def fillInUI(self, parent): import Pmw, Tkinter row = 0 Tkinter.Label(parent, text="Create plane for selected atoms...").grid( row=row, columnspan=2) row += 1 from chimera.tkoptions import StringOption, BooleanOption self.nameOpt = StringOption(parent, row, "Plane name", "plane", None) row += 1 self.replaceExistingOpt = BooleanOption(parent, row, "Replace existing planes", False, None) row += 1 from chimera.tkoptions import ColorOption, FloatOption self.colorOpt = ColorOption(parent, row, "Color", None, None, balloon="Plane color. If No Color, then the plane" " will be colored to match the structure") row += 1 self.autoRadiusOpt = BooleanOption(parent, row, "Set disk size to enclose atom projections", True, self._radCB) row += 1 self.radRow = row self.radOffsetOpt = FloatOption(parent, row, "Extra radius" " (padding)", 0.0, None) self.radiusOpt = FloatOption(parent, row, "Fixed radius", 10.0, None) self.radiusOpt.forget() row += 1 self.thicknessOpt = FloatOption(parent, row, "Disk thickness", prefs[PLANE_THICKNESS], None)
def fillInUI(self, parent): import Tkinter row = 0 from VolumeViewer import Volume_Menu self.volumeMenu = Volume_Menu(parent, 'Volume data', open_button=True) self.volumeMenu.frame.grid(row=row, columnspan=2) row += 1 from chimera.tkoptions import StringOption self.nameOption = StringOption(parent, row, 'Column name', 'Density', None, width=10) row += 1
class RenameDialog(ModelessDialog):
buttons = ('OK', 'Cancel')
default = 'OK'
def __init__(self, geomUI, item):
self.title = "Rename '%s'" % item.name
self.geomUI = geomUI
self.item = item
ModelessDialog.__init__(self)
def map(self, e=None):
self.renameOpt._option.focus_set()
def fillInUI(self, parent):
from chimera.tkoptions import StringOption
self.renameOpt = StringOption(parent, 0,
"Rename %s to" % self.item.name, "", None)
def Apply(self):
newName = self.renameOpt.get().strip()
if not newName:
self.enter()
from chimera import UserError
raise UserError("Must supply a new item name or click Cancel")
self.geomUI._renameItemCB(self.item, newName)
def destroy(self):
self.item = None
self.geomUI = None
ModelessDialog.destroy(self)
def fillInUI(self, parent): Tkinter.Label(parent, text="Collect positions of selected" " atoms over trajectory", relief="ridge", bd=4).grid( row=0, column=0, columnspan=2, sticky="ew") startFrame = self.movie.startFrame endFrame = self.movie.endFrame from chimera.tkoptions import IntOption, BooleanOption, \ FloatOption, StringOption self.startFrame = IntOption(parent, 1, "Starting frame", startFrame, None, min=startFrame, max=endFrame, width=6) numFrames = endFrame - startFrame + 1 defStride = 1 + int(numFrames/300) self.stride = IntOption(parent, 2, "Step size", defStride, None, min=1, max=numFrames, width=3) self.endFrame = IntOption(parent, 3, "Ending frame", endFrame, None, min=startFrame, max=endFrame, width=6) self.doCutoff = BooleanOption(parent, 4, 'Limit data collection' ' to within cutoff distance of any "held steady" atoms', True, None) self.cutoff = FloatOption(parent, 5, "Cutoff distance", prefs[VOLUME_CUTOFF], None, width=4) self.resolution = FloatOption(parent, 6, "Volume grid spacing", prefs[VOLUME_RESOLUTION], None, min=0.0001, width=4) self.volumeName = StringOption(parent, 7, "Volume data name", self.movie.ensemble.name, None, width=20) self.byAtomType = BooleanOption(parent, 8, "Collect data" " separately for each atom type in selection", True, None, balloon="Create a volume data set for" " each type of atom type\n(sp2 oxygen, aromatic carbon," " etc.) in current selection")
class RenameDialog(ModelessDialog):
buttons = ('OK', 'Cancel')
default = 'OK'
def __init__(self, regionBrowser, region):
self.title = "Rename '%s' Region" % regionName(region,
regionBrowser.seqCanvas.mav.prefs)
self.regionBrowser = regionBrowser
self.region = region
ModelessDialog.__init__(self)
def map(self, e=None):
self.renameOpt._option.focus_set()
def fillInUI(self, parent):
from chimera.tkoptions import StringOption
