def fillInUI(self, parent): import Pmw, Tkinter SaveModeless.fillInUI(self, parent) self.clientArea.columnconfigure(0, weight=1) row = 0 from chimera.widgets import ModelOptionMenu self.surfList = ModelOptionMenu(self.clientArea, labelpos='w', label_text="Save surface:", filtFunc=lambda m: isinstance(m, MSMSModel)) self.surfList.grid(row=row, column=0) row += 1 self.saveNormalsVar = Tkinter.IntVar(self.clientArea) self.saveNormalsVar.set(True) Tkinter.Checkbutton(self.clientArea, text="Save normals", variable=self.saveNormalsVar).grid(row=row) row += 1 self.displayedOnlyVar = Tkinter.IntVar(self.clientArea) self.displayedOnlyVar.set(True) Tkinter.Checkbutton(self.clientArea, text="Limit output to" " displayed surface sections", variable=self.displayedOnlyVar).grid(row=row) row += 1
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeOptionMenu
self.modelMenu = MoleculeOptionMenu(
self.clientArea,
labelpos='w',
label_text="Save model:",
command=lambda m: self.configure(self.modelMenu.getvalue(),
refreshList=False))
self.modelMenu.grid(row=row, column=0, sticky='w')
row += 1
from AddCharge import knownChargeModels, defaultChargeModel
from chimera import dialogs
self.parmsetOption = Pmw.OptionMenu(
self.clientArea,
labelpos='w',
label_text="Select force field type: ",
initialitem=defaultChargeModel,
items=knownChargeModels)
# not always shown; remember row number
self._msmRow = row
self.parmsetOption.grid(row=row, column=0, sticky='w')
row += 1
def __init__(self, histDialog):
# make dialog hidden initially
self.histDialog = histDialog
SaveModeless.__init__(self,
clientPos='s',
clientSticky="ew",
initialfile="chimera.cmd")
def fillInUI(self, parent):
import Tkinter as Tk
import Pmw
from HtmlText import HtmlText
SaveModeless.fillInUI(self, parent)
parent = self.clientArea
self.notes = Pmw.ScrolledText(parent,
text_pyclass=HtmlText,
text_relief=Tk.FLAT,
text_wrap=Tk.WORD,
text_height=4,
text_width=10,
text_highlightthickness=0)
self.notes.pack(side=Tk.TOP,
anchor=Tk.NW,
fill=Tk.BOTH,
expand=True,
pady=5,
padx=10)
self.notes.configure(text_state=Tk.DISABLED,
hscrollmode='dynamic',
vscrollmode='dynamic',
text_background=parent.cget('background'))
import exports
self.notes.settext(exports.getNotes(self.getFilter()))
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
self.clientArea.columnconfigure(0, weight=1)
row = 0
from chimera.widgets import ModelOptionMenu
self.surfList = ModelOptionMenu(
self.clientArea,
labelpos='w',
label_text="Save surface:",
filtFunc=lambda m: isinstance(m, MSMSModel))
self.surfList.grid(row=row, column=0)
row += 1
self.saveNormalsVar = Tkinter.IntVar(self.clientArea)
self.saveNormalsVar.set(True)
Tkinter.Checkbutton(self.clientArea,
text="Save normals",
variable=self.saveNormalsVar).grid(row=row)
row += 1
self.displayedOnlyVar = Tkinter.IntVar(self.clientArea)
self.displayedOnlyVar.set(True)
Tkinter.Checkbutton(self.clientArea,
text="Limit output to"
" displayed surface sections",
variable=self.displayedOnlyVar).grid(row=row)
row += 1
def __init__(self, mav):
self.mav = mav
self.title = "Save Association Info of %s" % mav.title
defaultFile = os.path.splitext(self.mav.title or "alignment")[0]
SaveModeless.__init__(self,
clientPos='s',
initialfile=defaultFile + ".asc")
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
self.clientArea.columnconfigure(0, weight=1)
self.clientArea.columnconfigure(1, weight=1)
self.amount = Pmw.RadioSelect(self.clientArea,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
pady=0,
label_text="Record")
self.amount.add("selected commands")
self.amount.add("all commands")
self.amount.invoke(1)
self.amount.grid(row=0, column=0)
self.commandStyle = Pmw.RadioSelect(self.clientArea,
orient='vertical',
command=self._adjustFileName,
buttontype='radiobutton',
labelpos='w',
pady=0,
label_text="Record as")
self.commandStyle.add("Chimera commands")
self.commandStyle.add("Python commands")
self.commandStyle.invoke(0)
self.commandStyle.grid(row=1, column=0)
self.appending = Tkinter.IntVar(parent)
self.appending.set(0)
Tkinter.Checkbutton(self.clientArea,
variable=self.appending,
text="Append to file").grid(row=0,
column=1,
rowspan=2)
def __init__(self, mav):
self.mav = mav
self.title = "Save EPS of %s" % mav.title
defaultFile = os.path.splitext(self.mav.title or "alignment")[0]
SaveModeless.__init__(self,
clientPos='s',
initialfile=defaultFile,
filters=[("EPS", "*.eps", ".eps")])
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
from CGLtk import Hybrid
br = Hybrid.Entry(self.clientArea, 'Bit rate (Kb/sec):', 6,
self.default_bit_rate)
br.frame.grid(row=0, column=0, sticky='w')
self.bit_rate = br.variable
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
from CGLtk import Hybrid
br = Hybrid.Entry(self.clientArea, 'Bit rate (Kb/sec):', 6,
self.default_bit_rate)
br.frame.grid(row = 0, column = 0, sticky = 'w')
self.bit_rate = br.variable
def __init__(self):
self.default_bit_rate = 6000
from MovieRecorder import RecorderGUI
filters = map(lambda f: (f[0], '*.%s' % f[1], '.%s' % f[1]),
RecorderGUI.formats)
SaveModeless.__init__(self, clientPos = 's', clientSticky = 'w',
filters = filters, historyID = "MorphMap")
def __init__(self):
self.prefs = preferences.addCategory("write PDB dialog",
preferences.HiddenCategory,
optDict={"multiSavePDB": "multiple"})
self.haveTraj = False
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("PDB", "*.pdb", ".pdb")])
openModels.addAddHandler(self._modelsChange, None),
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def __init__(self):
self.prefs = preferences.addCategory("write Mol2 dialog",
preferences.HiddenCategory,
optDict={"multiSaveMol2": "multiple",
"hydrogen naming": "sybyl",
"residue numbers": True})
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Mol2", "*.mol2", ".mol2")])
openModels.addAddHandler(self._modelsChange, None)
