ValueError:
from chimera import UserError
raise UserError("Probability must be >= 0 and < 100")
from Aniso import prob2scale
self._modFromCalc = True
self.scaling.setvalue("%g" % prob2scale(prob))
self._modFromCalc = False
def _scaleTypingCB(self):
if not self._modFromCalc:
self.calculator.setvalue("")
def fillInUI(self, parent):
import Pmw, Tkinter
row = 0
Tkinter.Label(parent, text="Create axis for...").grid(row=row,
sticky='w')
row += 1
self.modeVar = Tkinter.IntVar(parent)
self.modeVar.set(self.MODE_HELICES)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='nsew')
row += 1
Tkinter.Radiobutton(f,
text="Each helix in:",
command=self._helixCB,
variable=self.modeVar,
value=self.MODE_HELICES).grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(f,
listbox_selectmode='extended')
self.molList.grid(row=0, column=1, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
f.rowconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='w')
row += 1
Tkinter.Radiobutton(f,
text="Selected atoms (axis name:",
command=self._selCB,
variable=self.modeVar,
value=self.MODE_SELECTION).grid(row=0, column=0)
self.axisNameVar = Tkinter.StringVar(parent)
self.axisNameVar.set("axis")
Tkinter.Entry(f, textvariable=self.axisNameVar,
width=10).grid(row=0, column=1)
Tkinter.Label(f, text=")").grid(row=0, column=2)
paramGroup = Pmw.Group(parent, tag_text="Axis Parameters")
paramGroup.grid(row=row, column=0)
row += 1
paramFrame = paramGroup.interior()
prow = 0
butFrame = Tkinter.Frame(paramFrame)
butFrame.grid(row=prow, column=0, columnspan=3)
prow += 1
self.massWeighting = Tkinter.IntVar(parent)
self.massWeighting.set(False)
self._mwButton = Tkinter.Checkbutton(butFrame,
command=self._mwCB,
text="Mass weighting",
variable=self.massWeighting)
self._mwButton.grid(row=0, column=0, sticky='w')
self._mwButton.grid_remove()
self.helixCorrection = Tkinter.IntVar(parent)
self.helixCorrection.set(True)
Tkinter.Checkbutton(butFrame,
text="Use helical correction",
command=self._hcCB,
variable=self.helixCorrection).grid(row=1,
column=0,
sticky='w')
self.replaceExisting = Tkinter.IntVar(parent)
self.replaceExisting.set(True)
Tkinter.Checkbutton(butFrame,
text="Replace existing axes",
variable=self.replaceExisting).grid(row=2,
column=0,
sticky='w')
f = Tkinter.Frame(paramFrame)
f.grid(row=prow, column=0, columnspan=3)
prow += 1
from chimera.tkoptions import ColorOption, FloatOption
self.colorOpt = ColorOption(
f,
prow,
"Color",
None,
None,
balloon="Axis color. If No Color, then the axis"
" will be colored to match the structure")
Tkinter.Label(paramFrame, text="Radius:").grid(row=prow,
column=0,
rowspan=2)
self.fixedRadiusVar = Tkinter.IntVar(parent)
self.fixedRadiusVar.set(False)
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=False).grid(row=prow, column=1)
Tkinter.Label(paramFrame,
text="average axis-atom distance").grid(row=prow,
column=2,
sticky='w')
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=True).grid(row=prow + 1, column=1)
f = Tkinter.Frame(paramFrame)
f.grid(row=prow + 1, column=2, sticky='w')
self.radiusOpt = FloatOption(f,
0,
"angstroms",
prefs[AXIS_RADIUS],
None,
min=0.01)
def fillInUI(self, parent):
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption
Tkinter.Label(parent,
text="Create RMSD map of trajectory "
"against itself",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.minRmsd = FloatOption(parent,
4, "Lower RMSD threshold"
" (white)",
prefs[RMSD_MIN],
None,
width=6)
self.maxRmsd = FloatOption(parent,
5, "Upper RMSD threshold"
" (black)",
prefs[RMSD_MAX],
None,
width=6)
self.useSel = BooleanOption(
parent, 6, "Restrict map to "
"current selection, if any", True, None)
self.ignoreBulk = BooleanOption(parent, 7, "Ignore solvent/"
"ions", True, None)
self.ignoreHyds = BooleanOption(parent, 8, "Ignore hydrogens", True,
None)
self.recolor = BooleanOption(parent, 9, "Auto-recolor for"
" contrast", prefs[RMSD_AUTOCOLOR], None)
class EspDialog(ModelessDialog):
title = "Coulombic Surface Coloring"
name = "ESP computation"
help = "ContributedSoftware/coulombic/coulombic.html"
HB = "estimated from H-bonds"
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(
parent,
labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew", columnspan=2)
Pmw.OptionMenu(parent,
command=self._menuCB,
initialitem="3",
items=[str(x) for x in range(2, 12)],
labelpos='w',
label_text="Number of colors/values:").grid(
row=1, column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(
parent,
3,
"Distance-dependent dielectric",
True,
None,
balloon="If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant", 4.0,
None)
self.surfDist = FloatOption(parent,
5,
"Distance from surface",
1.4,
None,
balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(
interior,
text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))), slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="name",
text="Residue name-based",
command=self._switchHisList).grid(row=1,
sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f,
text="HID/HIE/HIP = delta/epsilon/both").grid(row=0,
sticky='w')
self.hisDefault = Pmw.OptionMenu(
f,
initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"],
labelpos='w',
label_text="HIS = ",
command=lambda a, s=self: setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="pick",
textvariable=self._pickText,
command=self._switchHisList).grid(row=3,
sticky='w')
Tkinter.Button(parent,
pady=0,
command=self._colorKeyCB,
text="Create corresponding color key").grid(
row=7, column=0, columnspan=2)
self.hisChanged = False
def Apply(self):
for entry in self.values:
entry.invoke()
colors = [w.rgba for w in self.wells]
values = [float(e.getvalue()) for e in self.values]
if self.hisProtVar.get() == "name":
hisScheme = {
self.HB: None,
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP'
}[self.hisDefault.getvalue()]
else:
hisScheme = self.hisListingData
from ESP import colorEsp
for surf in self.surfListBox.getvalue():
if self.hisChanged:
# clear out charge values so that histidines
# get new charges
for a in surf.atoms:
a.charge = None
colorEsp(surf,
colors,
values,
dielectric=self.dielectric.get(),
distDep=self.distDep.get(),
surfDist=self.surfDist.get(),
hisScheme=hisScheme)
self.hisChanged = False
def _colorKeyCB(self):
for entry in self.values:
entry.invoke()
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure(
zip([w.rgba for w in self.wells],
[e.getvalue() for e in self.values]))
def _menuCB(self, val):
newNum = int(val)
oldSettings = []
for well, entry in zip(self.wells, self.values):
entry.invoke()
oldSettings.append((well.rgba, float(entry.getvalue())))
well.grid_forget()
well.destroy()
entry.grid_forget()
entry.destroy()
import Pmw
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.values = []
scale = (len(oldSettings) - 1.0) / (newNum - 1.0)
f = self.interpFrame
for i in range(newNum):
index = i * scale
if index == int(index) \
or int(index) >= len(oldSettings):
color, value = oldSettings[int(index)]
else:
lowc, lowv = oldSettings[int(index)]
highc, highv = oldSettings[int(index) + 1]
frac = index - int(index)
color = []
for lowcomp, highcomp in zip(lowc, highc):
color.append((1.0 - frac) * lowcomp + frac * highcomp)
value = (1.0 - frac) * lowv + frac * highv
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
def _selSurfCB(self):
if self.surfListBox.getvalue():
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK']['state'] = state
self.buttonWidgets['Apply']['state'] = state
self._updateHisListing()
def _select(self, hisType):
for r, vars in self._vars.items():
dv, ev = vars
if hisType == "delta":
dv.set(True)
ev.set(False)
self.hisListingData[r] = "HID"
elif hisType == "epsilon":
dv.set(False)
ev.set(True)
self.hisListingData[r] = "HIE"
else:
dv.set(True)
ev.set(True)
self.hisListingData[r] = "HIP"
def _switchHisList(self):
self.hisChanged = True
if not hasattr(self, 'hisListing'):
if self.hisProtVar.get() != "pick":
return
self.hisListingData = {}
import Tix, Tkinter
self.hisFrame = Tkinter.Frame(self.hisGroup.interior())
self.hisListing = Tix.ScrolledHList(self.hisFrame,
width="3i",
options="""hlist.columns 4
hlist.header 1
hlist.indicator 1""")
self.hisListing.hlist.configure(
selectbackground=self.hisListing['background'],
selectborderwidth=0)
self.hisListing.grid(row=0, column=0, columnspan=3, sticky="nsew")
self.hisFrame.rowconfigure(1, weight=1)