self.renameOpt = StringOption(parent, 0, "Rename region to",
"", None)
def Apply(self):
newName = self.renameOpt.get().strip()
if not newName:
self.enter()
from chimera import UserError
raise UserError("Must supply a new region name or "
"click Cancel")
self.regionBrowser.renameRegion(self.region, newName)
def destroy(self):
self.region = None
self.regionBrowser = None
ModelessDialog.destroy(self)
def fillInUI(self, parent): self.refMenu = Pmw.OptionMenu(parent, command=self._newRefCB, labelpos="nw", label_text="Reference structure:") self.refMenu.grid(row=0, column=0) self.alignList = Pmw.ScrolledListBox(parent, items=[], labelpos="nw", listbox_height=6, label_text="Structures to evaluate:", listbox_exportselection=0, listbox_selectmode='extended') self.alignList.grid(row=1, column=0, sticky="nsew") parent.rowconfigure(1, weight=1) parent.columnconfigure(0, weight=1) subFrame = Tkinter.Frame(parent) subFrame.grid(row=2, column=0) from chimera.tkoptions import StringOption self.attrNameOption = StringOption(subFrame, 2, "Create residue attribute named", "matchDist", None, balloon="Create a residue attribute" " measuring the CA/C4' distance between\nreference and" " evaluated structures. The attribute will be shown\n" "in the select-by-attribute dialog after you hit OK.") Tkinter.Label(parent, text="The attribute-selection dialog will" " display when OK is chosen").grid(row=3, column=0) self.refresh(initial=1) self.assocHandlerID = self.mav.triggers.addHandler(MOD_ASSOC, self.refresh, None)
class Projection(ModalDialog):
buttons = ('Cancel', 'Apply')
def __init__(self):
self.name = None
self.filename = None
ModalDialog.__init__(self)
def fillInUI(self, parent):
from chimera.tkoptions import StringOption
Tkinter.Label(parent, text='Data projection',
relief="ridge", bd=4).grid(row=0, column=0)
self.name = StringOption(parent, 1, "Name for the projection", 'Projection', None)
self.filename = Tkinter.Button(parent, text='Open data file',
command=lambda: self.get_filename(parent)).grid(row=2, column=0)
self.read_header = Tkinter.BooleanVar()
self.check_header = Tkinter.Checkbutton(parent,
text="Read header to define names for n-dim features",
var=self.read_header).grid(row=3, column=0)
def get_filename(self, parent):
self.filename = askopenfilename()
Tkinter.Label(parent, text='Filename: %s'%self.filename,
relief="ridge", bd=4).grid(row=2, column=1)
def Apply(self):
name = self.name.get()
ModalDialog.Cancel(self, value=(name, self.filename, self.read_header.get()))
def destroy(self):
ModelessDialog.destroy(self)
def fillInUI(self, parent):
from chimera.tkoptions import StringOption
Tkinter.Label(parent, text='Data projection',
relief="ridge", bd=4).grid(row=0, column=0)
self.name = StringOption(parent, 1, "Name for the projection", 'Projection', None)
self.filename = Tkinter.Button(parent, text='Open data file',
command=lambda: self.get_filename(parent)).grid(row=2, column=0)
self.read_header = Tkinter.BooleanVar()
self.check_header = Tkinter.Checkbutton(parent,
text="Read header to define names for n-dim features",
var=self.read_header).grid(row=3, column=0)
def fillInUI(self, parent):
self.refMenu = Pmw.OptionMenu(parent,
command=self._newRefCB,
labelpos="nw",
label_text="Reference structure:")
self.refMenu.grid(row=0, column=0)
self.alignList = Pmw.ScrolledListBox(
parent,
items=[],
labelpos="nw",
listbox_height=6,
label_text="Structures to evaluate:",
listbox_exportselection=0,
listbox_selectmode='extended')
self.alignList.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
subFrame = Tkinter.Frame(parent)
subFrame.grid(row=2, column=0)
from chimera.tkoptions import StringOption
self.attrNameOption = StringOption(
subFrame,
2,
"Create residue attribute named",
"matchDist",
None,
balloon="Create a residue attribute"
" measuring the CA/C4' distance between\nreference and"
" evaluated structures. The attribute will be shown\n"
"in the select-by-attribute dialog after you hit OK.")