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def __init__(self):
self.default_bit_rate = 6000
from MovieRecorder import RecorderGUI
filters = map(lambda f: (f[0], '*.%s' % f[1], '.%s' % f[1]),
RecorderGUI.formats)
SaveModeless.__init__(self,
clientPos='s',
clientSticky='w',
filters=filters,
historyID="MorphMap")
def enter(self):
# if any new export types have been added,
# then add them to the dialog
import exports
filterInfo = exports.getFilterInfo()
for pos, fi in enumerate(filterInfo):
if fi[0] in self.addedSceneTypes:
continue
self.addedSceneTypes.add(fi[0])
self.addFilter(fi, pos)
# next do the normal enter stuff
SaveModeless.enter(self)
def _save(text): global _saveDialog if not _saveDialog: from OpenSave import SaveModeless _saveDialog = SaveModeless( title="Choose Attribute Calculator Save File", command=_fileChosen, initialfile="attrcalc.txt", historyID="Attribute Calculator Output") else: _saveDialog.enter() _saveDialog._text = text
def fillInUI(self, parent): SaveModeless.fillInUI(self, parent) self.saveTypes = Pmw.RadioSelect(self.clientArea, pady=0, buttontype='checkbutton', labelpos='w', orient='vertical', label_text="Save:") self.saveTypes.grid(row=0, column=0) for name in self.structMeasure.notebook.pagenames(): mode = 'normal' if name not in [DISTANCES, ANGLES, BONDROTS, GEOMETRIES]: mode = 'disabled' self.saveTypes.add(name, state=mode) if mode == 'normal': self.saveTypes.invoke(name)
def __init__(self, **kw):
import exports
self.notes = None
filterInfo = exports.getFilterInfo()
self.addedSceneTypes = set([i[0] for i in filterInfo])
SaveModeless.__init__(self,
clientPos='s',
clientSticky='ew',
filters=filterInfo,
defaultFilter='X3D',
command=self._command,
setFilterCommand=self._setFilterCB,
**kw)
def export_cb(self):
def save(okay, dialog, self=self):
if okay:
paths = dialog.getPaths()
if paths:
self.write_comma_separated_values(paths[0])
from segment_dialog import current_segmentation
seg = current_segmentation()
if seg is None:
idir = ifile = None
elif hasattr(seg, 'path'):
import os.path
idir, ifile = os.path.split(seg.path)
ifile = os.path.splitext(ifile)[0] + '.csv'
else:
import os.path
idir = None
ifile = os.path.splitext(seg.name)[0] + '.csv'
from OpenSave import SaveModeless
SaveModeless(title='Export Comma Separated Values',
initialdir=idir,
initialfile=ifile,
command=save)
def write_grasp_surface_file():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes=[SurfaceModel])
if len(mlist) == 0:
from chimera import replyobj
replyobj.status('No displayed surfaces')
return
varray, tarray, narray = surface_geometry(mlist)
if len(tarray) == 0:
from chimera import replyobj
replyobj.status('No displayed triangles')
return
def save_geometry(okay, d, varray=varray, tarray=tarray, narray=narray):
if not okay:
return # User canceled action.
path = d.getPaths()[0]
f = grasp_surface_file(varray, tarray, narray)
file = open(path, 'wb')
file.write(f)
file.close()
from OpenSave import SaveModeless
SaveModeless(title="Save Surface",
filters=[('GRASP surface', ['*.srf'], '.srf')],
command=save_geometry)
def saveDemoAs(self):
from OpenSave import SaveModeless
SaveModeless(command=self._saveCB,
title="Choose Demo Save Location",
dialogKw={'oneshot': 1},
historyID="Demo Save As",
defaultFilter=0,
filters=[("Demo", ["*.src"], ".src")])
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
from MovieRecorder import RecorderGUI
formats = []
exts = []
for fmtInfo in RecorderGUI.formats:
fmt, ext = fmtInfo[:2]
formats.append(fmt)
exts.append("." + ext)
filters = []
for i, fmt in enumerate(formats):
ext = exts[i]
filters.append((fmt, '*'+ext, ext))
SaveModeless.__init__(self, clientPos='s', clientSticky='ew',
defaultFilter=prefs[RECORDER_FORMAT],
filters=filters, historyID="MD recorder")
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
from chimera.tkoptions import SymbolicEnumOption, BooleanOption
class ColorModeOption(SymbolicEnumOption):
values = ["color", "gray", "mono"]
labels = ["color", "grayscale", "black & white"]
self.colorMode = ColorModeOption(self.clientArea,
0,
"color mode",
"color",
None,
balloon="output color range")
self.orientation = BooleanOption(
self.clientArea,
1,
"rotate 90",
False,
None,
balloon="If true, output will be rotated 90 degrees\n"
"(i.e. landscape mode)")
class ExtentOption(SymbolicEnumOption):
values = ["visible", "all"]
labels = ["visible region", "entire alignment"]
self.extent = ExtentOption(
self.clientArea,
2,
"extent",
"visible",
None,
balloon="save the entire alignment or just the visible part")
self.hideNodes = BooleanOption(
self.clientArea,
3,
"hide tree control nodes",
True,
None,
balloon="Hide square boxes used as controls for tree")
if not self.mav.seqCanvas.treeShown:
self.hideNodes.forget()
self._nodesHandler = self.mav.triggers.addHandler(
DISPLAY_TREE, self._treeDispCB, None)
def fillInUI(self, parent): SaveModeless.fillInUI(self, parent) self.selUnsel = Pmw.OptionMenu(self.clientArea, items=[ "selected", "unselected"], labelpos='w', label_text= "Write") self.selUnsel.grid(row=0, column=0, sticky='e') self.classMenu = Pmw.OptionMenu(self.clientArea, items= map(lambda c: c.__name__.lower() + "s", classes)) self.classMenu.grid(row=0, column=1, sticky='w') from tkoptions import NamingStyleOption if self.prefs[self.PREF_NAMING] in NamingStyleOption.values: default = self.prefs[self.PREF_NAMING] else: default = None self.naming = NamingStyleOption(self.clientArea, 1, None, default, None)
def fillInUI(self, *args): if isinstance(self, SaveModeless): SaveModeless.fillInUI(self, *args) else: SaveModal.fillInUI(self, *args) import Tkinter self.saveRegion = Tkinter.IntVar(self.clientArea) self.saveRegion.set(False) Tkinter.Checkbutton(self.clientArea, variable=self.saveRegion, text="Restrict save to active region").grid(row=0, sticky='w') self.omitGaps = Tkinter.IntVar(self.clientArea) self.omitGaps.set(True) Tkinter.Checkbutton(self.clientArea, variable=self.omitGaps, text="Omit all-gap columns").grid(row=1, sticky='w') self.appendNumberings = Tkinter.IntVar(self.clientArea) Tkinter.Checkbutton(self.clientArea, variable=self.appendNumberings, text="Append sequence" " numberings to sequence names").grid(row=2, sticky='w')
