def get(image, master, allowRelativePath=False):
"""Get image from standard locations.
get(image, master) => TkImage
image can be either a filename (or URL) or a Image.Image. Filenames
are searched for by chimera.pathFinder(). Master is the widget the
result TkImage will be created for. The master is needed for the Tk
interpreter to place the image in and to find out the background color
to blend the image with if it is semi-transparent.
"""
if isinstance(image, basestring):
import os.path
if allowRelativePath or os.path.isabs(image):
filename = image
else:
filename = chimera.pathFinder().firstExistingFile(
"chimera",
os.path.join("images", image),
False, False)
if not filename:
import errno
raise IOError(errno.ENOENT,
os.strerror(errno.ENOENT), image)
try:
image = Image.open(filename)
except IOError, e:
# PIL's IOError is missing the filename
e = IOError(*(e.args + (filename,)))
raise e
def create():
global root
global _reply
global splash
root = Tk.Tk(screenName=chimera.screen, className=chimera.AppName,
sync=chimera.debug)
splash = Tk.Frame(root, background="white")
splash.columnconfigure(0, weight=1)
splash.columnconfigure(2, weight=1)
splash.rowconfigure(0, weight=1)
root.title(chimera.title)
if chimera.geometry:
root.geometry(chimera.geometry)
splash.master.protocol("WM_DELETE_WINDOW", _earlyExit)
status = Tk.Label(splash, background="white", foreground="black",
font="Helvetica -14 italic", anchor=Tk.W,
justify=Tk.LEFT, borderwidth=0, text='startup status')
status.grid(row=1, column=0, columnspan=2, sticky=Tk.EW)
import chimage
icon = chimage.get('chimera48.png', splash)
logo = Tk.Label(splash, image=icon, borderwidth=0)
logo.__image = icon
logo.grid(row=0, column=0, sticky=Tk.E)
icon = chimage.get('titleChimera.png', root)
title = Tk.Label(splash, image=icon, borderwidth=0)
title.__image = icon
title.grid(row=0, column=1, sticky=Tk.EW)
icon2 = chimage.get('brand.png', root)
brand = Tk.Label(splash, image=icon2, borderwidth=0)
brand.__image = icon2
brand.grid(row=0, rowspan=2, column=2, sticky=Tk.W)
winsys = splash.tk.call('tk', 'windowingsystem')
if winsys == 'win32':
import os.path
filename = chimera.pathFinder().firstExistingFile("chimera",
os.path.join("Icons", "chimera32.ico"),
False, False)
if filename:
# this requires Tcl/Tk 8.3.3 (or newer)
# top.wm_iconbitmap(filename)
root.tk.call('wm', 'iconbitmap', root._w, filename)
elif winsys == 'aqua':
# in Tk 8.5 (8.6 carbon?), need to set useCustomMDEF for
# images and colors in menus entries
splash.tk.call("set", "::tk::mac::useCustomMDEF", "1")
splash.tk.createcommand('::tk::mac::OpenDocument',
_openDocument)
splashReply = replyobj.SplashReply(status)
_reply = replyobj.pushReply(splashReply, takeStdout=0, takeStderr=0)
splash.pack(expand=True, fill=Tk.BOTH)
if not splash.winfo_viewable():
splash.wait_visibility()
def icon(self):
import chimera
import os.path
file = chimera.pathFinder().firstExistingFile(
"chimera", os.path.join("images", "sideview.png"), False, False)
if not file:
return None
return file
def icon(self):
import chimera
import os.path
file = chimera.pathFinder().firstExistingFile("chimera",
os.path.join("images", "sideview.png"),
False, False)
if not file:
return None
return file
def setup():
import StdTools
preferences.addCategory("Tools", ToolsCategory, aliases=["Extensions"],
manager=manager)
manager.loadDirectory(chimera.pathFinder().dataRoot)
StdTools.registerStandardTools()
if chimera.nogui:
return
manager.createMenu()
manager.showToolbarButtons()
def _getCacheDir():
global _cacheDir
if _cacheDir is None:
import chimera
pf = chimera.pathFinder()
paths = pf.pathList("", "ccdcache", False, False, True)
if paths:
_cacheDir = paths[0]
else:
_cacheDir = ""
return _cacheDir
def _getCacheDir():
global _cacheDir
if _cacheDir is None:
import chimera
pf = chimera.pathFinder()
paths = pf.pathList("", "ccdcache", False, False, True)
if paths:
_cacheDir = paths[0]
else:
_cacheDir = ""
return _cacheDir
def __init__(self):
from chimera import pathFinder
import os.path
import SwishE
pf = pathFinder()
data_root = pf.dataRoot
idx_file = os.path.join(data_root,"chimera","helpdir","chimera-docs.idx")
self.index = idx_file
self.index = self.index.replace("\\","/")
self.swisher = SwishE.new(repr(self.index))
def setup():
import StdTools
preferences.addCategory("Tools",
ToolsCategory,
aliases=["Extensions"],
manager=manager)
manager.loadDirectory(chimera.pathFinder().dataRoot)
StdTools.registerStandardTools()
if chimera.nogui:
return
manager.createMenu()
manager.showToolbarButtons()
def checkRegistration(nag=1):
"Check registration status."