Tkinter.Label(parent,
text="The attribute-selection dialog will"
" display when OK is chosen").grid(row=3, column=0)
self.refresh(initial=1)
self.assocHandlerID = self.mav.triggers.addHandler(
MOD_ASSOC, self.refresh, None)
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
group = Pmw.Group(self.clientArea, tag_text='Further info')
group.grid(row=0, column=0, sticky='nsew')
self.catName = StringOption(group.interior(), 0, "group name", None,
None)
class PBLineWidthOption(LineWidthOption):
default = prefs["line width"]
balloon = "Width of pseudobonds (in pixels)"
self.lineWidth = PBLineWidthOption(group.interior(), 1, None, None,
None)
self.clearCat = BooleanOption(group.interior(), 2,
"clear group of previous pseudobonds", 1,
None)
self.leftModel = IntOption(group.interior(), 3,
"first column specifiers default to model",
0, None)
self.rightModel = IntOption(
group.interior(), 4, "second column specifiers default to model",
0, None)
class PBreaderDialog(OpenModeless):
title = "Pseudobond Reader"
help = "ContributedSoftware/pbreader/pbreader.html"
def __init__(self):
OpenModeless.__init__(self,
title="Pseudobond File to Read",
historyID="PBReader open",
clientPos='s')
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
group = Pmw.Group(self.clientArea, tag_text='Further info')
group.grid(row=0, column=0, sticky='nsew')
self.catName = StringOption(group.interior(), 0, "group name", None,
None)
class PBLineWidthOption(LineWidthOption):
default = prefs["line width"]
balloon = "Width of pseudobonds (in pixels)"
self.lineWidth = PBLineWidthOption(group.interior(), 1, None, None,
None)
self.clearCat = BooleanOption(group.interior(), 2,
"clear group of previous pseudobonds", 1,
None)
self.leftModel = IntOption(group.interior(), 3,
"first column specifiers default to model",
0, None)
self.rightModel = IntOption(
group.interior(), 4, "second column specifiers default to model",
0, None)
def Apply(self):
if not self.getPaths():
replyobj.error("No pseudobond file chosen\n")
lineWidth = self.lineWidth.get()
prefs["line width"] = lineWidth
for path in self.getPaths():
readPBinfo(path,
category=self.catName.get(),
clearCategory=self.clearCat.get(),
lineWidth=lineWidth,
drawMode=None,
leftModel=str(self.leftModel.get()),
rightModel=str(self.rightModel.get()),
defColor=None)
def fillInUI(self, parent): from chimera.widgets import MoleculeScrolledListBox self.molListBox = MoleculeScrolledListBox(parent, listbox_selectmode='extended', labelpos='w', label_text="Molecules to combine/copy:") if self.initModels: self.molListBox.setvalue(self.initModels) self.molListBox.grid(row=0, column=0, columnspan=2, sticky="nsew") parent.rowconfigure(0, weight=1) parent.columnconfigure(1, weight=1) from chimera.tkoptions import StringOption, IntOption self.molNameEntry = StringOption(parent, 1, "New model's" " name", "combination", None) curIDs = set([i1 for i1, i2 in openModels.listIds()]) mid = 0 while mid in curIDs: mid += 1 self.modelID = IntOption(parent, 2, "New model's ID", mid, None) from chimera.widgets import MoleculeOptionMenu self.refMolMenu = MoleculeOptionMenu(parent, labelpos='w', label_text="Coordinate system of:", initialitem=self.initModels[0]) self.refMolMenu.grid(row=3, column=0, columnspan=2, sticky='w') import Pmw chb = self.chainHandlingButtons = Pmw.RadioSelect(parent, buttontype="radiobutton", labelpos='w', label_text="If original molecules have duplicate\n" "single-letter chain IDs, then:", orient="vertical") self.buttonTexts = ["rename them uniquely", "retain them (residues may be renumbered)"] for bt in self.buttonTexts: chb.add(bt) chb.setvalue(self.buttonTexts[0]) chb.grid(row=4, column=0, columnspan=2) import Tkinter self.closeModelsVar = Tkinter.IntVar(parent) self.closeModelsVar.set(False) Tkinter.Checkbutton(parent, text="Close source models", variable=self.closeModelsVar).grid( row=5, column=0, columnspan=2)
def fillInUI(self, parent): OpenModeless.fillInUI(self, parent) group = Pmw.Group(self.clientArea, tag_text='Further info') group.grid(row=0, column=0, sticky='nsew') self.catName = StringOption(group.interior(), 0, "group name", None, None) class PBLineWidthOption(LineWidthOption): default = prefs["line width"] balloon = "Width of pseudobonds (in pixels)" self.lineWidth = PBLineWidthOption(group.interior(), 1, None, None, None) self.clearCat = BooleanOption(group.interior(), 2, "clear group of previous pseudobonds", 1, None) self.leftModel = IntOption(group.interior(), 3, "first column specifiers default to model", 0, None) self.rightModel = IntOption(group.interior(), 4, "second column specifiers default to model", 0, None)
class PBreaderDialog(OpenModeless):
title = "Pseudobond Reader"
help = "ContributedSoftware/pbreader/pbreader.html"
def __init__(self):
OpenModeless.__init__(self, title="Pseudobond File to Read",
historyID="PBReader open", clientPos='s')
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
group = Pmw.Group(self.clientArea, tag_text='Further info')
group.grid(row=0, column=0, sticky='nsew')
self.catName = StringOption(group.interior(), 0,
"group name", None, None)
class PBLineWidthOption(LineWidthOption):
default = prefs["line width"]
balloon = "Width of pseudobonds (in pixels)"