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
from MovieRecorder import RecorderGUI
formats = []
exts = []
for fmtInfo in RecorderGUI.formats:
fmt, ext = fmtInfo[:2]
formats.append(fmt)
exts.append("." + ext)
filters = []
for i, fmt in enumerate(formats):
ext = exts[i]
filters.append((fmt, '*' + ext, ext))
SaveModeless.__init__(self,
clientPos='s',
clientSticky='ew',
defaultFilter=prefs[RECORDER_FORMAT],
filters=filters,
historyID="MD recorder")
def fillInUI(self, parent): SaveModeless.fillInUI(self, parent) from chimera.tkoptions import SymbolicEnumOption self.headerChoice = SymbolicEnumOption(self.clientArea, 0, "Save", None, None) self.omitNoValueVar = Tkinter.IntVar(self.clientArea) self.omitNoValueVar.set(True) frame = Tkinter.Frame(self.clientArea) frame.grid(row=1, column=0, columnspan=2) ckb = Tkinter.Checkbutton(frame, variable=self.omitNoValueVar, text="Omit no-value positions") ckb.grid() chimera.help.register(ckb, balloon= "If on, conservations positions without\n" "values will not have lines in the output file") self._populateMenu() from MAViewer import SHOW_HEADERS, HIDE_HEADERS for trig in [SHOW_HEADERS, HIDE_HEADERS]: self.mav.triggers.addHandler(trig, self._populateMenu, None)
def browse(self):
if hasattr(self, '_saveDialog'):
self._saveDialog.enter()
return
from OpenSave import SaveModeless
self._saveDialog = SaveModeless(
command=self._saveCB,
historyID='Delphi output %s' % self.name,
title='Save %s' % self.name,
initialfile=self.default,
filters=[(self.name, '*', self.defaultextension)],
compressed=self.compressed)
def fillInUI(self, parent): import Pmw, Tkinter SaveModeless.fillInUI(self, parent) row = 0 from chimera.widgets import MoleculeOptionMenu self.modelMenu = MoleculeOptionMenu(self.clientArea, labelpos='w', label_text="Save model:", command=lambda m: self.configure( self.modelMenu.getvalue(), refreshList=False)) self.modelMenu.grid(row=row, column=0, sticky='w') row += 1 from AddCharge import knownChargeModels, defaultChargeModel from chimera import dialogs self.parmsetOption = Pmw.OptionMenu(self.clientArea, labelpos='w', label_text="Select force field type: ", initialitem=defaultChargeModel, items=knownChargeModels) # not always shown; remember row number self._msmRow = row self.parmsetOption.grid(row=row, column=0, sticky='w') row += 1
def fillInUI(self, *args):
if isinstance(self, SaveModeless):
SaveModeless.fillInUI(self, *args)
else:
SaveModal.fillInUI(self, *args)
import Tkinter
self.saveRegion = Tkinter.IntVar(self.clientArea)
self.saveRegion.set(False)
Tkinter.Checkbutton(self.clientArea,
variable=self.saveRegion,
text="Restrict save to active region").grid(
row=0, sticky='w')
self.omitGaps = Tkinter.IntVar(self.clientArea)
self.omitGaps.set(True)
Tkinter.Checkbutton(self.clientArea,
variable=self.omitGaps,
text="Omit all-gap columns").grid(row=1,
sticky='w')
self.appendNumberings = Tkinter.IntVar(self.clientArea)
Tkinter.Checkbutton(self.clientArea,
variable=self.appendNumberings,
text="Append sequence"
" numberings to sequence names").grid(row=2,
sticky='w')
def save_fits_cb(self):
lfits = self.selected_listbox_fits()
mlist = sum([f.fit_molecules() for f in lfits], [])
if len(mlist) == 0:
from chimera.replyobj import warning
warning('No fits of molecules chosen from list.')
return
idir = ifile = None
vlist = [f.volume for f in lfits]
pmlist = [m for m in mlist + vlist if hasattr(m, 'openedAs')]
if pmlist:
for m in pmlist:
import os.path
dpath, fname = os.path.split(m.openedAs[0])
base, suf = os.path.splitext(fname)
if ifile is None:
suffix = '_fit%d.pdb' if len(lfits) > 1 else '_fit.pdb'
ifile = base + suffix
if dpath and idir is None:
idir = dpath
def save(okay, dialog, lfits=lfits):
if okay:
paths = dialog.getPaths()
if paths:
path = paths[0]
import Midas
if len(lfits) > 1 and path.find('%d') == -1:
base, suf = os.path.splitext(path)
path = base + '_fit%d' + suf
for i, fit in enumerate(lfits):
p = path if len(lfits) == 1 else path % (i + 1)
fit.place_models(self.session)
Midas.write(fit.fit_molecules(),
relModel=fit.volume,
filename=p)
from OpenSave import SaveModeless
SaveModeless(title='Save Fit Molecules',
filters=[('PDB', '*.pdb', '.pdb')],
initialdir=idir,
initialfile=ifile,
command=save)
def _save(output, show): global _saveDialog if not _saveDialog: from OpenSave import SaveModeless _saveDialog = SaveModeless( title="Choose Surface Area/Volume Save File", command=_fileChosen, initialfile="output.html", historyID="Surface Area/Volume Output") else: _saveDialog.enter() _saveDialog._output = output _saveDialog._show = show
def select_save_path_modeless(save_cb):
from fileformats import file_writers
filters = map(lambda fw: (fw[0], ['*' + fw[2]], fw[2]), file_writers)
def save(okay, d, save_cb=save_cb):
if not okay:
return
paths_and_types = d.getPathsAndTypes()
if len(paths_and_types) == 0:
return
path, file_type = paths_and_types[0]
save_cb(path, file_type)
from OpenSave import SaveModeless
d = SaveModeless(title="Save Volume Data",
filters=filters,
defaultFilter=0,
command=save)
def Save(self):
if self.image is None:
return
def save(okay, dialog, self=self):
if not okay:
return
paths_and_types = dialog.getPathsAndTypes()
if len(paths_and_types) == 0:
return
path, format = paths_and_types[0]
self.image.save(path, format)
from OpenSave import SaveModeless
SaveModeless(title='Save Image',
filters=[('JPEG', '*.jpg', '.jpg'),
('PNG', '*.png', '.png'),
('TIFF', '*.tif', '.tif')],
command=save)
def show_save_dialog(seg, saved_cb=None):
def save(okay, dialog, saved_cb=saved_cb):
if okay:
paths = dialog.getPaths()
