class SeqPickerDialog(ModelessDialog):
title = 'Show Model Sequence'
buttons = ('Show', 'Close')
default = 'Show'
keepShown = 'Show'
name = "model sequence chooser"
help = "ContributedSoftware/multalignviewer/multalignviewer.html#individual"
def fillInUI(self, parent):
from chimera.widgets import MoleculeChainScrolledListBox
self.molListBox = MoleculeChainScrolledListBox(
parent,
listbox_selectmode="extended",
labelpos="w",
# some fancy footwork so that double click honors
# the "keep shown" dialog setting
dblclickcommand=lambda *args: getattr(self, 'Show')(),
label_text="Show sequence for:")
self.molListBox.grid(row=0, column=0, sticky="news")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def Apply(self):
from base import seqCmd
seqCmd(self.molListBox.getvalue())
def fillInUI(self, parent):
from chimera.widgets import MoleculeChainScrolledListBox
self.molListBox = MoleculeChainScrolledListBox(
parent,
listbox_selectmode="extended",
labelpos="w",
# some fancy footwork so that double click honors
# the "keep shown" dialog setting
dblclickcommand=lambda *args: getattr(self, 'Show')(),
label_text="Show sequence for:")
self.molListBox.grid(row=0, column=0, sticky="news")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
titles = self.Servers.keys()
titles.sort()
self.serverChooser = Pmw.OptionMenu(parent,
labelpos="w",
label_text="Compute:",
items=titles,
command=self._changeServer)
self.serverChooser.pack(fill="x", expand=False)
self.paramHolder = Tkinter.Frame(parent, padx=10, pady=2)
self.paramHolder.pack(fill="x", expand=False)
self.paramFrames = {}
for name, val in self.Servers.iteritems():
self.paramFrames[name] = val[2](self, self.paramHolder)
self.propertyName = Pmw.EntryField(parent,
labelpos="w",
label_text="As attribute:",
value=self.Servers[titles[0]][0],
validate=self._validatePropName)
self.propertyName.pack(fill="x", expand=False)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("rba",
text="Open Render/Select by Attribute")
self.outputOptions.add("save",
text="Save server output to file")
self.outputOptions.add("show",
text="Show server output in browser")
self.outputOptions.setvalue(["rba"])
self._changeServer(titles[0])
def fillInUI(self, parent): from chimera.widgets import MoleculeChainScrolledListBox self.molListBox = MoleculeChainScrolledListBox(parent, listbox_selectmode="extended", labelpos="w", # some fancy footwork so that double click honors # the "keep shown" dialog setting dblclickcommand=lambda *args: getattr(self, 'Show')(), label_text="Show sequence for:") self.molListBox.grid(row=0, column=0, sticky="news") parent.rowconfigure(0, weight=1) parent.columnconfigure(0, weight=1)
class SeqPickerDialog(ModelessDialog):
title = 'Show Model Sequence'
buttons = ('Show', 'Close')
default = 'Show'
keepShown = 'Show'
name = "model sequence chooser"
help = "ContributedSoftware/multalignviewer/multalignviewer.html#individual"
def fillInUI(self, parent):
from chimera.widgets import MoleculeChainScrolledListBox
self.molListBox = MoleculeChainScrolledListBox(parent,
listbox_selectmode="extended", labelpos="w",
# some fancy footwork so that double click honors
# the "keep shown" dialog setting
dblclickcommand=lambda *args: getattr(self, 'Show')(),
label_text="Show sequence for:")
self.molListBox.grid(row=0, column=0, sticky="news")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def Apply(self):
from base import seqCmd
seqCmd(self.molListBox.getvalue())
class MatchMaker(ModelessDialog):
name = "match structures"
buttons = ('OK', 'Apply', 'Cancel')
title = "MatchMaker"
help = 'ContributedSoftware/matchmaker/matchmaker.html'
def __init__(self, **kw):
ModelessDialog.__init__(self, **kw)
def Apply(self):
cp = self.chainMatchVar.get()
alg = self.seqAlgorithmMenu.getvalue()
showSeq = self.showSeqVar.get()
iterate = self.iterVar.get()
computeSS = self.computeSSVar.get()
for entry in self._entries:
entry.invoke()
if iterate:
iterArg = float(self.iterEntry.getvalue())
else:
iterArg = None
helixOpen, strandOpen, otherOpen = self.ssParams.getGaps()
matrix = self.matrixMenu.getvalue()
gapOpen = float(self.gapOpenEntry.getvalue())