self.lineWidth = PBLineWidthOption(group.interior(), 1, None,
None, None)
self.clearCat = BooleanOption(group.interior(), 2,
"clear group of previous pseudobonds", 1, None)
self.leftModel = IntOption(group.interior(), 3,
"first column specifiers default to model", 0, None)
self.rightModel = IntOption(group.interior(), 4,
"second column specifiers default to model", 0, None)
def Apply(self):
if not self.getPaths():
replyobj.error("No pseudobond file chosen\n")
lineWidth = self.lineWidth.get()
prefs["line width"] = lineWidth
for path in self.getPaths():
readPBinfo(path, category=self.catName.get(),
clearCategory=self.clearCat.get(),
lineWidth=lineWidth, drawMode=None,
leftModel=str(self.leftModel.get()),
rightModel=str(self.rightModel.get()),
defColor=None)
class NewAnnotationDialog(ModelessDialog):
title = "New Annotation"
buttons = ('OK', 'Cancel')
default = 'OK'
help = "ContributedSoftware/multalignviewer/multalignviewer.html#anno-ali"
def __init__(self, noteDialog):
self.noteDialog = noteDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.tkoptions \
import StringOption
self.noteOption = StringOption(parent,
0, "New annotation name", "",
None)
def Apply(self):
name = self.noteOption.get().strip()
if not name:
self.enter()
from chimera import UserError
raise UserError("No annotation"
" name specified")
self.noteDialog._addAttrWidgets(name,"")
self.uiMaster().update_idletasks()
top, bottom = self.noteDialog.attrFrame\
.yview()
if bottom < 1.0:
newTop = top + 1.0 - bottom
self.noteDialog.attrFrame.yview(
mode='moveto',
value=newTop)
self.noteDialog.attrWidgets[name][1]\
.focus()
def destroy(self):
self.noteDialog = None
ModelessDialog.destroy(self)
class VolumeDialog(ModelessDialog):
title = "Volume Map Selection"
buttons = ("OK", "Apply", "Close")
help = "ContributedSoftware/rotamers/rotamers.html#density"
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter
row = 0
from VolumeViewer import Volume_Menu
self.volumeMenu = Volume_Menu(parent, 'Volume data',
open_button=True)
self.volumeMenu.frame.grid(row=row, columnspan=2)
row += 1
from chimera.tkoptions import StringOption
self.nameOption = StringOption(parent, row, 'Column name',
'Density', None, width=10)
row += 1
def Apply(self):
from chimera import UserError
dr = self.volumeMenu.data_region()
if not dr:
self.enter()
raise UserError("No volume chosen")
name = self.nameOption.get().strip()
if not name:
self.enter()
raise UserError("Column name must not be blank")
self.rotDialog.addVolumeColumn(name, dr)
def destroy(self):
self.rotDialog = None
ModelessDialog.destroy(self)
class NewAnnotationDialog(ModelessDialog):
title = "New Annotation"
buttons = ('OK', 'Cancel')
default = 'OK'
help = "ContributedSoftware/multalignviewer/multalignviewer.html#anno-ali"
def __init__(self, noteDialog):
self.noteDialog = noteDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.tkoptions \
import StringOption
self.noteOption = StringOption(parent, 0,
"New annotation name", "",
None)
def Apply(self):
name = self.noteOption.get().strip()
if not name:
self.enter()
from chimera import UserError
raise UserError("No annotation" " name specified")
self.noteDialog._addAttrWidgets(name, "")
self.uiMaster().update_idletasks()
top, bottom = self.noteDialog.attrFrame\
.yview()
if bottom < 1.0:
newTop = top + 1.0 - bottom
self.noteDialog.attrFrame.yview(mode='moveto',
value=newTop)
self.noteDialog.attrWidgets[name][1]\
.focus()
def destroy(self):
self.noteDialog = None
ModelessDialog.destroy(self)
class VolumeDialog(ModelessDialog):
title = "Calculate Atomic Occupancy"
help = "ContributedSoftware/movie/movie.html#occupancy"
provideStatus = True
statusPosition = "left"
buttons = ('OK', 'Close')
default = 'OK'
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def map(self, e=None):
if not self.movie.holdingSteady:
self.status("No atoms being held steady -- see Help", color="red")
def fillInUI(self, parent):
Tkinter.Label(parent,
text="Collect positions of selected"
" atoms over trajectory",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.doCutoff = BooleanOption(
parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms', True,
None)
self.cutoff = FloatOption(parent,
5,
"Cutoff distance",
prefs[VOLUME_CUTOFF],
None,
width=4)
self.resolution = FloatOption(parent,
6,
"Volume grid spacing",
prefs[VOLUME_RESOLUTION],
None,
min=0.0001,
width=4)
self.volumeName = StringOption(parent,
7,
"Volume data name",
self.movie.ensemble.name,
None,
width=20)
self.byAtomType = BooleanOption(
parent,
8, "Collect data"
" separately for each atom type in selection",
True,
None,
balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
def Apply(self):
from chimera import UserError
atoms = chimera.selection.currentAtoms()
if not atoms:
self.enter()
raise UserError("No atoms selected")
startFrame = self.startFrame.get()
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less" " than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside" " of trajectory")
if self.doCutoff.get():
bound = prefs[VOLUME_CUTOFF] = self.cutoff.get()
else:
bound = None
prefs[VOLUME_RESOLUTION] = self.resolution.get()
step = self.stride.get()
spacing = self.resolution.get()
name = self.volumeName.get()
atomTypes = {}