pf = chimera.pathFinder()
filenames = pf.allExistingFiles('', RegistrationFile)
if not filenames:
if nag:
return _checkUsage(pf)
else:
return
import x509
store = x509.CAStore()
smime = x509.SMIME(store)
for filename in filenames:
try:
text, signers = smime.verifyFile(filename)
except x509.error, emsg:
if emsg == 'Verify error:Certificate has expired':
replyobj.warning('Registration file "%s" '
'has expired.\n' % filename)
continue
valid = 0
for cert in signers:
fromUC = 0
fromCGL = 0
fields = string.split(cert.subject(), '/')
for f in fields:
if f == 'O=University of California, San Francisco':
fromUC = 1
elif f == 'OU=Computer Graphics Laboratory':
fromCGL = 1
if fromUC and fromCGL:
valid = 1
break
if not valid:
replyobj.warning('Registration file "%s" '
'is not signed by CGL.\n' % filename)
lines = string.split(text, '\r\n')
param = {}
for line in lines:
try:
key, value = map(string.strip, string.split(line, ':'))
except ValueError:
pass
else:
param[key] = value
if param.has_key('Expires') \
and time.time() > float(param['Expires']):
replyobj.warning('Registration file "%s" '
'has expired.\n' % filename)
# Other parameter-dependent processing can go here
return param
def __init__(self):
from chimera import pathFinder
import os.path
import SwishE
pf = pathFinder()
data_root = pf.dataRoot
idx_file = os.path.join(data_root, "chimera", "helpdir",
"chimera-docs.idx")
self.index = idx_file
self.index = self.index.replace("\\", "/")
self.swisher = SwishE.new(repr(self.index))
def __init__(self):
dataFile = chimera.pathFinder().firstExistingFile("ResProp",
"schemaData.py", 0, 1)
if not dataFile:
raise ImportError, "Could not find schema data file"
execfile(dataFile)
for name, colorScheme in self.colorSchemes.items():
if _oldSelMain in colorScheme:
for old, new in _translationDict.items():
colorScheme[new] = colorScheme[old]
del colorScheme[old]
for schema in self.schemas:
self.registerSchemaAsSelector(schema)
def __init__(self):
dataFile = chimera.pathFinder().firstExistingFile(
"ResProp", "schemaData.py", 0, 1)
if not dataFile:
raise ImportError, "Could not find schema data file"
execfile(dataFile)
for name, colorScheme in self.colorSchemes.items():
if _oldSelMain in colorScheme:
for old, new in _translationDict.items():
colorScheme[new] = colorScheme[old]
del colorScheme[old]
for schema in self.schemas:
self.registerSchemaAsSelector(schema)
def filenames():
import chimera
pf = chimera.pathFinder()
paths = pf.pathList("", "gfxinfo.txt")
paths = paths[:-1] # skip system location
paths.reverse()
for p in paths:
if os.path.isabs(p):
name = p
else:
name = os.path.abspath(paths[0])
base = os.path.splitext(name)[0]
save = base + '.sav'
return name, save
def filenames():
import chimera
pf = chimera.pathFinder()
paths = pf.pathList("", "gfxinfo.txt")
paths = paths[:-1] # skip system location
paths.reverse()
for p in paths:
if os.path.isabs(p):
name = p
else:
name = os.path.abspath(paths[0])
base = os.path.splitext(name)[0]
save = base + '.sav'
return name, save
def __init__(self):
pf = pathFinder()
img_src = os.path.join(pf.dataRoot, "DBPuppet", "image_bs.gif")
WizShell.__init__(self, 4, 450, 175, img_src, img_bg_color='black')
self.ftm = FileTypeMan.FileTypeMan()
self.configStatus = True
self.configStatusString = ''
self.createPanelOne()
self.createPanelTwo()
self.createPanelThree()
self.createPanelFour()
def __init__(self):
pf = pathFinder()
img_src = os.path.join(pf.dataRoot, "DBPuppet", "image_bs.gif")
WizShell.__init__(self, 4, 450, 175, img_src, img_bg_color='black')
self.ftm = FileTypeMan.FileTypeMan()
self.configStatus = True
self.configStatusString = ''
self.createPanelOne()
self.createPanelTwo()
self.createPanelThree()
self.createPanelFour()
def revertToDefaults(self):