self.hisFrame.columnconfigure(0, weight=1)
self.hisFrame.columnconfigure(1, weight=1)
hlist = self.hisListing.hlist
hlist.header_create(0, itemtype="text", text="Model")
hlist.header_create(1, itemtype="text", text="Residue")
hlist.header_create(2, itemtype="text", text="Delta")
hlist.header_create(3, itemtype="text", text="Epsilon")
self._checkButtonStyle = Tix.DisplayStyle(
"window",
background=hlist['background'],
refwindow=self.hisListing,
anchor='center')
self._updateHisListing()
Tkinter.Button(self.hisFrame,
text="All Delta",
pady=0,
highlightthickness=0,
command=lambda p="delta": self._select(p)).grid(
row=1, column=0)
Tkinter.Button(self.hisFrame,
text="All Epsilon",
pady=0,
highlightthickness=0,
command=lambda p="epsilon": self._select(p)).grid(
row=1, column=1)
Tkinter.Button(self.hisFrame,
text="All Both",
pady=0,
highlightthickness=0,
command=lambda p="both": self._select(p)).grid(
row=1, column=2)
if self.hisProtVar.get() == "pick":
self._pickText.set("Specified individually:")
self.hisFrame.grid(row=4, sticky="nsew")
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=1)
self.uiMaster().rowconfigure(6, weight=4)
else:
self._pickText.set("Specified individually...")
self.hisFrame.grid_forget()
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=0)
self.uiMaster().rowconfigure(6, weight=0)
def _toggleDelta(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HID"
elif old == "HID":
new = "HIS"
elif old == "HIE":
new = "HIP"
else:
new = "HIE"
self.hisListingData[res] = new
def _toggleEpsilon(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HIE"
elif old == "HID":
new = "HIP"
elif old == "HIE":
new = "HIS"
else:
new = "HID"
self.hisListingData[res] = new
def _updateHisListing(self):
if not hasattr(self, 'hisListing'):
return
self._updateHisListingData()
hlist = self.hisListing.hlist
on = self.hisListing.tk.call('tix', 'getimage', 'ck_on')
off = self.hisListing.tk.call('tix', 'getimage', 'ck_off')
hlist.delete_all()
import Tkinter
row = 0
self._vars = {}
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
try:
hisType = self.hisListingData[r]
except KeyError:
continue
hlist.add(row,
itemtype="text",
text="%s (%s)" % (m.name, m.oslIdent()))
hlist.item_create(row,
1,
itemtype="text",
text=r.oslIdent(start=chimera.SelResidue))
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HID", "HIP"])
cmd = lambda r=r: self._toggleDelta(r)
self._vars[r] = [var]
toggle = Tkinter.Checkbutton(hlist,
command=cmd,
variable=var,
image=off,
selectimage=on,
selectcolor="",
indicatoron=False,
borderwidth=0)
hlist.item_create(row,
2,
itemtype="window",
window=toggle,
style=self._checkButtonStyle)
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HIE", "HIP"])
cmd = lambda r=r: self._toggleEpsilon(r)
self._vars[r].append(var)
toggle = Tkinter.Checkbutton(hlist,
command=cmd,
variable=var,
image=off,
selectimage=on,
selectcolor="",
indicatoron=False,
borderwidth=0)
hlist.item_create(row,
3,
itemtype="window",
window=toggle,
style=self._checkButtonStyle)
row += 1
def _updateHisListingData(self):
newData = {}
default = {
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP',
self.HB: 'HID'
}[self.hisDefault.getvalue()]
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
newData[r] = self.hisListingData[r]
except KeyError:
if r.type == 'HIS':
newData[r] = default
else:
newData[r] = r.type
self.hisListingData = newData
def fillInUI(self, master):
self._ModelTrigger = None
#self._SetupTrigger = None
self._SizeTrigger = None
self.raytrace = None
# Image Size
imageSetup = Tix.LabelFrame(master, label="Image Size")
imageSetup.pack(fill=Tk.X, ipadx=2, ipady=2)
subframe = imageSetup.frame
#subframe = Tk.Frame(imageSetup.frame)
#subframe.pack(fill=Tk.BOTH, expand=1)
# add in conversion factor for pixels and graphics screen
from chimera import tkgui
win = tkgui.app.graphics
res = tkgui.getScreenMMWidth() / win.winfo_screenwidth()
convert['pixels'] = mm2pt(res)
self.matchAspect = Tk.BooleanVar(master)
self.matchAspect.set(1)
self.usePrint = Tk.BooleanVar(master)
self.usePrint.set(preferences.get(IMAGE_SETUP, USE_PRINT_UNITS))
import itertools
row = itertools.count()