if paths:
write_segmentation(seg, paths[0])
if saved_cb:
saved_cb(seg)
if hasattr(seg, 'path'):
import os.path
idir, ifile = os.path.split(seg.path)
else:
idir = None
ifile = seg.name
from OpenSave import SaveModeless
SaveModeless(title='Save Segmentation %s' % seg.name,
filters=[('Segmentation', '*.seg', '.seg')],
initialdir=idir,
initialfile=ifile,
command=save)
def __init__(self, mav): self.mav = mav self.title = "Save Header of %s" % mav.title defaultFile = os.path.splitext(self.mav.title or "alignment")[0] SaveModeless.__init__(self, initialfile=defaultFile+".hdr", clientPos='s')
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(self.clientArea,
labelpos='w', label_text="Save models:",
listbox_selectmode='extended',
selectioncommand=lambda: self.configure(
self.modelList.getvalue(), refreshList=False))
self.modelList.grid(row=row, column=0, sticky='nsew')
self.clientArea.rowconfigure(row, weight=1)
self.clientArea.columnconfigure(0, weight=1)
row += 1
from chimera import dialogs
self.labelMap = {
"individual":
"a single file [individual @MOLECULE sections]",
"combined":
"a single file [combined @MOLECULE section]",
"multiple":
"multiple files [appending model number]"
}
preferred = self.labelMap[self.prefs["multiSaveMol2"]]
self.multiSaveMenu = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save multiple models in",
initialitem=preferred, items=self.labelMap.values())
# not always shown; remember row number
self._msmRow = row
row += 1
self.saveRelativeVar = Tkinter.IntVar(self.clientArea)
self.saveRelativeVar.set(False)
self.relativeFrame = f = Tkinter.Frame(self.clientArea)
Tkinter.Checkbutton(f, variable=self.saveRelativeVar,
text="Save relative to model:").grid(row=0,
column=0, sticky='e')
self.relModelMenu = ModelOptionMenu(f)
self.relModelMenu.grid(row=0, column=1, sticky='w')
self.saveUntransformedVar = Tkinter.IntVar(parent)
self.saveUntransformedVar.set(True)
self.untransformedButton = Tkinter.Checkbutton(self.clientArea,
variable=self.saveUntransformedVar,
text="Use untransformed coordinates")
self._rfRow = row
row += 1
self.sybylHydNamesVar = Tkinter.IntVar(self.clientArea)
self.sybylHydNamesVar.set(
self.prefs["hydrogen naming"] == "sybyl")
Tkinter.Checkbutton(self.clientArea,
variable=self.sybylHydNamesVar,
text="Use Sybyl-style hydrogen naming (e.g. HE12"
" rather than 2HE1)").grid(row=row, column=0,
sticky="w")
row += 1
self.resNumsVar = Tkinter.IntVar(self.clientArea)
self.resNumsVar.set(self.prefs["residue numbers"])
Tkinter.Checkbutton(self.clientArea, variable=self.resNumsVar,
text="Include residue sequence numbers in substructure"
" names").grid(row=row, column=0, sticky='w')
row += 1
self.writeGaffVar = Tkinter.IntVar(self.clientArea)
self.resNumsVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.writeGaffVar,
text="Write Amber/GAFF atom types instead of Sybyl atom types"
).grid(row=row, column=0, sticky='w')
row += 1
self.rigidVar = Tkinter.IntVar(self.clientArea)
self.rigidVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.rigidVar,
text="Write current selection to @SETS section of file"
).grid(row=row, column=0, sticky="w")
row += 1
def __init__(self, mav, **kw): self.mav = mav if isinstance(self, SaveModeless): SaveModeless.__init__(self, **kw) else: SaveModal.__init__(self, **kw)
def WriteRegionsFile(smod, fname=None):
if fname is None:
# Show save-file dialog.
def save(okay, dialog):
if okay:
paths = dialog.getPaths()
if paths:
WriteRegionsFile(smod, paths[0])
bname = smod.name[0:smod.name.rfind('_regions')]
prefix = smod.path + bname + "_regions_save_%d"
uupath = unusedFile(prefix)
from OpenSave import SaveModeless
d = SaveModeless(title='Save Regions',
initialdir=smod.path,
initialfile=os.path.basename(uupath),
command=save)
return
tot_write_regions = [0]
tot_e_size = 1
for region in smod.regions:
tot_e_size += RegionSize(region, tot_write_regions)
num_cons = 0
rcons = smod.region_contacts()
for r1, cr1 in rcons.iteritems():
for r2, o in cr1.iteritems():
if r1.rid < r2.rid:
num_cons = num_cons + 1
tot_e_size = tot_e_size + 1 + 4 * (num_cons)
print "Writing %d regions, %d grouped" % (tot_write_regions[0],
len(smod.regions))
if fname: print " - to", fname
e = numpy.zeros([tot_e_size], numpy.float32)
e[0] = float(tot_write_regions[0])
e_at = 1
rlist = renumberRegions(smod)
for region in rlist:
e_at = AddRegion(smod, region, e, e_at)
print " - writing %d contacts" % (num_cons)
e[e_at] = float(num_cons)
e_at = e_at + 1
#consa = []
for r1, cr1 in rcons.iteritems():
for r2, o in cr1.iteritems():
if r1.rid < r2.rid:
#consa = consa + [r1.rid, r2.rid, o.N, o.D]
e[e_at + 0] = float(r1.rid)
e[e_at + 1] = float(r2.rid)
e[e_at + 2] = o.N
e[e_at + 3] = o.D
e_at = e_at + 4
#consa = [len(consa)/4] + consa
#e = numpy.concatenate ( [ e, numpy.array ( consa, numpy.float32 ) ] )
e.tofile(fname)
print "Wrote %s" % os.path.basename(fname)
def __init__(self):
import preferences
options = { self.PREF_NAMING: "simple" }
self.prefs = preferences.addCategory("write selection dialog",
preferences.HiddenCategory, optDict=options)
SaveModeless.__init__(self, clientPos='s')
def _writeFileCB(self): if not hasattr(self, "_writeFileDialog"): from OpenSave import SaveModeless self._writeFileDialog = SaveModeless(command=self._writeFile, title="Write 2D Labels Info") self._writeFileDialog.enter()
class IlabelDialog(ModelessDialog):
name = "2D Labels/Color Key"
provideStatus = True
buttons = ("Delete", "Close")
LABELS = "Labels"
COLOR_KEY = "Color Key"
MOUSE_LABEL_TEXT = "Use mouse for label placement"
MOUSE_KEY_TEXT = "Use mouse for key placement"
EmphasisColor = "forest green"
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel,
None), icon=chimage.get(Image.open(os.path.join(myDir,
'ilabel.png')), tkgui.app))
addFunction('place key', (self._startOrGrabKey,
self._sizeOrMoveKey, None), icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