gapExtend = float(self.gapExtendEntry.getvalue())
pairings = {}
if cp == CP_SPECIFIC_SPECIFIC:
matchItems = []
for ref, menu in self.matchChainList.menus.items():
matchItems.append((ref, menu.getvalue()))
elif cp == CP_SPECIFIC_BEST:
# specific chain in reference;
# best seq-aligning chain in match model(s)
ref = self.refChainList.getvalue()
if not ref:
raise UserError("Must choose a reference chain")
matches = [
x for x in self.matchMolList.getvalue() if x != ref.molecule
]
matchItems = [ref, matches]
elif cp == CP_BEST:
# best seq-aligning pair of chains between
# reference and match structure(s)
ref = self.refMolList.getvalue()
matches = [x for x in self.matchMolList.getvalue() if x != ref]
matchItems = [ref, matches]
if self.ssParams.useSSVar.get():
ssFraction = self.ssParams.ssMixture.get()
ssMatrix = self.ssParams.getMatrix()
else:
ssMatrix = ssFraction = None
alignKw = {
'ssFraction': ssFraction,
'ssMatrix': ssMatrix,
'computeSS': computeSS
}
try:
matchInfo = match(cp,
matchItems,
matrix,
alg,
gapOpen,
gapExtend,
align=self._align,
iterate=iterArg,
gapOpenHelix=helixOpen,
gapOpenStrand=strandOpen,
gapOpenOther=otherOpen,
showAlignment=showSeq,
**alignKw)
except UserError:
self.enter()
raise
if not self.structSeqVar.get():
return
chains = set()
for matchAtoms, refAtoms, rmsd in matchInfo:
for r in (matchAtoms[0].residue, refAtoms[0].residue):
for mchain in r.molecule.sequences():
if r in mchain.resMap:
chains.add(mchain)
break
from StructSeqAlign import Match2Align
m2a = Match2Align()
m2a.chainList.setvalue(chains)
def fillInUI(self, parent):
self.refMolList = MoleculeScrolledListBox(
parent,
autoselect="single",
labelpos="nw",
label_text="Reference structure:")
self.refChainList = MoleculeChainScrolledListBox(
parent,
labelpos="nw",
label_text="Reference chain:",
listbox_selectmode='extended')
self.matchMolList = MoleculeScrolledListBox(
parent,
labelpos="nw",
label_text="Structure(s) to match:",
listbox_selectmode='extended')
self.matchChainList = ChainMenus(parent)
def doSync():
if self.chainMatchVar.get() != CP_SPECIFIC_SPECIFIC:
return
self.matchChainList.syncUp(self.refChainList)
self.refChainList.configure(selectioncommand=doSync)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
seqFrame = Tkinter.Frame(parent)
seqFrame.grid(row=1, column=0, columnspan=2, sticky="nsew")
seqFrame.columnconfigure(0, weight=1)
seqFrame.columnconfigure(1, weight=1)
pairingGroup = Pmw.Group(seqFrame, tag_text="Chain pairing")
pairingGroup.grid(row=0, column=0, columnspan=2, sticky="w", padx=2)
pairingGroup.interior().columnconfigure(0, weight=1)
self.chainMatchVar = Tkinter.StringVar(parent)
self.chainMatchVar.set(prefs[CHAIN_PAIRING])
radiobuttonInfo = [
(CP_BEST,
"Best-aligning pair of chains\n\tbetween reference and match structure"
),
(CP_SPECIFIC_BEST,
"Specific chain in reference structure\n\twith best-aligning chain in match structure"
),
(CP_SPECIFIC_SPECIFIC,
"Specific chain(s) in reference structure\n\twith specific chain(s) in match structure"
),
]
for i in range(len(radiobuttonInfo)):
val, text = radiobuttonInfo[i]
radio = Tkinter.Radiobutton(pairingGroup.interior(),
command=self._chainMatchCB,
text=text,
justify='left',
value=val,
variable=self.chainMatchVar)
radio.grid(row=i, column=0, sticky='w')
self._chainMatchCB()
self.seqAlgorithmMenu = Pmw.OptionMenu(
seqFrame,
initialitem=prefs[SEQUENCE_ALGORITHM],
labelpos='w',
label_text="Alignment algorithm:",
items=[SA_NEEDLEMAN_WUNSCH, SA_SMITH_WATERMAN])
self.seqAlgorithmMenu.grid(row=1, column=0, sticky='w')
matrixNames = SmithWaterman.matrices.keys()
matrixNames.sort()
if prefs[MATRIX] in SmithWaterman.matrices:
initialMatrix = prefs[MATRIX]
else:
if defaults[MATRIX] in SmithWaterman.matrices:
initialMatrix = defaults[MATRIX]
else:
initialMatrix = matrixNames[0]
prefs[MATRIX] = initialMatrix
self.matrixMenu = Pmw.OptionMenu(seqFrame,
initialitem=initialMatrix,
labelpos='w',
label_text="Matrix:",
items=matrixNames)
self.matrixMenu.grid(row=1, column=1, sticky='w')
gapFrame = Tkinter.Frame(seqFrame)
gapFrame.grid(row=2, column=0, columnspan=2, sticky='ew')
gapFrame.columnconfigure(0, weight=1)