self.showUsePrint = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.usePrint, highlightthickness=0,
text=USE_PRINT_UNITS,
command=self._updateUsePrint)
self.showUsePrint.grid(columnspan=2, row=row.next(), sticky=Tk.W)
w, h = chimera.viewer.windowSize
self.units = ImageUnitsOption(subframe, row.next(), UNITS,
'pixels', self.updateImageUnits)
self.iWidth = FloatOption(subframe, row.next(), 'Image width',
w, self.updateImageWidth, min=1e-10)
self.iHeight = FloatOption(subframe, row.next(), 'Image height',
h, self.updateImageHeight, min=1e-10)
matchAspect = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.matchAspect, highlightthickness=0,
text="Maintain current aspect ratio",
command=self.updateMatchAspect)
matchAspect.grid(columnspan=2, row=row.next(), sticky=Tk.W)
self.grow = Tk.Button(imageSetup.frame, text="Grow to Fit",
command=self.Resize, state=Tk.DISABLED)
fitrow = row.next()
self.grow.grid(row=fitrow, column=0, padx=2, pady=2,
sticky=Tk.NSEW)
self.shrink = Tk.Button(imageSetup.frame, text="Shrink to Fit",
command=lambda f=self.Resize: f(False),
state=Tk.DISABLED)
self.shrink.grid(row=fitrow, column=1, padx=2, pady=2,
sticky=Tk.NSEW)
#fetch = Tk.Button(imageSetup.frame, text="Get Pixels",
# command=self.fetchWindowSize)
#fetch.grid(row=row.next(), column=0, padx=2, pady=2, sticky=Tk.NSEW)
#calc = Tk.Button(imageSetup.frame, text="Image Setup",
# command=self.showImageSetupDialog)
#calc.grid(row=row.next(), column=1, padx=2, pady=2, sticky=Tk.NSEW)
self.printRes = FloatOption(subframe, row.next(), DPI,
preferences.get(IMAGE_SETUP, DPI),
self._updatePrint, min=1)
# Image Information
info = Tix.LabelFrame(master, label="Image Information")
info.pack(fill=Tk.X)
d = Tk.Label(info.frame, text="Description:")
d.grid(columnspan=2, row=0, column=0, sticky=Tk.W, padx=2,
pady=1)
self.description = Tk.Entry(info.frame)
info.frame.grid_columnconfigure(0, weight=1)
info.frame.grid_columnconfigure(1, weight=1)
self.description.grid(columnspan=2, row=1, column=0,
sticky=Tk.EW, padx=2, pady=2)
imageCredits = Tk.Button(info.frame,
text="Image Credits",
command=self.showImageCreditsDialog)
imageCredits.grid(row=2, column=0, padx=2, pady=2)
credit = Tk.Button(info.frame, text="Citing Chimera",
command=lambda: help.display("credits.html"))
credit.grid(row=2, column=1, padx=2, pady=2)
# Image camera
self.raytrace = BooleanOption(master, -1,
'Raytrace with POV-Ray', False,
self._updateRaytrace)
self.raytraceOptions = Tk.Button(master, text=POVRAY_SETUP,
command=self.showPOVRayOptions)
self.raytraceOptions.pack()
self.raytraceOptions.pack_forget()
self.supersample = SupersampleOption(master, -1, SUPERSAMPLE,
preferences.get(IMAGE_SETUP, SUPERSAMPLE),
self._updateSS)
self.adjustFOV = AdjustFOVOption(master, -1, ADJUST_FOV,
preferences.get(IMAGE_SETUP, ADJUST_FOV),
self._updateAdjustFOV)
self.printMode = _PrintModeOption(master, -1,
'Image camera mode', _PrintModeOption.SAME,
self._updatePrintMode)
self.lenticular = IntOption(master, -1,
'Number of lenticular images',
chimera.Camera.lenticularImageCount(),
self._updateLenticular, min=2, width=4)
self.lenticular.forget()
# switch to user's prefered units
self.adjust = convert['pixels']
units = preferences.get(IMAGE_SETUP, UNITS)
self._updateUsePrint()
self.units.set(units)
self.updateImageUnits()
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(
parent,
labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew", columnspan=2)
Pmw.OptionMenu(parent,
command=self._menuCB,
initialitem="3",
items=[str(x) for x in range(2, 12)],
labelpos='w',
label_text="Number of colors/values:").grid(
row=1, column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(
parent,
3,
"Distance-dependent dielectric",
True,
None,
balloon="If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant", 4.0,
None)
self.surfDist = FloatOption(parent,
5,
"Distance from surface",
1.4,
None,
balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(
interior,
text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))), slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="name",
text="Residue name-based",
command=self._switchHisList).grid(row=1,
sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f,
text="HID/HIE/HIP = delta/epsilon/both").grid(row=0,
sticky='w')
self.hisDefault = Pmw.OptionMenu(
f,
initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"],
labelpos='w',
label_text="HIS = ",
command=lambda a, s=self: setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="pick",
textvariable=self._pickText,
command=self._switchHisList).grid(row=3,
sticky='w')
Tkinter.Button(parent,
pady=0,
command=self._colorKeyCB,
text="Create corresponding color key").grid(
row=7, column=0, columnspan=2)
self.hisChanged = False
class EspDialog(ModelessDialog):
title = "Coulombic Surface Coloring"
name = "ESP computation"
help = "ContributedSoftware/coulombic/coulombic.html"
HB = "estimated from H-bonds"
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(parent, labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew",
columnspan=2)
Pmw.OptionMenu(parent, command=self._menuCB, initialitem="3",
items=[str(x) for x in range(2, 12)], labelpos='w',
label_text="Number of colors/values:").grid(row=1,
column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(parent, 3,
"Distance-dependent dielectric", True, None, balloon=
"If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant",
4.0, None)
self.surfDist = FloatOption(parent, 5, "Distance from surface",
1.4, None, balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(interior, text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))),
slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue name-based", command=
self._switchHisList).grid(row=1, sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f, text="HID/HIE/HIP = delta/epsilon/both").grid(
row=0, sticky='w')
self.hisDefault = Pmw.OptionMenu(f, initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"], labelpos='w',
label_text="HIS = ", command=lambda a, s=self:
setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList).grid(row=3, sticky='w')
Tkinter.Button(parent, pady=0, command=self._colorKeyCB,
text="Create corresponding color key").grid(row=7,
column=0, columnspan=2)
self.hisChanged = False
def Apply(self):
for entry in self.values:
entry.invoke()
colors = [w.rgba for w in self.wells]
values = [float(e.getvalue()) for e in self.values]
if self.hisProtVar.get() == "name":
hisScheme = {
self.HB: None,
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP'
}[self.hisDefault.getvalue()]
else:
hisScheme = self.hisListingData
from ESP import colorEsp
for surf in self.surfListBox.getvalue():
if self.hisChanged:
# clear out charge values so that histidines
# get new charges
for a in surf.atoms:
a.charge = None
colorEsp(surf, colors, values,
dielectric=self.dielectric.get(),
distDep=self.distDep.get(),
surfDist=self.surfDist.get(),
hisScheme=hisScheme)
self.hisChanged = False
def _colorKeyCB(self):
for entry in self.values:
entry.invoke()
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure(zip([w.rgba for w in self.wells],
[e.getvalue() for e in self.values]))
def _menuCB(self, val):
newNum = int(val)
oldSettings = []
for well, entry in zip(self.wells, self.values):
entry.invoke()
oldSettings.append((well.rgba, float(entry.getvalue())))
well.grid_forget()
well.destroy()
entry.grid_forget()
entry.destroy()
import Pmw
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.values = []
scale = (len(oldSettings) - 1.0) / (newNum - 1.0)
f = self.interpFrame
for i in range(newNum):
index = i * scale
if index == int(index) \
or int(index) >= len(oldSettings):
color, value = oldSettings[int(index)]
else:
lowc, lowv = oldSettings[int(index)]
highc, highv = oldSettings[int(index)+1]
frac = index - int(index)
color = []
for lowcomp, highcomp in zip(lowc, highc):
color.append((1.0 - frac) * lowcomp
+ frac * highcomp)
value = (1.0 - frac) * lowv + frac * highv
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
def _selSurfCB(self):
if self.surfListBox.getvalue():
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK']['state'] = state
self.buttonWidgets['Apply']['state'] = state
self._updateHisListing()
def _select(self, hisType):
for r, vars in self._vars.items():
dv, ev = vars
if hisType == "delta":
dv.set(True)
ev.set(False)