if self.byAtomType.get():
for a in atoms:
atomTypes.setdefault(a.idatmType, []).append(a)
if len(atomTypes) > 1:
for atomType, atAtoms in atomTypes.items():
self.movie.computeVolume(atAtoms,
startFrame=startFrame,
endFrame=endFrame,
step=step,
bound=bound,
spacing=spacing,
volumeName=name + " [" + atomType +
"]")
else:
self.movie.computeVolume(atoms,
startFrame=startFrame,
endFrame=endFrame,
step=step,
bound=bound,
spacing=spacing,
volumeName=name)
def fillInUI(self, parent): from chimera.tkoptions \ import StringOption self.noteOption = StringOption(parent, 0, "New annotation name", "", None)
def fillInUI(self, parent):
Tkinter.Label(parent,
text="Collect positions of selected"
" atoms over trajectory",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.doCutoff = BooleanOption(
parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms', True,
None)
self.cutoff = FloatOption(parent,
5,
"Cutoff distance",
prefs[VOLUME_CUTOFF],
None,
width=4)
self.resolution = FloatOption(parent,
6,
"Volume grid spacing",
prefs[VOLUME_RESOLUTION],
None,
min=0.0001,
width=4)
self.volumeName = StringOption(parent,
7,
"Volume data name",
self.movie.ensemble.name,
None,
width=20)
self.byAtomType = BooleanOption(
parent,
8, "Collect data"
" separately for each atom type in selection",
True,
None,
balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
class VolumeDialog(ModelessDialog):
title = "Calculate Atomic Occupancy"
help = "ContributedSoftware/movie/movie.html#occupancy"
provideStatus = True
statusPosition = "left"
buttons = ('OK', 'Close')
default= 'OK'
def __init__(self, movie):
self.movie = movie
movie.subdialogs.append(self)
ModelessDialog.__init__(self)
def map(self, e=None):
if not self.movie.holdingSteady:
self.status("No atoms being held steady -- see Help",
color="red")
def fillInUI(self, parent):
Tkinter.Label(parent, text="Collect positions of selected"
" atoms over trajectory", relief="ridge", bd=4).grid(
row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent, 1, "Starting frame",
startFrame, None, min=startFrame, max=endFrame, width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames/300)
self.stride = IntOption(parent, 2, "Step size", defStride,
None, min=1, max=numFrames, width=3)
self.endFrame = IntOption(parent, 3, "Ending frame", endFrame,
None, min=startFrame, max=endFrame, width=6)
self.doCutoff = BooleanOption(parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms',
True, None)
self.cutoff = FloatOption(parent, 5, "Cutoff distance",
prefs[VOLUME_CUTOFF], None, width=4)
self.resolution = FloatOption(parent, 6, "Volume grid spacing",
prefs[VOLUME_RESOLUTION], None, min=0.0001, width=4)
self.volumeName = StringOption(parent, 7, "Volume data name",
self.movie.ensemble.name, None, width=20)
self.byAtomType = BooleanOption(parent, 8, "Collect data"
" separately for each atom type in selection",
True, None, balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")
def Apply(self):
from chimera import UserError
atoms = chimera.selection.currentAtoms()
if not atoms:
self.enter()
raise UserError("No atoms selected")
startFrame = self.startFrame.get()
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less"
" than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside"
" of trajectory")
if self.doCutoff.get():
bound = prefs[VOLUME_CUTOFF] = self.cutoff.get()
else:
bound = None
prefs[VOLUME_RESOLUTION] = self.resolution.get()
step = self.stride.get()
spacing = self.resolution.get()
name = self.volumeName.get()
atomTypes = {}
if self.byAtomType.get():
for a in atoms:
atomTypes.setdefault(a.idatmType, []).append(a)
if len(atomTypes) > 1:
for atomType, atAtoms in atomTypes.items():
self.movie.computeVolume(atAtoms,
startFrame=startFrame,
endFrame=endFrame, step=step,
bound=bound, spacing=spacing,
volumeName=name+" ["+atomType+"]")
else:
self.movie.computeVolume(atoms, startFrame=startFrame,
endFrame=endFrame, step=step, bound=bound,
spacing=spacing, volumeName=name)
class AssessDialog(ModelessDialog):
"""Dialog to allow the user to show regions that are matched
closely or that are poorly matched
"""
buttons = ("OK", "Close")
default = "OK"
help = "ContributedSoftware/multalignviewer/multalignviewer.html" \
"#assessment"
def __init__(self, mav, *args, **kw):
self.mav = mav
self.title = "Show Match Quality for %s" % mav.title
ModelessDialog.__init__(self, *args, **kw)
def fillInUI(self, parent):
self.refMenu = Pmw.OptionMenu(parent,
command=self._newRefCB,
labelpos="nw",
label_text="Reference structure:")
self.refMenu.grid(row=0, column=0)
self.alignList = Pmw.ScrolledListBox(
parent,
items=[],
labelpos="nw",
listbox_height=6,
label_text="Structures to evaluate:",
listbox_exportselection=0,
listbox_selectmode='extended')
self.alignList.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
subFrame = Tkinter.Frame(parent)
subFrame.grid(row=2, column=0)
from chimera.tkoptions import StringOption
self.attrNameOption = StringOption(
subFrame,
2,
"Create residue attribute named",
"matchDist",
None,
balloon="Create a residue attribute"
" measuring the CA/C4' distance between\nreference and"
" evaluated structures. The attribute will be shown\n"
"in the select-by-attribute dialog after you hit OK.")