gapFrame.columnconfigure(1, weight=1)
self.gapOpenEntry = Pmw.EntryField(gapFrame,
labelpos='w',
label_text="Gap opening penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_OPEN]))
self.gapOpenEntry.grid(row=0, column=0)
self.gapExtendEntry = Pmw.EntryField(
gapFrame,
labelpos='w',
label_text="Gap extension penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_EXTEND]))
self.gapExtendEntry.grid(row=0, column=1)
self._entries = [self.gapOpenEntry, self.gapExtendEntry]
self.ssParams = SSParams(seqFrame, prefs, useSSCB=self._useSSCB)
self.ssParams.grid(row=3, column=0, columnspan=2, sticky='ew')
self.computeSSVar = Tkinter.IntVar(parent)
self.computeSSVar.set(prefs[COMPUTE_SS])
self._computeSSButton = Tkinter.Checkbutton(
seqFrame,
text="Compute secondary structure assignments",
variable=self.computeSSVar)
self._computeSSGridArgs = {'row': 4, 'sticky': 'w', 'columnspan': 2}
if self.ssParams.useSSVar.get():
self._computeSSButton.grid(**self._computeSSGridArgs)
self.showSeqVar = Tkinter.IntVar(parent)
self.showSeqVar.set(prefs[SHOW_SEQUENCE])
Tkinter.Checkbutton(seqFrame,
text="Show pairwise alignment(s)",
variable=self.showSeqVar).grid(row=5,
column=0,
sticky='w',
columnspan=2)
matchGroup = Pmw.Group(parent, tag_text="Matching")
matchGroup.grid(row=2, column=0, columnspan=2, sticky="nsew", padx=2)
matchGroup.interior().columnconfigure(0, weight=1)
self.iterVar = Tkinter.IntVar(parent)
self.iterVar.set(prefs[ITERATE])
Tkinter.Checkbutton(matchGroup.interior(),
justify="left",
text="Iterate by pruning long atom pairs"
" until no pair exceeds:",
variable=self.iterVar).grid(row=0,
column=0,
sticky='w')
self.iterEntry = Pmw.EntryField(matchGroup.interior(),
validate='real',
entry_width=3,
entry_justify="right",
value="%.1f" % prefs[ITER_CUTOFF],
labelpos='e',
label_text="angstroms")
self.iterEntry.grid(row=1, column=0)
self._entries.append(self.iterEntry)
self.structSeqVar = Tkinter.IntVar(parent)
self.structSeqVar.set(False)
Tkinter.Checkbutton(parent,
text="After superposition, compute"
" structure-based multiple sequence alignment",
variable=self.structSeqVar).grid(row=3,
sticky='w',
columnspan=2)
f = Tkinter.Frame(parent)
f.grid(row=4, column=0, columnspan=2, sticky='ew')
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)
# set up state of gap-open entry
self._useSSCB()
def _align(self, ref, match, matrix, alg, gapOpen, gapExtend, ksdsspCache,
**alignKw):
replyobj.status(
"test match %s %s to %s %s" %
(ref.molecule.name, ref.name, match.molecule.name, match.name))
return align(ref, match, matrix, alg, gapOpen, gapExtend, ksdsspCache,
**alignKw)
def _chainMatchCB(self):
matching = self.chainMatchVar.get()
if matching == CP_SPECIFIC_SPECIFIC:
ref = self.refChainList
match = self.matchChainList
ref.component("listbox").config(selectmode="extended")
self.matchChainList.syncUp(self.refChainList)
elif matching == CP_SPECIFIC_BEST:
ref = self.refChainList
match = self.matchMolList
ref.component("listbox").config(selectmode="browse")
else:
ref = self.refMolList
match = self.matchMolList
for slave in self.uiMaster().grid_slaves(row=0):
slave.grid_forget()
ref.grid(row=0, column=0, sticky="nsew")
match.grid(row=0, column=1, sticky="nsew")
def _restoreSettings(self):
self.ssParams.resetParams()
self.chainMatchVar.set(defaults[CHAIN_PAIRING])
self._chainMatchCB()
self.seqAlgorithmMenu.setvalue(defaults[SEQUENCE_ALGORITHM])
self.showSeqVar.set(defaults[SHOW_SEQUENCE])
self.iterVar.set(defaults[ITERATE])
self.computeSSVar.set(defaults[COMPUTE_SS])
for entry in self._entries:
entry.invoke()
self.iterEntry.setvalue(str(defaults[ITER_CUTOFF]))
self.ssParams.useSSVar.set(defaults[USE_SS])
self.matrixMenu.setvalue(defaults[MATRIX])
self.gapOpenEntry.setvalue(str(defaults[GAP_OPEN]))
self.gapExtendEntry.setvalue(str(defaults[GAP_EXTEND]))
self.structSeqVar.set(False)
def _saveSettings(self):
prefs[CHAIN_PAIRING] = self.chainMatchVar.get()
prefs[SEQUENCE_ALGORITHM] = self.seqAlgorithmMenu.getvalue()
prefs[SHOW_SEQUENCE] = self.showSeqVar.get()
prefs[ITERATE] = self.iterVar.get()
prefs[COMPUTE_SS] = self.computeSSVar.get()
for entry in self._entries:
entry.invoke()