def fillInUI(self, parent):
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.fileMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Write...", command=self._writeFileCB)
self.fileMenu.add_command(label="Read...", command=self._readFileCB)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row=0)
from ColorKey import KeyModel
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
# _pageRaisedCB uses mouseModeVar, so define first
self.mouseLabelingVar = Tkinter.IntVar(parent)
self.mouseLabelingVar.set(True)
self.mlLabelVar = Tkinter.StringVar(parent)
self.mouseModeButton = Tkinter.Checkbutton(parent,
command=self._mouseFuncCB,
variable=self.mouseLabelingVar,
textvariable=self.mlLabelVar)
self.mouseModeButton.grid(row=2, column=0)
self.notebook = Pmw.NoteBook(parent,
raisecommand=self._pageRaisedCB)
self.notebook.add(self.LABELS, tab_text=self.LABELS)
self.notebook.add(self.COLOR_KEY, tab_text=self.COLOR_KEY)
self.notebook.grid(row=1, column=0, sticky="nsew")
self._fillLabelsPage(self.notebook.page(self.LABELS))
self.keyModel = KeyModel(self)
self.keyPosition = None
self._fillColorKeyPage(self.notebook.page(self.COLOR_KEY))
def _fillLabelsPage(self, page):
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
page.columnconfigure(2, weight=1)
row = 0
from CGLtk.Table import SortableTable
self.labelTable = SortableTable(page, automultilineHeaders=False)
self.labelTable.addColumn("Label [(x, y) text]", self._labelListing,
anchor='w')
self.labelTable.addColumn("Shown", "shown", format=bool)
self.labelTable.setData(self.model.labels)
self.labelTable.launch(browseCmd=self._tableCB, selectMode="single")
self.labelTable.grid(row=row, column=0, columnspan=3, sticky="nsew")
page.rowconfigure(row, weight=1)
row += 1
self.labelText = Pmw.ScrolledText(page, labelpos='w',
label_text="Text", text_height=3, text_width=20,
text_wrap='none', text_state='disabled',
text_exportselection=False)
text = self.labelText.component('text')
text.bind("<<Modified>>", self._textCB)
text.bind("<<Selection>>", self._updateTextAttrWidgets)
self.labelText.grid(row=row, column=0,
sticky='nsew', columnspan=3)
page.rowconfigure(row, weight=1)
row += 1
self.labelSymbolMenu = Pmw.OptionMenu(page, labelpos='w',
label_text="Insert symbol:", command=self._insertSymbol,
items=[
u'\N{GREEK SMALL LETTER ALPHA}',
u'\N{GREEK SMALL LETTER BETA}',
u'\N{GREEK SMALL LETTER GAMMA}',
u'\N{GREEK SMALL LETTER DELTA}',
u'\N{GREEK SMALL LETTER EPSILON}',
u'\N{GREEK SMALL LETTER PI}',
u'\N{GREEK SMALL LETTER PHI}',
u'\N{GREEK SMALL LETTER CHI}',
u'\N{GREEK SMALL LETTER PSI}',
u'\N{GREEK SMALL LETTER OMEGA}',
u'\N{LEFTWARDS ARROW}',
u'\N{RIGHTWARDS ARROW}',
u'\N{LEFT RIGHT ARROW}',
u'\N{UPWARDS ARROW}',
u'\N{DOWNWARDS ARROW}',
u'\N{SUPERSCRIPT TWO}',
u'\N{SUPERSCRIPT THREE}',
u'\N{DEGREE SIGN}',
u'\N{LATIN CAPITAL LETTER A WITH RING ABOVE}',
"more..."
])
self.labelSymbolMenu.grid(row=row, column=0, columnspan=3)
row += 1
colorHouse = Pmw.LabeledWidget(page, labelpos='w',
label_text="Color")
colorHouse.grid(row=row, column=0, rowspan=3)
from CGLtk.color.ColorWell import ColorWell
self.colorWell = ColorWell(colorHouse.interior(),
color=self._contrastWithBG(), callback=self._colorCB)
self.colorWell.grid()
from chimera.tkoptions import IntOption
self.labelFontSize = IntOption(page, row, "Font size", 24,
self._labelChangeCB, startCol=1, min=1,
attribute="size", width=3)
row += 1
self.labelFontStyle = FontStyle(page, row, "Font style",
oglFont.normal, self._labelChangeCB, startCol=1)
row += 1
self.labelFontTypeface = FontTypeface(page, row, "Font typeface",
FONT_TYPEFACE_VALUES[0],
self._labelChangeCB, startCol=1)
row += 1
if self.model.curLabel:
self.changeToLabel(self.model.curLabel, force=True)
def _fillColorKeyPage(self, page):
from chimera.tkoptions import IntOption, EnumOption, \
BooleanOption, RGBAOption
f = Tkinter.Frame(page)
f.grid(row=0, columnspan=2)
self.numComponents = IntOption(f, 0, "Number of colors/labels",
3, self._componentsCB, min=2, width=2)
self.componentsFrame = Tkinter.Frame(page)
self.componentsFrame.grid(row=1, column=0, sticky="nsew",
columnspan=2)
page.columnconfigure(0, weight=1)
self.componentsFrame.columnconfigure(1, weight=1)
class ColorTreatment(EnumOption):
values = ("distinct", "blended")
self.colorTreatment = ColorTreatment(page, 2,
"Color range depiction", "blended", self._keyChangeCB,
balloon="Should colors be shown as distinct rectangles"
" or as a continuous range")
class LabelPosition(EnumOption):
values = ("left/top", "right/bottom")
self.labelPos = LabelPosition(page, 3, "Label positions",
"right/bottom", self._keyChangeCB, balloon="Position of"
" labels relative to color key.\nLabels always"
" positioned adjacent to long side.")
self.labelColor = RGBAOption(page, 4, "Label color",
self._contrastWithBG(), self._keyChangeCB, balloob=
"Label color. If set to 'No color', use corresponding"
" key color", noneOkay=True)
class LabelJustification(EnumOption):
values = ("left", "decimal point", "right")
self.justification = LabelJustification(page, 5,
"Label justification", "decimal point",
self._keyChangeCB, balloon="Justification of label text"
" in a vertical key layout.\nHorizontal key labels will"
" always be center justified.")
self.labelOffset = IntOption(page, 6, "Label offset", 0,
self._keyChangeCB, width=3, balloon="Additional offset"
" of labels from color bar, in pixels")
self.keyFontSize = IntOption(page, 7, "Font size", 24,
self._keyChangeCB, width=3)
self.keyFontStyle = FontStyle(page, 8, "Font style",
oglFont.normal, self._keyChangeCB)
self.keyFontTypeface = FontTypeface(page, 9, "Font typeface",
FONT_TYPEFACE_VALUES[0], self._keyChangeCB)
self.borderColor = RGBAOption(page, 10, "Border color",
None, self._keyChangeCB, balloon="Color of border"
" around color key (not each individual color).\n"
"If 'no color', then no border is drawn.")