Tkinter.Label(parent,
text="The attribute-selection dialog will"
" display when OK is chosen").grid(row=3, column=0)
self.refresh(initial=1)
self.assocHandlerID = self.mav.triggers.addHandler(
MOD_ASSOC, self.refresh, None)
def destroy(self):
self.mav.triggers.deleteHandler(MOD_ASSOC, self.assocHandlerID)
self.mav = None
ModelessDialog.destroy(self)
def refresh(self, trig1=None, trig2=None, trig3=None, initial=0):
self.matchMaps = {}
self.mols = {}
sortableNames = []
for aseq in self.mav.seqs:
if not hasattr(aseq, 'matchMaps'):
continue
for mol, matchMap in aseq.matchMaps.items():
name = "%s (%s), %s" % (mol.name, mol.oslIdent(),
matchMap['mseq'].name)
sortableNames.append((mol.oslIdent(), name))
self.matchMaps[name] = matchMap
self.mols[name] = mol
if len(sortableNames) < 2:
self.mav._disableAssessDialog()
return
sortableNames.sort(oslModelCmp)
self.names = []
for osl, name in sortableNames:
self.names.append(name)
if initial:
self.refMenu.setitems(self.names)
self._newRefCB(self.names[0])
else:
refsel = self.refMenu.getvalue()
if refsel in self.names:
selItem = refsel
else:
selItem = self.names[0]
self.refMenu.setitems(self.names, index=selItem)
self._newRefCB(selItem)
def Apply(self):
from chimera import UserError
attrName = self.attrNameOption.get()
from chimera.misc import stringToAttr
fixedAttrName = stringToAttr(attrName, collapse=False)
if fixedAttrName != attrName:
self.enter()
raise UserError("Attribute name must be composed only"
" of letters, digits, and underscores and must"
" not start with a digit.")
refName = self.refMenu.getvalue()
sels = self.alignList.getcurselection()
if len(sels) == 0:
self.enter()
raise UserError('Select at least one evaluation '
'structure to assess')
refMol = self.mols[refName]
evalMols = []
for sel in sels:
evalMols.append(self.mols[sel])
self.mav.assessMatch(refMol, evalMols, attrName)
from chimera import dialogs
from ShowAttr import ShowAttrDialog
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=evalMols,
attrsOf="residues",
attrName=attrName,
mode="Select")
def _newRefCB(self, ref):
self.alignList.setlist([n for n in self.names if n != ref])
lb = self.alignList.component("listbox")
lb.selection_set(0, 'end')
class RecorderDialog(SaveModeless):
title = "Record Animation of Trajectory"
help = "ContributedSoftware/movie/movie.html#recording"
default = "Record"
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 map(self, e=None):
from MovieRecorder import checkLicense
if not checkLicense():
self.Close()
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)
def Apply(self):
from chimera import UserError
startFrame = self.startFrame.get()
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less" " than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside" " of trajectory")
path, format = self.getPathsAndTypes()[0]
prefs[RECORDER_FORMAT] = format
recordArgs = self.recordArgs.get()
prefs[RECORDER_RECORD_ARGS] = recordArgs
encodeArgs = self.encodeArgs.get()
prefs[RECORDER_ENCODE_ARGS] = encodeArgs
roundtrip = self.roundtrip.get()
prefs[RECORDER_ROUNDTRIP] = roundtrip
supersample = self.supersample.get()
prefs[RECORDER_SUPERSAMPLE] = supersample
if supersample:
samples = self.samples.get()
prefs[RECORDER_SAMPLES] = samples
recordArgs = " ".join([recordArgs, "supersample", str(samples)])
raytrace = self.raytrace.get()
prefs[RECORDER_RAYTRACE] = raytrace
from MovieRecorder import RecorderGUI
for ext, fmtInfo in RecorderGUI.command_formats.items():
if fmtInfo[0] == format:
break
recordArgs = " ".join([recordArgs, "raytrace", str(raytrace)])
reprPath = repr(path)
if reprPath[0] == 'u':
# strip unicode indicator
reprPath = reprPath[1:]
encodeArgs = " ".join([
encodeArgs, "roundtrip",
str(roundtrip), "mformat", ext, "output", reprPath
])
self.movie.recordAnimation(startFrame=startFrame,
endFrame=endFrame,
step=self.stride.get(),
recordArgs=recordArgs,
encodeArgs=encodeArgs)
Record = SaveModeless.Save
def supersampleCB(self, *args):
if self.supersample.get():
self.samples.enable()