prefs[ITER_CUTOFF] = float(self.iterEntry.getvalue())
prefs[HELIX_OPEN], prefs[STRAND_OPEN], prefs[OTHER_OPEN] = \
self.ssParams.getGaps()
prefs[USE_SS] = self.ssParams.useSSVar.get()
prefs[SS_MIXTURE] = self.ssParams.ssMixture.get()
ssMatrix = self.ssParams.getMatrix()
if ssMatrix != prefs[SS_SCORES]:
prefs[SS_SCORES] = ssMatrix
prefs[MATRIX] = self.matrixMenu.getvalue()
prefs[GAP_OPEN] = float(self.gapOpenEntry.getvalue())
prefs[GAP_EXTEND] = float(self.gapExtendEntry.getvalue())
def _useSSCB(self):
if self.ssParams.useSSVar.get():
state = 'disabled'
self._computeSSButton.grid(**self._computeSSGridArgs)
else:
state = 'normal'
self._computeSSButton.grid_forget()
self.gapOpenEntry.configure(label_state=state, entry_state=state)
def fillInUI(self, parent):
self.refMolList = MoleculeScrolledListBox(
parent,
autoselect="single",
labelpos="nw",
label_text="Reference structure:")
self.refChainList = MoleculeChainScrolledListBox(
parent,
labelpos="nw",
label_text="Reference chain:",
listbox_selectmode='extended')
self.matchMolList = MoleculeScrolledListBox(
parent,
labelpos="nw",
label_text="Structure(s) to match:",
listbox_selectmode='extended')
self.matchChainList = ChainMenus(parent)
def doSync():
if self.chainMatchVar.get() != CP_SPECIFIC_SPECIFIC:
return
self.matchChainList.syncUp(self.refChainList)
self.refChainList.configure(selectioncommand=doSync)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
seqFrame = Tkinter.Frame(parent)
seqFrame.grid(row=1, column=0, columnspan=2, sticky="nsew")
seqFrame.columnconfigure(0, weight=1)
seqFrame.columnconfigure(1, weight=1)
pairingGroup = Pmw.Group(seqFrame, tag_text="Chain pairing")
pairingGroup.grid(row=0, column=0, columnspan=2, sticky="w", padx=2)
pairingGroup.interior().columnconfigure(0, weight=1)
self.chainMatchVar = Tkinter.StringVar(parent)
self.chainMatchVar.set(prefs[CHAIN_PAIRING])
radiobuttonInfo = [
(CP_BEST,
"Best-aligning pair of chains\n\tbetween reference and match structure"
),
(CP_SPECIFIC_BEST,
"Specific chain in reference structure\n\twith best-aligning chain in match structure"
),
(CP_SPECIFIC_SPECIFIC,
"Specific chain(s) in reference structure\n\twith specific chain(s) in match structure"
),
]
for i in range(len(radiobuttonInfo)):
val, text = radiobuttonInfo[i]
radio = Tkinter.Radiobutton(pairingGroup.interior(),
command=self._chainMatchCB,
text=text,
justify='left',
value=val,
variable=self.chainMatchVar)
radio.grid(row=i, column=0, sticky='w')
self._chainMatchCB()
self.seqAlgorithmMenu = Pmw.OptionMenu(
seqFrame,
initialitem=prefs[SEQUENCE_ALGORITHM],
labelpos='w',
label_text="Alignment algorithm:",
items=[SA_NEEDLEMAN_WUNSCH, SA_SMITH_WATERMAN])
self.seqAlgorithmMenu.grid(row=1, column=0, sticky='w')
matrixNames = SmithWaterman.matrices.keys()
matrixNames.sort()
if prefs[MATRIX] in SmithWaterman.matrices:
initialMatrix = prefs[MATRIX]
else:
if defaults[MATRIX] in SmithWaterman.matrices:
initialMatrix = defaults[MATRIX]
else:
initialMatrix = matrixNames[0]
prefs[MATRIX] = initialMatrix
self.matrixMenu = Pmw.OptionMenu(seqFrame,
initialitem=initialMatrix,
labelpos='w',
label_text="Matrix:",
items=matrixNames)
self.matrixMenu.grid(row=1, column=1, sticky='w')
gapFrame = Tkinter.Frame(seqFrame)
gapFrame.grid(row=2, column=0, columnspan=2, sticky='ew')
gapFrame.columnconfigure(0, weight=1)
gapFrame.columnconfigure(1, weight=1)
self.gapOpenEntry = Pmw.EntryField(gapFrame,
labelpos='w',
label_text="Gap opening penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_OPEN]))
self.gapOpenEntry.grid(row=0, column=0)
self.gapExtendEntry = Pmw.EntryField(
gapFrame,
labelpos='w',
label_text="Gap extension penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_EXTEND]))
self.gapExtendEntry.grid(row=0, column=1)
self._entries = [self.gapOpenEntry, self.gapExtendEntry]
self.ssParams = SSParams(seqFrame, prefs, useSSCB=self._useSSCB)
self.ssParams.grid(row=3, column=0, columnspan=2, sticky='ew')
self.computeSSVar = Tkinter.IntVar(parent)
self.computeSSVar.set(prefs[COMPUTE_SS])
self._computeSSButton = Tkinter.Checkbutton(
seqFrame,
text="Compute secondary structure assignments",