self.hisListingData[r] = "HID"
elif hisType == "epsilon":
dv.set(False)
ev.set(True)
self.hisListingData[r] = "HIE"
else:
dv.set(True)
ev.set(True)
self.hisListingData[r] = "HIP"
def _switchHisList(self):
self.hisChanged = True
if not hasattr(self, 'hisListing'):
if self.hisProtVar.get() != "pick":
return
self.hisListingData = {}
import Tix, Tkinter
self.hisFrame = Tkinter.Frame(self.hisGroup.interior())
self.hisListing = Tix.ScrolledHList(self.hisFrame,
width="3i",
options="""hlist.columns 4
hlist.header 1
hlist.indicator 1""")
self.hisListing.hlist.configure(
selectbackground=self.hisListing['background'],
selectborderwidth=0)
self.hisListing.grid(row=0, column=0, columnspan=3,
sticky="nsew")
self.hisFrame.rowconfigure(1, weight=1)
self.hisFrame.columnconfigure(0, weight=1)
self.hisFrame.columnconfigure(1, weight=1)
hlist = self.hisListing.hlist
hlist.header_create(0, itemtype="text", text="Model")
hlist.header_create(1, itemtype="text", text="Residue")
hlist.header_create(2, itemtype="text", text="Delta")
hlist.header_create(3, itemtype="text", text="Epsilon")
self._checkButtonStyle = Tix.DisplayStyle("window",
background=hlist['background'],
refwindow=self.hisListing, anchor='center')
self._updateHisListing()
Tkinter.Button(self.hisFrame, text="All Delta",
pady=0, highlightthickness=0,
command=lambda p="delta": self._select(p)
).grid(row=1, column=0)
Tkinter.Button(self.hisFrame, text="All Epsilon",
pady=0, highlightthickness=0,
command=lambda p="epsilon": self._select(p)
).grid(row=1, column=1)
Tkinter.Button(self.hisFrame, text="All Both",
pady=0, highlightthickness=0,
command=lambda p="both": self._select(p)
).grid(row=1, column=2)
if self.hisProtVar.get() == "pick":
self._pickText.set("Specified individually:")
self.hisFrame.grid(row=4, sticky="nsew")
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=1)
self.uiMaster().rowconfigure(6, weight=4)
else:
self._pickText.set("Specified individually...")
self.hisFrame.grid_forget()
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=0)
self.uiMaster().rowconfigure(6, weight=0)
def _toggleDelta(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HID"
elif old == "HID":
new = "HIS"
elif old == "HIE":
new = "HIP"
else:
new = "HIE"
self.hisListingData[res] = new
def _toggleEpsilon(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HIE"
elif old == "HID":
new = "HIP"
elif old == "HIE":
new = "HIS"
else:
new = "HID"
self.hisListingData[res] = new
def _updateHisListing(self):
if not hasattr(self, 'hisListing'):
return
self._updateHisListingData()
hlist = self.hisListing.hlist
on = self.hisListing.tk.call('tix', 'getimage', 'ck_on')
off = self.hisListing.tk.call('tix', 'getimage', 'ck_off')
hlist.delete_all()
import Tkinter
row = 0
self._vars = {}
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
try:
hisType = self.hisListingData[r]
except KeyError:
continue
hlist.add(row, itemtype="text", text="%s (%s)"
% (m.name, m.oslIdent()))
hlist.item_create(row, 1, itemtype="text",
text=r.oslIdent(
start=chimera.SelResidue))
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HID", "HIP"])
cmd = lambda r=r: self._toggleDelta(r)
self._vars[r] = [var]
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 2, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HIE", "HIP"])
cmd = lambda r=r: self._toggleEpsilon(r)
self._vars[r].append(var)
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 3, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
row += 1
def _updateHisListingData(self):
newData = {}
default = {
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP',
self.HB: 'HID'
}[self.hisDefault.getvalue()]
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
newData[r] = self.hisListingData[r]
except KeyError:
if r.type == 'HIS':
newData[r] = default
else:
newData[r] = r.type
self.hisListingData = newData
class VolumeDialog(ModelessDialog):
title = "Calculate Atomic Occupancy"
help = "ContributedSoftware/movie/movie.html#occupancy"
provideStatus = True
statusPosition = "left"
buttons = ('OK', 'Close')
default = 'OK'
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def map(self, e=None):
if not self.movie.holdingSteady:
self.status("No atoms being held steady -- see Help", color="red")
def fillInUI(self, parent):
Tkinter.Label(parent,
text="Collect positions of selected"
" atoms over trajectory",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.doCutoff = BooleanOption(
parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms', True,
None)
self.cutoff = FloatOption(parent,
5,
"Cutoff distance",
prefs[VOLUME_CUTOFF],
None,
width=4)
self.resolution = FloatOption(parent,
6,
"Volume grid spacing",
prefs[VOLUME_RESOLUTION],
None,
min=0.0001,
width=4)
self.volumeName = StringOption(parent,
7,
"Volume data name",
self.movie.ensemble.name,
None,
width=20)
self.byAtomType = BooleanOption(
parent,
8, "Collect data"
" separately for each atom type in selection",
True,
None,
balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
def Apply(self):
from chimera import UserError
atoms = chimera.selection.currentAtoms()
if not atoms:
self.enter()
raise UserError("No atoms selected")
startFrame = self.startFrame.get()
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")
if self.doCutoff.get():
bound = prefs[VOLUME_CUTOFF] = self.cutoff.get()
else:
bound = None
prefs[VOLUME_RESOLUTION] = self.resolution.get()
step = self.stride.get()
spacing = self.resolution.get()
name = self.volumeName.get()
atomTypes = {}
if self.byAtomType.get():
for a in atoms:
atomTypes.setdefault(a.idatmType, []).append(a)
if len(atomTypes) > 1:
for atomType, atAtoms in atomTypes.items():
self.movie.computeVolume(atAtoms,
startFrame=startFrame,
endFrame=endFrame,
step=step,
bound=bound,
spacing=spacing,
volumeName=name + " [" + atomType +
"]")
else:
self.movie.computeVolume(atoms,
startFrame=startFrame,
endFrame=endFrame,
step=step,
bound=bound,
spacing=spacing,
volumeName=name)
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(parent, labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew",
columnspan=2)
Pmw.OptionMenu(parent, command=self._menuCB, initialitem="3",
items=[str(x) for x in range(2, 12)], labelpos='w',
label_text="Number of colors/values:").grid(row=1,
column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(parent, 3,
"Distance-dependent dielectric", True, None, balloon=
"If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant",
4.0, None)
self.surfDist = FloatOption(parent, 5, "Distance from surface",
1.4, None, balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(interior, text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))),
slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue name-based", command=
self._switchHisList).grid(row=1, sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f, text="HID/HIE/HIP = delta/epsilon/both").grid(
row=0, sticky='w')
self.hisDefault = Pmw.OptionMenu(f, initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"], labelpos='w',
label_text="HIS = ", command=lambda a, s=self:
setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList).grid(row=3, sticky='w')
Tkinter.Button(parent, pady=0, command=self._colorKeyCB,
text="Create corresponding color key").grid(row=7,
column=0, columnspan=2)
self.hisChanged = False
def fillInUI(self, parent):
import Pmw, Tkinter
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.presetsMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Presets", menu=self.presetsMenu)
presets = self.builtinPresets + prefs[PRESETS]
for label, kw in presets:
self.presetsMenu.add_command(
label=label, command=lambda kw=kw: self.preset(**kw))
self.presetsMenu.add_separator()
self.presetsMenu.add_command(label="Preset from current settings...",
command=self.startDefinePreset)
self.presetsMenu.add_command(label="Delete user preset...",
command=self.startDeletePreset)
from chimera.tkgui import aquaMenuBar
row = aquaMenuBar(menubar, parent, row=0, columnspan=2)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
self._modFromCalc = False
self.scaling = Pmw.EntryField(parent,
labelpos='w',
value='1',
label_text="Scale factor:",
entry_width=5,
validate={
'validator': 'real',
'min': 0.0
},
modifiedcommand=self._scaleTypingCB,
command=self.ShowEllipsoids)
self.scaling.grid(row=row, column=0)
self.smoothing = Pmw.EntryField(parent,
labelpos='w',