self.borderWidth = IntOption(page, 11, "Border width", 3,
self._keyChangeCB, balloon="in pixels")
self.tickMarks = BooleanOption(page, 12, "Show tick marks",
False, self._keyChangeCB, balloon="Show tick marks"
" pointing from key to labels")
self._componentsCB(self.numComponents)
def destroy(self, *args):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
chimera.triggers.deleteHandler(SAVE_SESSION,
self._sessionHandlerID)
chimera.triggers.deleteHandler(CLOSE_SESSION,
self._closeHandlerID)
chimera.triggers.deleteHandler(BEGIN_RESTORE_SESSION,
self._beginRestoreHandlerID)
chimera.openModels.close([self.model, self.keyModel])
ModelessDialog.destroy(self)
def map(self, e=None):
self._pageRaisedCB(self.notebook.getcurselection())
def unmap(self, e=None):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
def changeToLabel(self, nextLabel, force=False):
if nextLabel == self.model.curLabel and not force:
return
if self.model.curLabel and not unicode(self.model.curLabel) \
and self.model.curLabel != nextLabel:
# remove previous label if empty
self.removeLabel(self.model.curLabel)
self.model.changeToLabel(nextLabel)
self.labelText.component('text').configure(state='normal')
self.labelTable.select(nextLabel)
self.labelText.settext(unicode(nextLabel))
text = self.labelText.component('text')
lineIndex = 1
for line in self.model.curLabel.lines:
charIndex = 0
for c in line:
text.tag_add(id(c),
"%d.%d" % (lineIndex, charIndex))
charIndex += 1
text.tag_add(id(line), "%d.%d" % (lineIndex, charIndex))
lineIndex += 1
def Delete(self):
if self.notebook.getcurselection() == self.LABELS:
self.labelText.clear()
if not self.model.curLabel:
self.status("No label to delete", color="red",
blankAfter=10)
return
self.removeLabel(self.model.curLabel)
self.labelText.component('text').configure(
state='disabled')
else:
self.keyPosition = None
self._keyChangeCB()
def Help(self):
helpLoc = "ContributedSoftware/2dlabels/2dlabels.html"
if self.notebook.getcurselection() == self.COLOR_KEY:
helpLoc += "#colorkey"
chimera.help.display(helpLoc)
def keyConfigure(self, data, pageChange=True):
self._componentsCB(len(data), update=False)
for datum, well, label in zip(data, self.wells, self.labels):
color, text = datum
well.showColor(color, doCallback=False)
label.variable.set(text, invoke_callbacks=False)
self._keyChangeCB()
if pageChange:
self.notebook.selectpage(self.COLOR_KEY)
def makeChar(self, char, model):
attrs = {}
try:
attrs['rgba'] = self.colorWell.rgba
except AttributeError: # multi or None
if model:
attrs['rgba'] = model.rgba
size = self.labelFontSize.get()
if size is not None:
attrs['size'] = size
style = self.labelFontStyle.get()
if style is not None:
attrs['style'] = style
fontName = self.labelFontTypeface.get()
if fontName is not None:
attrs['fontName'] = fontName
return Character(char, **attrs)
def newLabel(self, pos):
label = self.model.newLabel(pos)
self.labelTable.setData(self.model.labels)
self.status("Mouse drag to reposition label",
color=self.EmphasisColor)
return label
def removeLabel(self, label):
self.model.removeLabel(label)
self.labelTable.setData(self.model.labels)
if self.model.curLabel is not None:
self.labelTable.select(self.model.curLabel)
def reverseKey(self):
data = zip([w.rgba for w in self.wells],
[l.variable.get() for l in self.labels])
data.reverse()
self.keyConfigure(data)
def setLabelFromText(self):
curLabel = self.model.curLabel
text = self.labelText.component('text')
# delete parts of label not in text...
#
# newlines first...
while len(curLabel.lines) > 1:
for i, line in enumerate(curLabel.lines[:-1]):
if not text.tag_ranges(id(line)):
curLabel.lines[i+1][:0] = line
del curLabel.lines[i]
break
else:
break
# characters...
for line in curLabel.lines:
for c in line[:]:
if not text.tag_ranges(id(c)):
line.remove(c)
# get new parts of text into label
model = None
targets = []
lines = curLabel.lines
for line in lines:
targets.extend([id(c) for c in line])
if not model and line:
model = line[0]
if line is not lines[-1]:
targets.append(id(line))
contents = self.labelText.get()[:-1] # drop trailing newline
if targets:
target = targets.pop(0)
else:
target = None
textLine = 1
textIndex = -1
curLine = lines[0]
for c in contents:
textIndex += 1
if str(target) in text.tag_names("%d.%d"
% (textLine, textIndex)):
if targets:
target = targets.pop(0)
else:
target = None
if c == '\n':
textLine += 1
textIndex = -1
curLine = lines[[id(l)
for l in lines].index(
id(curLine))+1]
elif curLine:
model = curLine[textIndex]
elif c == '\n':
insertLine = curLine[0:textIndex]
lines.insert(textLine-1, insertLine)
del curLine[0:textIndex]
text.tag_add(id(insertLine), "%d.%d"
% (textLine, textIndex))
textLine += 1
textIndex = -1
else:
labelChar = self.makeChar(c, model)
curLine.insert(textIndex, labelChar)
text.tag_add(id(labelChar), "%d.%d"
% (textLine, textIndex))
self.model.setMajorChange()
def updateGUI(self, source="gui"):
curLabel = self.model.curLabel
if curLabel and source == "gui":
self.setLabelFromText()
self.labelTable.setData(self.model.labels)
if curLabel:
self.labelTable.select(curLabel)
self._updateTextAttrWidgets()
def _colorCB(self, color):
curLabel = self.model.curLabel
if not curLabel:
self.status("No label to color", color='red')
return
self.model.setMajorChange()
for c in self._selChars():
c.rgba = color
def _componentsCB(self, opt, update=True):
cf = self.componentsFrame
if hasattr(self, 'wells'):
for well in self.wells:
well.grid_forget()
well.destroy()
for label in self.labels:
label.frame.grid_forget()
self.reverseButton.grid_forget()
self.reverseButton.destroy()
else:
Tkinter.Label(cf, text="Colors").grid(row=0)
Tkinter.Label(cf, text="Labels").grid(row=0, column=1)
if isinstance(opt, int):
numComponents = opt
self.numComponents.set(opt)
else:
numComponents = opt.get()
wellSize = min(38, int( (7 * 38) / numComponents ))
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.labels = []
from CGLtk import Hybrid
for i in range(numComponents):
well = ColorWell(cf, width=wellSize, height=wellSize,
callback=self._keyChangeCB, color='white')
well.grid(row=i+1)
self.wells.append(well)
label = Hybrid.Entry(cf, "", 10)
label.variable.add_callback(self._keyTypingCB)
label.frame.grid(row=i+1, column=1, sticky='ew')
self.labels.append(label)
self.reverseButton = Tkinter.Button(cf, command=self.reverseKey,
text="Reverse ordering of above", pady=0)
self.reverseButton.grid(row=numComponents+1, column=0,
columnspan=2)
self.notebook.setnaturalsize()
if update:
self._keyChangeCB()
def _contrastWithBG(self):
bg = chimera.viewer.background
if bg:
bgColor = bg.rgba()
else:
bgColor = (0, 0, 0)
if bgColor[0]*2 + bgColor[1]*3 + bgColor[2] < 0.417:
return (1, 1, 1)
else:
return (0, 0, 0)
def _eventToPos(self, viewer, event, offset = (0, 0)):
w, h = viewer.windowSize
return (event.x - offset[0]) / float(w), \
(h - event.y - offset[1]) / float(h)
def _handleTextChange(self):
self.updateGUI()
self.labelText.edit_modified(False)
def _insertSymbol(self, item):
if len(item) > 1:
from chimera import help
help.display("ContributedSoftware/2dlabels/symbols.html")
return
if not self.model.labels:
self.status("No labels have been created yet", color="red")
return
if not self.labelTable.selected():
self.status("No labels active", color="red")
self.labelText.insert("insert", item)
self.setLabelFromText()
def _keyChangeCB(self, *args):
self.keyModel.setMajorChange()
def _keyTypingCB(self, fromAfter=False):
# wait for a pause in typing before updating key...
if fromAfter:
self._typingHandler = None
self._keyChangeCB()
return
handle = getattr(self, '_typingHandler', None)
if handle:
self.componentsFrame.after_cancel(handle)
self._typingHandler = self.componentsFrame.after(500,
lambda: self._keyTypingCB(fromAfter=True))
def _labelChangeCB(self, option):
curLabel = self.model.curLabel
self.model.setMajorChange()
val = option.get()
attrName = option.attribute
for c in self._selChars():
setattr(c, attrName, val)
def _labelListing(self, label):
text = unicode(label)
if '\n' in text:
newline = text.index('\n')
text= text[:newline] + "..."