variable=self.computeSSVar)
self._computeSSGridArgs = {'row': 4, 'sticky': 'w', 'columnspan': 2}
if self.ssParams.useSSVar.get():
self._computeSSButton.grid(**self._computeSSGridArgs)
self.showSeqVar = Tkinter.IntVar(parent)
self.showSeqVar.set(prefs[SHOW_SEQUENCE])
Tkinter.Checkbutton(seqFrame,
text="Show pairwise alignment(s)",
variable=self.showSeqVar).grid(row=5,
column=0,
sticky='w',
columnspan=2)
matchGroup = Pmw.Group(parent, tag_text="Matching")
matchGroup.grid(row=2, column=0, columnspan=2, sticky="nsew", padx=2)
matchGroup.interior().columnconfigure(0, weight=1)
self.iterVar = Tkinter.IntVar(parent)
self.iterVar.set(prefs[ITERATE])
Tkinter.Checkbutton(matchGroup.interior(),
justify="left",
text="Iterate by pruning long atom pairs"
" until no pair exceeds:",
variable=self.iterVar).grid(row=0,
column=0,
sticky='w')
self.iterEntry = Pmw.EntryField(matchGroup.interior(),
validate='real',
entry_width=3,
entry_justify="right",
value="%.1f" % prefs[ITER_CUTOFF],
labelpos='e',
label_text="angstroms")
self.iterEntry.grid(row=1, column=0)
self._entries.append(self.iterEntry)
self.structSeqVar = Tkinter.IntVar(parent)
self.structSeqVar.set(False)
Tkinter.Checkbutton(parent,
text="After superposition, compute"
" structure-based multiple sequence alignment",
variable=self.structSeqVar).grid(row=3,
sticky='w',
columnspan=2)
f = Tkinter.Frame(parent)
f.grid(row=4, column=0, columnspan=2, sticky='ew')
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)
# set up state of gap-open entry
self._useSSCB()
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()])
class Interface(ModelessDialog):
title = "Compute Surface Area and Volume"
help = "ContributedSoftware/surfvol/surfvol.html"
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
titles = self.Servers.keys()
titles.sort()
self.serverChooser = Pmw.OptionMenu(parent,
labelpos="w",
label_text="Compute:",
items=titles,
command=self._changeServer)
self.serverChooser.pack(fill="x", expand=False)
self.paramHolder = Tkinter.Frame(parent, padx=10, pady=2)
self.paramHolder.pack(fill="x", expand=False)
self.paramFrames = {}
for name, val in self.Servers.iteritems():
self.paramFrames[name] = val[2](self, self.paramHolder)
self.propertyName = Pmw.EntryField(parent,
labelpos="w",
label_text="As attribute:",
value=self.Servers[titles[0]][0],
validate=self._validatePropName)
self.propertyName.pack(fill="x", expand=False)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("rba",
text="Open Render/Select by Attribute")
self.outputOptions.add("save",
text="Save server output to file")
self.outputOptions.add("show",
text="Show server output in browser")
self.outputOptions.setvalue(["rba"])
self._changeServer(titles[0])
def _changeServer(self, name):
self.propertyName.setvalue(self.Servers[name][0])
for n, (frame, parts) in self.paramFrames.iteritems():
if n == name:
frame.pack(fill="x", expand=True)
else:
frame.forget()
def _validatePropName(self, text):
if len(text) == 0:
return Pmw.PARTIAL
if text[0] not in NameFirstChar:
return Pmw.ERROR
for c in text[1:]:
if c not in NameChar:
return Pmw.ERROR
return Pmw.OK
def Apply(self):
if not self.propertyName.valid():
raise chimera.UserError(
"Please enter valid attribute name")
propName = self.propertyName.getvalue()
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = self.chainChooser.getvalue()
if not target:
raise chimera.UserError(
"Please select molecule or chain")
opts = self.outputOptions.getvalue()
rba = "rba" in opts
save = "save" in opts
show = "show" in opts
serverName = self.serverChooser.getcurselection()
f = self.Servers[serverName][1]
parts = self.paramFrames[serverName][1]
opts = self.Servers[serverName][3](self, parts)
output = f(target, opts, propName, rba)
if save:
_save(output, show)
elif show:
# create temporary file and invoke browser
from OpenSave import osTemporaryFile
filename = osTemporaryFile(suffix=".html")
f = open(filename, "w")
f.write(output)
f.close()
import urllib
from chimera import help
help.display("file:" + urllib.pathname2url(filename))
_paramMsmsParams = [
( "Surface probe size:",
"msms_probe",
( ( "1.3", "1.3" ),
( "1.4", "1.4" ),
( "1.5", "1.5" ),