else:
self.samples.disable()
def fillInUI(self, parent): from chimera.tkoptions import StringOption self.renameOpt = StringOption(parent, 0, "Rename region to", "", None)
def fillInUI(self, parent): from chimera.tkoptions import StringOption self.renameOpt = StringOption(parent, 0, "Rename %s to" % self.item.name, "", None)
class CreatePlaneDialog(ModelessDialog):
title = "Define Plane"
help = "ContributedSoftware/structuremeas/structuremeas.html#define-plane"
provideStatus = True
statusPosition = "above"
def fillInUI(self, parent):
import Pmw, Tkinter
row = 0
Tkinter.Label(parent, text="Create plane for selected atoms...").grid(
row=row, columnspan=2)
row += 1
from chimera.tkoptions import StringOption, BooleanOption
self.nameOpt = StringOption(parent, row, "Plane name", "plane", None)
row += 1
self.replaceExistingOpt = BooleanOption(parent, row,
"Replace existing planes", False, None)
row += 1
from chimera.tkoptions import ColorOption, FloatOption
self.colorOpt = ColorOption(parent, row, "Color", None, None,
balloon="Plane color. If No Color, then the plane"
" will be colored to match the structure")
row += 1
self.autoRadiusOpt = BooleanOption(parent, row,
"Set disk size to enclose atom projections", True, self._radCB)
row += 1
self.radRow = row
self.radOffsetOpt = FloatOption(parent, row, "Extra radius"
" (padding)", 0.0, None)
self.radiusOpt = FloatOption(parent, row, "Fixed radius", 10.0, None)
self.radiusOpt.forget()
row += 1
self.thicknessOpt = FloatOption(parent, row, "Disk thickness",
prefs[PLANE_THICKNESS], None)
def Apply(self):
from chimera import UserError
if self.replaceExistingOpt.get():
planeManager.removePlanes(planeManager.planes)
kw = {
'color': self.colorOpt.get(),
'thickness': self.thicknessOpt.get()
}
prefs[PLANE_THICKNESS] = kw['thickness']
if self.autoRadiusOpt.get():
kw['radiusOffset'] = self.radOffsetOpt.get()
else:
kw['radius'] = self.radiusOpt.get()
replyobj.info("Creating plane\n")
selAtoms = selection.currentAtoms()
if len(selAtoms) < 3:
self.enter()
raise UserError("Need to select at least three"
" atoms to define a plane")
planeManager.createPlane(self.nameOpt.get().strip(), selAtoms, **kw)
def _radCB(self, opt):
if opt.get():
self.radiusOpt.forget()
self.radOffsetOpt.manage()
else:
self.radOffsetOpt.forget()
self.radiusOpt.manage()
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)
class RecorderDialog(SaveModeless):
title = "Record Animation of Trajectory"
help = "ContributedSoftware/movie/movie.html#recording"
default = "Record"
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 map(self, e=None):
from MovieRecorder import checkLicense
if not checkLicense():
self.Close()
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)
def Apply(self):
from chimera import UserError
startFrame = self.startFrame.get()
endFrame = self.endFrame.get()
if endFrame <= startFrame:
self.enter()
raise UserError("Start frame must be less"
" than end frame")
if startFrame < self.movie.startFrame \
or endFrame > self.movie.endFrame:
self.enter()
raise UserError("Start or end frame outside"
" of trajectory")
path, format = self.getPathsAndTypes()[0]
prefs[RECORDER_FORMAT] = format
recordArgs = self.recordArgs.get()
prefs[RECORDER_RECORD_ARGS] = recordArgs
encodeArgs = self.encodeArgs.get()
prefs[RECORDER_ENCODE_ARGS] = encodeArgs
roundtrip = self.roundtrip.get()
prefs[RECORDER_ROUNDTRIP] = roundtrip
supersample = self.supersample.get()
prefs[RECORDER_SUPERSAMPLE] = supersample
if supersample:
samples = self.samples.get()
prefs[RECORDER_SAMPLES] = samples
recordArgs = " ".join([recordArgs,
"supersample", str(samples)])
raytrace = self.raytrace.get()
prefs[RECORDER_RAYTRACE] = raytrace
from MovieRecorder import RecorderGUI
for ext, fmtInfo in RecorderGUI.command_formats.items():
if fmtInfo[0] == format:
break
recordArgs = " ".join([recordArgs, "raytrace", str(raytrace)])
reprPath = repr(path)
if reprPath[0] == 'u':
# strip unicode indicator
reprPath = reprPath[1:]