if not text:
text = "<empty>"
return "(%.2f, %.2f) %s" % (label.pos[0], label.pos[1], text)
def _mouseFuncCB(self):
self.status("")
if not self.mouseLabelingVar.get():
if hasattr(self, "_prevMouse"):
setButtonFunction("1", (), self._prevMouse)
delattr(self, "_prevMouse")
elif self.mlLabelVar.get() == self.MOUSE_LABEL_TEXT:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place text")
else:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place key")
def _moveLabel(self, viewer, event):
pos = self._eventToPos(viewer, event, self._moveOffset)
self.model.moveLabel(pos)
curLabel = self.model.curLabel
self.labelTable.setData(self.model.labels)
self.labelTable.select(curLabel)
def _pageRaisedCB(self, pageName):
if pageName == "Labels":
pageItem = self.MOUSE_LABEL_TEXT
if not self.model.labels:
self.status("Click mouse button 1 in graphics\n"
"window to place first label",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end')+1):
self.fileMenu.entryconfigure(index, state='normal')
else:
pageItem = self.MOUSE_KEY_TEXT
self.status("Drag mouse to position/size key",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end')+1):
self.fileMenu.entryconfigure(index, state='disabled')
self.mlLabelVar.set(pageItem)
# just setting the var doesn't cause the callback, and
# yet using invoke() toggles the var, so set it _opposite_
# to what's desired before calling invoke()
self.mouseLabelingVar.set(False)
self.mouseModeButton.invoke()
def _pickLabel(self, viewer, event):
w, h = viewer.windowSize
pos = self._eventToPos(viewer, event)
label, self._moveOffset = self.model.pickLabel(pos, w, h)
if label is None:
label = self.newLabel(pos)
self._moveOffset = (0, 0)
self.changeToLabel(label)
self.labelText.component('text').focus_set()
def _readFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import readFiles
readFiles(dialog.getPaths(), clear=dialog.deleteExistingVar.get())
def _readFileCB(self):
if not hasattr(self, "_readFileDialog"):
self._readFileDialog = ReadFileDialog(
command=self._readFile, clientPos='s')
self._readFileDialog.enter()
def _restoreSession(self, info):
if info["sel ranges"]:
self.labelText.tag_add("sel", *info["sel ranges"])
self._updateTextAttrWidgets()
self._suppressMap = True
self.labelText.edit_modified(False)
if "key position" not in info:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return
self.keyPosition = info["key position"]
self.colorTreatment.set(info["color depiction"])
self.labelPos.set(info["label positions"])
self.labelColor.set(info["label color"])
self.justification.set(info["label justification"])
self.labelOffset.set(info["label offset"])
self.keyFontSize.set(info["font size"])
self.keyFontStyle.set(info["font typeface"])
if "font name" in info:
self.keyFontTypeface.set(info["font name"])
self.borderColor.set(info["border color"])
self.borderWidth.set(info["border width"])
self.tickMarks.set(info["show ticks"])
self.keyConfigure(info["colors/labels"])
if self.keyPosition:
self.notebook.selectpage(self.COLOR_KEY)
else:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return info
def _saveSession(self, triggerName, myData, sessionFile):
print>>sessionFile, """
def restore2DLabelDialog(info):
from chimera.dialogs import find, display
from Ilabel.gui import IlabelDialog
dlg = find(IlabelDialog.name)
if dlg is not None:
dlg.destroy()
dlg = display(IlabelDialog.name)
dlg._restoreSession(info)
import SimpleSession
SimpleSession.registerAfterModelsCB(restore2DLabelDialog, %s)
""" % repr(self._sessionInfo())
def _selChars(self):
chars = []
curLabel = self.model.curLabel
if curLabel:
sel = self.labelText.tag_ranges("sel")
if sel:
sline, schar = [int(x)
for x in str(sel[0]).split('.')]
eline, echar = [int(x)
for x in str(sel[1]).split('.')]
sline -= 1
eline -= 1
for li, line in enumerate(curLabel.lines):
if li < sline:
continue
if li > eline:
break
if sline == eline:
chars.extend(line[schar:echar])
elif li == sline:
chars.extend(line[schar:])
elif li == eline:
chars.extend(line[:echar])
else:
chars.extend(line)
else:
for l in curLabel.lines:
chars.extend(l)
return chars
def _sessionInfo(self):
info = {}
info["sel ranges"] = tuple([str(tr)
for tr in self.labelText.tag_ranges("sel")])
if self.mouseLabelingVar.get():
info["mouse func"] = "labeling"
else:
info["mouse func"] = "normal"
info["key position"] = self.keyPosition
info["colors/labels"] = [(w.rgba, l.variable.get())
for w, l in zip(self.wells, self.labels)]
info["color depiction"] = self.colorTreatment.get()
info["label positions"] = self.labelPos.get()
info["label color"] = self.labelColor.get()
info["label justification"] = self.justification.get()
info["label offset"] = self.labelOffset.get()
info["font size"] = self.keyFontSize.get()
info["font typeface"] = self.keyFontStyle.get()
info["font name"] = self.keyFontTypeface.get()
info["border color"] = self.borderColor.get()
info["border width"] = self.borderWidth.get()
info["show ticks"] = self.tickMarks.get()
return info
def _sizeOrMoveKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.grabPos:
deltas = [pos[axis] - self.grabPos[axis]
for axis in [0, 1]]
for posIndex in [0, 1]:
old = self.keyPosition[posIndex]
self.keyPosition[posIndex] = (
old[0] + deltas[0], old[1] + deltas[1])
self.grabPos = pos
elif len(self.keyPosition) == 1:
self.keyPosition.append(pos)
else:
self.keyPosition[1] = pos
self._keyChangeCB()
def _startOrGrabKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.keyPosition and len(self.keyPosition) == 2:
# possible grab;
# see if in middle third of long side...
p1, p2 = self.keyPosition
x1, y1 = p1
x2, y2 = p2
if abs(x2 - x1) < abs(y2 - y1):
longAxis = 1
ymin = min(y2, y1)
ymax = max(y2, y1)
b1 = (2* ymin + ymax) / 3.0
b2 = (2* ymax + ymin) / 3.0
o1 = min(x1, x2)
o2 = max(x1, x2)
else:
longAxis = 0
xmin = min(x2, x1)
xmax = max(x2, x1)
b1 = (2* xmin + xmax) / 3.0
b2 = (2* xmax + xmin) / 3.0
o1 = min(y1, y2)
o2 = max(y1, y2)
if b1 < pos[longAxis] < b2 \
and o1 < pos[1-longAxis] < o2:
self.grabPos = pos
return
self.grabPos = None
self.keyPosition = [pos]
self._keyChangeCB()
self.status("Grab middle of key to reposition",
color=self.EmphasisColor)
def _tableCB(self, sel):
if not sel:
return
self.changeToLabel(sel)
def _textCB(self, e):
text = self.labelText.component('text')
if not text.tk.call((text._w, 'edit', 'modified')):
#if not text.edit_modified():
return
# this callback can happen _before_ the change
# actually occurs, so do the processing after idle
text.after_idle(self._handleTextChange)
def _updateTextAttrWidgets(self, e=None):
rgba = None
multiple = False
for c in self._selChars():
if rgba is None:
rgba = c.rgba
elif rgba != c.rgba:
multiple = True
break
if rgba is not None:
self.colorWell.showColor(rgba, multiple=multiple,
doCallback=False)
self.labelFontSize.display(self._selChars())
self.labelFontStyle.display(self._selChars())
self.labelFontTypeface.display(self._selChars())
def _writeFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import writeFile
writeFile(dialog.getPaths()[0])
def _writeFileCB(self):
if not hasattr(self, "_writeFileDialog"):
from OpenSave import SaveModeless
self._writeFileDialog = SaveModeless(command=self._writeFile,
title="Write 2D Labels Info")
self._writeFileDialog.enter()
def __init__(self):
SaveModeless.__init__(self, command=_saveCB,
filters=[("Chimera session", ["*.py"], ".py")],
historyID="SimpleSession", compressed=True)
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(self.clientArea,
labelpos='w', label_text="Save models:",
listbox_selectmode='extended',
selectioncommand=lambda: self.configure(
self.modelList.getvalue(), refreshList=False))
self.modelList.grid(row=row, column=0, sticky='nsew')
self.clientArea.rowconfigure(row, weight=1)
self.clientArea.columnconfigure(0, weight=1)
row += 1
import Tkinter, Pmw
self.dispOnlyVar = Tkinter.IntVar(parent)
self.dispOnlyVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.dispOnlyVar,
text="Save displayed atoms only").grid(row=row,
column=0, sticky='w')
row += 1
self.selOnlyVar = Tkinter.IntVar(parent)
self.selOnlyVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.selOnlyVar,
text="Save selected atoms only").grid(row=row,
column=0, sticky='w')
row += 1
self.saveRelativeVar = Tkinter.IntVar(parent)
self.saveRelativeVar.set(False)
self.relativeFrame = f = Tkinter.Frame(self.clientArea)
Tkinter.Checkbutton(f, variable=self.saveRelativeVar,
text="Save relative to model:"
).grid(row=0, column=0, sticky='e')
self.relModelMenu = ModelOptionMenu(f)
self.relModelMenu.grid(row=0, column=1, sticky='w')
self.saveUntransformedVar = Tkinter.IntVar(parent)
self.saveUntransformedVar.set(True)
self.untransformedButton = Tkinter.Checkbutton(self.clientArea,
variable=self.saveUntransformedVar,
text="Use untransformed coordinates")
self._rfRow = row
row += 1
self.frameSave = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save",
initialitem="current frame",
items=["current frame", "all frames"])
# not always shown; remember row number
self._fsRow = row
row += 1
from chimera import dialogs
self.labelMap = {
"single": "a single file",
"multiple":
"multiple files [appending model number]"
}
preferred = self.labelMap[self.prefs["multiSavePDB"]]
self.multiSaveMenu = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save multiple models in",
initialitem=preferred, items=self.labelMap.values())
# not always shown; remember row number
self._msmRow = row
row += 1
def __init__(self, mav): self.mav = mav self.title = "Save Association Info of %s" % mav.title defaultFile = os.path.splitext(self.mav.title or "alignment")[0] SaveModeless.__init__(self, clientPos='s', initialfile=defaultFile+".asc")
def fillInUI(self, parent): SaveModeless.fillInUI(self, parent) from chimera.tkoptions import NamingStyleOption self.namingStyle = NamingStyleOption(self.clientArea, 0, None, None, None)
def __init__(self, info, callback, **kw): self.info = info self.callback = callback SaveModeless.__init__(self, clientPos='s', **kw)
def __init__(self):
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("DMS", "*.dms", ".dms")])
def __init__(self):
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Prmtop", "*.prmtop", ".prmtop")])
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
self.clientArea.columnconfigure(1, weight=1)
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(self.clientArea, 0,
"Starting frame", startFrame, None,
min=startFrame, max=endFrame, width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames/300)
self.stride = IntOption(self.clientArea, 2, "Step size",
defStride, None, min=1, max=numFrames, width=3)
self.endFrame = IntOption(self.clientArea, 3, "Ending frame",
endFrame, None, min=startFrame, max=endFrame, width=6)
self.roundtrip = BooleanOption(self.clientArea, 4, "Encode"
' forward then backward ("roundtrip")', prefs[
RECORDER_ROUNDTRIP], None, balloon=
"Encode the frames in forward and then reverse\n"
"order so that if the movie is played as a loop\n"
"the motion seems continuous")
class FrameQuality(BooleanOption):
labels = ["screen", "supersampled"]
self.supersample = FrameQuality(self.clientArea, 5,
"Frame quality", prefs[RECORDER_SUPERSAMPLE],
self.supersampleCB, balloon=
"Whether each frame should be taken as is from\n"
"the screen (fast) or redrawn at higher quality\n"
"with several samples per pixel.")
from chimera.printer import SupersampleOption
self.samples = SupersampleOption(self.clientArea, 6,
"Samples", prefs[RECORDER_SAMPLES], None)
self.supersampleCB()
self.raytrace = BooleanOption(self.clientArea, 7, "Raytrace"
" with POV-Ray", prefs[RECORDER_RAYTRACE], None)
def povOptCB():
from chimera.dialogs import display
d = display("preferences")
from chimera.printer import POVRAY_SETUP
d.setCategoryMenu(POVRAY_SETUP)
Tkinter.Button(self.clientArea, text="POV-Ray Options", pady=0,
command=povOptCB).grid(row=8, column=0, columnspan=2)
self.recordArgs = StringOption(self.clientArea, 9,
"Additional recording options",
prefs[RECORDER_RECORD_ARGS], None, balloon=
"Options (other than 'supersample' and 'raytrace')\n"
"for recording frames as per Chimera's 'movie record'"
" command")
self.encodeArgs = StringOption(self.clientArea, 10,
"Additional encoding options",
prefs[RECORDER_ENCODE_ARGS], None, balloon=
"Options (other than 'mformat', 'output', and\n"
"'roundtrip') for composing the frames into the\n"
"final animation as per Chimera's 'movie encode'\n"
"command")
Tkinter.Label(self.clientArea, text=
"On some computers it may be necessary to make sure"
" that no\nwindows occlude the main Chimera graphics"
" window (even\npartially) during non-raytraced movie"
" recording").grid(row=11, column=0, columnspan=2)