( "1.6", "1.6" ) ),
"1.5"
),
( "Atoms to use:",
"msms_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"No Hetatms"
),
]
_paramGersteinSurfaceParams = [
( "Surface probe size:",
"surf_Gerstein_probe",
( ( "1.3", "1.3" ),
( "1.4", "1.4" ),
( "1.5", "1.5" ),
( "1.6", "1.6" ) ),
"1.4"
),
( "Atoms to use:",
"surf_Gerstein_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"All atoms except waters"
),
]
_paramGersteinVolumeParams = [
( "Method:",
"vol_Gerstein_method",
( ( "Normal Voronoi", "1" ),
( "Method B", "2" ),
( "Radical Plane", "3" ),
( "Modified Method B", "4" ) ),
"Method B"
),
( "Radii:",
"vol_Gerstein_radii",
( ( "Chothia Radii", "" ),
( "Richards Radii", "-RichardsRadii" ) ),
"Chothia Radii"
),
( "Atoms to use:",
"vol_Gerstein_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"No Hetatms"
),
]
def _paramMakeMsms(self, group):
return self._paramMake(group, self._paramMsmsParams)
def _paramGetMsms(self, parts):
return self._paramGet(parts, self._paramMsmsParams)
def _paramMakeGersteinSurface(self, group):
return self._paramMake(group, self._paramGersteinSurfaceParams)
def _paramGetGersteinSurface(self, parts):
return self._paramGet(parts, self._paramGersteinSurfaceParams)
def _paramMakeGersteinVolume(self, group):
return self._paramMake(group, self._paramGersteinVolumeParams)
def _paramGetGersteinVolume(self, parts):
return self._paramGet(parts, self._paramGersteinVolumeParams)
def _paramMake(self, parent, params):
g = Pmw.Group(parent, tag_text="Parameters")
parts = []
for label, cgiTag, items, default in params:
m = Pmw.OptionMenu(g.interior(),
labelpos="w",
label_text=label,
items=[ item[0] for item in items ])
m.setvalue(default)
m.pack(fill="x", expand=False)
parts.append(m)
Pmw.alignlabels(parts)
return g, parts
def _paramGet(self, parts, params):
args = []
for i, m in enumerate(parts):
sel = m.getvalue()
label, cgiTag, items, default = params[i]
for name, value in items:
if name == sel:
args.append((cgiTag, None, value))
break
else:
raise ChimeraError("unexpected option value")
return args
Servers = {
"Surface Area (MSMS)":
( "msmsArea",
StrucTools.msms,
_paramMakeMsms,
_paramGetMsms,
),
"Accessible Surface (Gerstein)":
( "accessibleSurface",
StrucTools.surface,
_paramMakeGersteinSurface,
_paramGetGersteinSurface,
),
"Voronoi Volume (Gerstein)":
( "voronoiVolume",
StrucTools.volume,
_paramMakeGersteinVolume,
_paramGetGersteinVolume,
),
}
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("solid", text="Solid surface (rather than mesh)")
self.outputOptions.add("track", text="Reuse last surface (if any)")
self.outputOptions.add("atoms", text="Select interface atoms")
self.outputOptions.add("prune", text="Residue centroid distance pruning")
self.outputOptions.setvalue(["solid", "track"])
self.pruneDistance = Pmw.EntryField(parent,
labelpos="w",
label_text="Prune distance:",
value="30.0",
validate=self._validatePruneDistance)
self.pruneDistance.pack(fill="x", expand=False)
self.moleculeBias = Pmw.Counter(parent,
labelpos="w",
label_text="Molecule bias:",
datatype="real",
increment = 0.1,
entryfield_value="0.5",
entryfield_validate={'validator' : 'real',
'min' : '0.0', 'max' : '1.0',
'separator' : '.'})
self.moleculeBias.pack(fill="x", expand=False)
histKw = {
'minlabel': True,
'maxlabel': True,
'scaling': 'linear',
}
self.histogram = MarkedHistogram(parent, **histKw)
self.histogramMarkers = self.histogram.addmarkers(activate=True,
coordtype='relative')
self.histogramMarkers.extend([
((1.0, 0.0), (0.0, 0.0, 0.33, 1.0)),
((0.0, 0.0), (1.0, 0.0, 0.0, 1.0))])
self.histogram.pack(expand=True, fill="both")
self._trackedPiece = None
self._trackedModel = None
self.models = {}
chimera.openModels.addRemoveHandler(self._removeModel, None)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.saveSession, None)
chimera.triggers.addHandler("Molecule",
self._moleculeChanged, None)
class Interface(ModelessDialog):
title = "Compute Interface Surface"
help = "ContributedSoftware/intersurf/intersurf.html"
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("solid", text="Solid surface (rather than mesh)")