encodeArgs = " ".join([encodeArgs, "roundtrip", str(roundtrip),
"mformat", ext, "output", reprPath])
self.movie.recordAnimation(startFrame=startFrame,
endFrame=endFrame, step=self.stride.get(),
recordArgs=recordArgs, encodeArgs=encodeArgs)
Record = SaveModeless.Save
def supersampleCB(self, *args):
if self.supersample.get():
self.samples.enable()
else:
self.samples.disable()
class AssessDialog(ModelessDialog):
"""Dialog to allow the user to show regions that are matched
closely or that are poorly matched
"""
buttons = ("OK", "Close")
default = "OK"
help = "ContributedSoftware/multalignviewer/multalignviewer.html" \
"#assessment"
def __init__(self, mav, *args, **kw):
self.mav = mav
self.title = "Show Match Quality for %s" % mav.title
ModelessDialog.__init__(self, *args, **kw)
def fillInUI(self, parent):
self.refMenu = Pmw.OptionMenu(parent, command=self._newRefCB,
labelpos="nw", label_text="Reference structure:")
self.refMenu.grid(row=0, column=0)
self.alignList = Pmw.ScrolledListBox(parent, items=[],
labelpos="nw", listbox_height=6,
label_text="Structures to evaluate:",
listbox_exportselection=0,
listbox_selectmode='extended')
self.alignList.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
subFrame = Tkinter.Frame(parent)
subFrame.grid(row=2, column=0)
from chimera.tkoptions import StringOption
self.attrNameOption = StringOption(subFrame, 2,
"Create residue attribute named", "matchDist", None,
balloon="Create a residue attribute"
" measuring the CA/C4' distance between\nreference and"
" evaluated structures. The attribute will be shown\n"
"in the select-by-attribute dialog after you hit OK.")
Tkinter.Label(parent, text="The attribute-selection dialog will"
" display when OK is chosen").grid(row=3, column=0)
self.refresh(initial=1)
self.assocHandlerID = self.mav.triggers.addHandler(MOD_ASSOC,
self.refresh, None)
def destroy(self):
self.mav.triggers.deleteHandler(MOD_ASSOC, self.assocHandlerID)
self.mav = None
ModelessDialog.destroy(self)
def refresh(self, trig1=None, trig2=None, trig3=None, initial=0):
self.matchMaps = {}
self.mols = {}
sortableNames = []
for aseq in self.mav.seqs:
if not hasattr(aseq, 'matchMaps'):
continue
for mol, matchMap in aseq.matchMaps.items():
name = "%s (%s), %s" % (mol.name,
mol.oslIdent(), matchMap['mseq'].name)
sortableNames.append((mol.oslIdent(), name))
self.matchMaps[name] = matchMap
self.mols[name] = mol
if len(sortableNames) < 2:
self.mav._disableAssessDialog()
return
sortableNames.sort(oslModelCmp)
self.names = []
for osl, name in sortableNames:
self.names.append(name)
if initial:
self.refMenu.setitems(self.names)
self._newRefCB(self.names[0])
else:
refsel = self.refMenu.getvalue()
if refsel in self.names:
selItem = refsel
else:
selItem = self.names[0]
self.refMenu.setitems(self.names, index=selItem)
self._newRefCB(selItem)
def Apply(self):
from chimera import UserError
attrName = self.attrNameOption.get()
from chimera.misc import stringToAttr
fixedAttrName = stringToAttr(attrName, collapse=False)
if fixedAttrName != attrName:
self.enter()
raise UserError("Attribute name must be composed only"
" of letters, digits, and underscores and must"
" not start with a digit.")
refName = self.refMenu.getvalue()
sels = self.alignList.getcurselection()
if len(sels) == 0:
self.enter()
raise UserError('Select at least one evaluation '
'structure to assess')
refMol = self.mols[refName]
evalMols = []
for sel in sels:
evalMols.append(self.mols[sel])
self.mav.assessMatch(refMol, evalMols, attrName)
from chimera import dialogs
from ShowAttr import ShowAttrDialog
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=evalMols, attrsOf="residues",
attrName=attrName, mode="Select")
def _newRefCB(self, ref):
self.alignList.setlist([n for n in self.names if n != ref])
lb = self.alignList.component("listbox")
lb.selection_set(0, 'end')
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)
def fillInUI(self, parent):
from chimera.tkoptions \
import StringOption
self.noteOption = StringOption(parent, 0,
"New annotation name", "",
None)