label_text="Smoothing level:",
validate={
'validator': 'numeric',
'min': 1,
'max': 100
},
value='3',
entry_width=2,
command=self.ShowEllipsoids)
self.smoothing.grid(row=row, column=1)
row += 1
self.calculator = Pmw.EntryField(
parent,
labelpos='w',
label_text="Set scale factor for probability (%):",
entry_width=4,
command=self._prob2scaling)
self.calculator.grid(row=row, column=0, columnspan=2)
row += 1
from chimera.tkoptions import SymbolicEnumOption, \
FloatOption, RGBAOption
self.showEllipsoidVar = Tkinter.IntVar(parent)
self.showEllipsoidVar.set(True)
ellipsoidGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict ellipsoids",
tag_variable=self.showEllipsoidVar)
ellipsoidGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = ellipsoidGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.ellipsoidColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
class TransparencyOption(SymbolicEnumOption):
values = [
None, 0.0, 10.0, 20.0, 30.0, 40.0, 50.0, 60.0, 70.0, 80.0,
90.0, 100.0
]
labels = [
"same as color", "0%", "10%", "20%", "30%", "40%", "50%",
"60%", "70%", "80%", "90%", "100%"
]
self.transparencyOpt = TransparencyOption(inside, 1, "Transparency",
None, None)
self.showAxesVar = Tkinter.IntVar(parent)
self.showAxesVar.set(False)
axesGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict principal axes",
tag_variable=self.showAxesVar)
axesGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = axesGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.axisColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
self.axisFactorOpt = FloatOption(inside,
1,
"Length factor",
1.5,
self.ShowEllipsoids,
balloon="relative to ellipsoids",
sticky="w")
self.axisThicknessOpt = FloatOption(inside,
2,
"Thickness",
0.01,
self.ShowEllipsoids,
sticky="w")
self.showEllipsesVar = Tkinter.IntVar(parent)
self.showEllipsesVar.set(False)
ellipsesGroup = Pmw.Group(parent,
tag_pyclass=Tkinter.Checkbutton,
tag_text="Depict principal ellipses",
tag_variable=self.showEllipsesVar)
ellipsesGroup.grid(row=row, column=0, columnspan=2, sticky="ew")
row += 1
inside = ellipsesGroup.interior()
inside.columnconfigure(0, weight=1, uniform=1)
inside.columnconfigure(1, weight=1, uniform=1)
self.ellipseColorOpt = RGBAOption(
inside,
0,
'Color',
None,
None,
noneOkay=True,
balloon='"No color" means use atom colors')
self.ellipseFactorOpt = FloatOption(inside,
1,
"Size factor",
1.0,
self.ShowEllipsoids,
balloon="relative to ellipsoids",
sticky="w")
self.ellipseThicknessOpt = FloatOption(inside,
2,
"Thickness",
0.02,
self.ShowEllipsoids,
sticky="w")
self.selRestrictVar = Tkinter.IntVar(parent)
self.selRestrictVar.set(False)
Tkinter.Checkbutton(parent,
text="Restrict Show/Hide to current"
" selection, if any",
variable=self.selRestrictVar).grid(row=row,
column=0,
columnspan=2)
row += 1
class RmsdStarter(ModelessDialog):
title = "Get RMSD Map Parameters"
help = "ContributedSoftware/movie/movie.html#rmsd"
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption
Tkinter.Label(parent, text="Create RMSD map of trajectory "
"against itself", relief="ridge", bd=4).grid(row=0,
column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
self.startFrame = IntOption(parent, 1, "Starting frame",
startFrame, None, min=startFrame, max=endFrame, width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames/300)
self.stride = IntOption(parent, 2, "Step size", defStride,
None, min=1, max=numFrames, width=3)
self.endFrame = IntOption(parent, 3, "Ending frame", endFrame,
None, min=startFrame, max=endFrame, width=6)
self.minRmsd = FloatOption(parent, 4, "Lower RMSD threshold"
" (white)", prefs[RMSD_MIN], None, width=6)
self.maxRmsd = FloatOption(parent, 5, "Upper RMSD threshold"
" (black)", prefs[RMSD_MAX], None, width=6)
self.useSel = BooleanOption(parent, 6, "Restrict map to "
"current selection, if any", True, None)
self.ignoreBulk = BooleanOption(parent, 7, "Ignore solvent/"
"ions", True, None)
self.ignoreHyds = BooleanOption(parent, 8, "Ignore hydrogens",
True, None)
self.recolor = BooleanOption(parent, 9, "Auto-recolor for"
" contrast", prefs[RMSD_AUTOCOLOR], None)
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])