self.outputOptions.add("track", text="Reuse last surface (if any)")
self.outputOptions.add("atoms", text="Select interface atoms")
self.outputOptions.add("prune", text="Residue centroid distance pruning")
self.outputOptions.setvalue(["solid", "track"])
self.pruneDistance = Pmw.EntryField(parent,
labelpos="w",
label_text="Prune distance:",
value="30.0",
validate=self._validatePruneDistance)
self.pruneDistance.pack(fill="x", expand=False)
self.moleculeBias = Pmw.Counter(parent,
labelpos="w",
label_text="Molecule bias:",
datatype="real",
increment = 0.1,
entryfield_value="0.5",
entryfield_validate={'validator' : 'real',
'min' : '0.0', 'max' : '1.0',
'separator' : '.'})
self.moleculeBias.pack(fill="x", expand=False)
histKw = {
'minlabel': True,
'maxlabel': True,
'scaling': 'linear',
}
self.histogram = MarkedHistogram(parent, **histKw)
self.histogramMarkers = self.histogram.addmarkers(activate=True,
coordtype='relative')
self.histogramMarkers.extend([
((1.0, 0.0), (0.0, 0.0, 0.33, 1.0)),
((0.0, 0.0), (1.0, 0.0, 0.0, 1.0))])
self.histogram.pack(expand=True, fill="both")
self._trackedPiece = None
self._trackedModel = None
self.models = {}
chimera.openModels.addRemoveHandler(self._removeModel, None)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.saveSession, None)
chimera.triggers.addHandler("Molecule",
self._moleculeChanged, None)
def _validatePruneDistance(self, text):
if len(text) == 0:
return Pmw.PARTIAL
try:
float(text)
except:
return Pmw.ERROR
return Pmw.OK
def _show_geometry(self, vertices, triangles, vertex_colors, solid=0, track=0):
import numpy
varray = numpy.array(vertices, numpy.float32)
tarray = numpy.array(triangles, numpy.int32)
carray = numpy.array(vertex_colors, numpy.float32)
import chimera
if track and self._trackedPiece:
sm = self._trackedModel
g = self._trackedPiece
g.geometry = varray, tarray
g.vertexColors = carray
if solid:
g.displayStyle = g.Solid
else:
g.displayStyle = g.Mesh
else:
import _surface
sm = _surface.SurfaceModel()
g = sm.addPiece(varray, tarray, (1, 1, 1, 1))
g.vertexColors = carray
if solid:
g.displayStyle = g.Solid
else:
g.displayStyle = g.Mesh
sm.name = "Interface Surface"
chimera.openModels.add([sm])
self._trackedPiece = g
self._trackedModel = sm
sm.openState.xform = chimera.Xform.identity()
self.models[sm] = (vertices, triangles, vertex_colors, solid)
return sm, g
def Apply(self):
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = self.chainChooser.getvalue()
if not target:
raise chimera.UserError("Please select two molecules/chains")
if len(target) != 2:
raise chimera.UserError("Please select exactly two molecules/chains")
opts = self.outputOptions.getvalue()
solid = "solid" in opts
prune = "prune" in opts
track = "track" in opts
selAtoms = "atoms" in opts
if not self.moleculeBias.valid():
raise chimera.UserError("Please enter a valid bias toward the second molecule")
bias = float(self.moleculeBias.getvalue())
if prune:
if not self.pruneDistance.valid():
raise chimera.UserError("Please enter a valid prune distance")
pruneDistance = float(self.pruneDistance.getvalue())
else:
pruneDistance = 0
self.doApply(target, solid, track, selAtoms,
bias, prune, pruneDistance)
def doApply(self, target, solid, track, selAtoms,
bias, prune, pruneDistance):
m1, m2 = target
if prune:
m1_list = SurfMaker.GetAtomList(m1, m2, pruneDistance)
m2_list = SurfMaker.GetAtomList(m2, m1, pruneDistance)
else:
m1_list = SurfMaker.GetAtomList(m1)
m2_list = SurfMaker.GetAtomList(m2)
if not m1_list or not m2_list:
raise chimera.UserError("No interface surface found")
p = SurfMaker.UnpackIntersurfData(m1_list, m2_list)
tetras = SurfMaker.ComputeTetrahedralization(p)
surfPoints, surfTriangles, surfAtoms = SurfMaker.ComputeSurface(p, tetras, bias)
surfMetric = [ getDistance(x[0], x[1]) for x in surfAtoms ]
lo = min(surfMetric)
hi = max(surfMetric)
scale = hi - lo
markers = [ (lo + m['xy'][0] * scale, m['rgba'])
for m in self.histogramMarkers ]
surfColors = [ getHistogramColor(x, markers)
for x in surfMetric ]
self.histogramData = (lo, hi, surfMetric)
def myMakeBars(numBins, data=self.histogramData):
return makeBars(numBins, data)
self.histogram["datasource"] = (lo, hi, myMakeBars)
self._show_geometry(surfPoints, surfTriangles, surfColors, solid, track)
if selAtoms:
from chimera import selection
atomSet = set([])
for a1, a2 in surfAtoms:
atomSet.add(a1)
atomSet.add(a2)
sel = selection.ItemizedSelection()
sel.add(atomSet)
sel.addImplied(vertices=False)
selection.setCurrent(sel)
def _removeModel(self, trigger, data, models):
for m in models:
if self._trackedModel is m:
self._trackedModel = None
self._trackedPiece = None
try:
del self.models[m]
except KeyError:
pass
def _moleculeChanged(self, trigger, data, models):
if 'activeCoordSet changed' not in models.reasons:
return
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = [ c.molecule for c in self.chainChooser.getvalue() ]
else:
return
for m in models.modified:
if m in target:
break
else:
return
self.Apply()
def saveSession(self, trigger, data, file):
isMapped = self.uiMaster().winfo_ismapped()
if not isMapped and not self.models:
# Not visible and no displayed surfaces
return
from SessionUtil import stateclasses, objecttree
restoring_code = \
"""
def restoreIntersurfSession(state):
import SimpleSession
from Intersurf import Intersurf
SimpleSession.registerAfterModelsCB(Intersurf.restoreSession, state)
risArgs = (%s)
try:
restoreIntersurfSession(risArgs)
except:
reportRestoreError("Error restoring Intersurf extension")
"""
pageName = self.notebook.getcurselection()
chosenMolecules = self.molChooser.getcurselection()
chosenChains = self.chainChooser.getcurselection()
opts = self.outputOptions.getvalue()
pruneDistance = self.pruneDistance.getvalue()
bias = self.moleculeBias.getvalue()
if isinstance(self.histogram["datasource"], basestring):
histogramData = self.histogram["datasource"]
else:
histogramData = self.histogramData
markerValues = []
markers, selectedMarker = self.histogram.currentmarkerinfo()
if markers:
for m in markers:
markerValues.append((m["xy"], m["rgba"]))
ms = stateclasses.Model_State()
modelData = []
trackedIndex = -1
n = 0
for m, v in self.models.iteritems():
if self._trackedModel is m:
trackedIndex = n
ms.state_from_model(m)
bt = objecttree.instance_tree_to_basic_tree(ms)
modelData.append((v, bt))
n += 1
state = (pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
histogramData, markerValues,
modelData, trackedIndex, isMapped)
file.write(restoring_code % repr(state))
def restoreSession(self, state):
from SessionUtil import stateclasses, objecttree
if len(state) == 10:
(pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
dataSource, markerValues,
modelData, trackedIndex) = state
if modelData:
isMapped = True
else:
isMapped = False
else:
(pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
histogramData, markerValues,
modelData, trackedIndex, isMapped) = state
# Call get method to make sure items are updated
self.molChooser.get()
self.molChooser.setvalue(chosenMolecules)
self.chainChooser.get()
self.chainChooser.setvalue(chosenChains)
self.notebook.selectpage(pageName)
self.outputOptions.setvalue(list(opts))
self.pruneDistance.setvalue(pruneDistance)
self.moleculeBias.setvalue(bias)
if isinstance(histogramData, basestring):
dataSource = histogramData
else:
lo, hi, surfMetric = histogramData
self.histogramData = (lo, hi, surfMetric)
def myMakeBars(numBins, data=self.histogramData):
return makeBars(numBins, data)
dataSource = (lo, hi, myMakeBars)
self.histogram["datasource"] = dataSource
if markerValues:
oldMarkers = self.histogram.currentmarkerinfo()[0]
newMarkers = self.histogram.addmarkers()
newMarkers.extend(markerValues)
self.histogram.deletemarkers(oldMarkers)
self.histogramMarkers = newMarkers
trackedModel = None
trackedPiece = None
nameToClass = {
"Model_State": stateclasses.Model_State,
"Xform_State": stateclasses.Xform_State,
}
for n, mState in enumerate(modelData):
if len(mState) == 2:
v, bt = mState
else:
v = mState
bt = None
sm, g = self._show_geometry(*v)
if trackedIndex == n:
trackedModel = sm
trackedPiece = g
if bt is not None:
ms = objecttree.basic_tree_to_instance_tree(bt,
nameToClass)
ms.restore_state(sm)
if trackedModel:
self._trackedModel = trackedModel
self._trackedPiece = trackedPiece
if not isMapped:
self.Close()