# temporarily protect 'self' from the execfile()
s = self
class dummyClass:
pass
self = dummyClass()
dataFile = chimera.pathFinder().firstExistingFile("ResProp",
"schemaData.py", 0, 0)
if not dataFile:
raise ImportError, "Could not find schema data file"
execfile(dataFile)
data = self
self = s
for schema in data.schemas:
if schema in self.schemas:
self.deleteSchema(schema)
self.addSchema(schema, data.selections[schema],
data.colorSchemes[schema])
def __init__(self):
pf = chimera.pathFinder()
ROOT = pf.dataRoot
img_src = os.path.join(ROOT, "BugReport", "1bug1.png")
WizShell.__init__(self, 3, 200, 300, img_src, img_bg_color="white")
self.createIntroPanel()
if not self.checkConnection():
self.introText.configure(state='normal')
self.introText.delete(0.0, 'end')
self.introText.insert(0.0, "<font color=\"red\" size=\"+4\">"
"Can't find network connection!</font>"
"<p>Thank you for assisting us in the development process"
" by using our feedback submission system."
" It does not appear that you are connected to the internet."
" A network connection is needed in order to send the"
" feedback to the UCSF Computer Graphics Lab."
" Please try again when your computer is connected to a"
" network.</p>"
"<p>If you <i>do have</i> a network connection,"
" but use a proxy to connect to the web,"
" you can try configuring the proxy settings in the"
" <a href=\"python:import dialogs, chimera;dialogs.display('preferences')."
"setCategoryMenu(chimera.initprefs.WEBACCESS_PREF)\" "
"title=\"Click to open 'Web Access' preferences\"> "
"Web Access</a> preference category."
" More information on how to do this can be found in the"
" <a href=\"python:chimera.help.display('UsersGuide/preferences.html#Web Access')\""
" title=\"'Web Access' Preference category documentation\">"
" Preferences documentation</a>.</p>"
)
self.introText.configure(state='disabled')
self.buttonWidgets['Next'].configure(state='disabled')
self.buttonWidgets['Cancel'].configure(text='Try again later')
self.createReportPanel()
self.createResultPanel()
def __init__(self):
pf = chimera.pathFinder()
ROOT = pf.dataRoot
img_src = os.path.join(ROOT, "BugReport", "1bug1.png")
WizShell.__init__(self, 3, 200, 300, img_src, img_bg_color="white")
self.createIntroPanel()
if not self.checkConnection():
self.introText.configure(state='normal')
self.introText.delete(0.0, 'end')
self.introText.insert(
0.0, "<font color=\"red\" size=\"+4\">"
"Can't find network connection!</font>"
"<p>Thank you for assisting us in the development process"
" by using our feedback submission system."
" It does not appear that you are connected to the internet."
" A network connection is needed in order to send the"
" feedback to the UCSF Computer Graphics Lab."
" Please try again when your computer is connected to a"
" network.</p>"
"<p>If you <i>do have</i> a network connection,"
" but use a proxy to connect to the web,"
" you can try configuring the proxy settings in the"
" <a href=\"python:import dialogs, chimera;dialogs.display('preferences')."
"setCategoryMenu(chimera.initprefs.WEBACCESS_PREF)\" "
"title=\"Click to open 'Web Access' preferences\"> "
"Web Access</a> preference category."
" More information on how to do this can be found in the"
" <a href=\"python:chimera.help.display('UsersGuide/preferences.html#Web Access')\""
" title=\"'Web Access' Preference category documentation\">"
" Preferences documentation</a>.</p>")
self.introText.configure(state='disabled')
self.buttonWidgets['Next'].configure(state='disabled')
self.buttonWidgets['Cancel'].configure(text='Try again later')
self.createReportPanel()
self.createResultPanel()
def revertToDefaults(self):
# temporarily protect 'self' from the execfile()
s = self
class dummyClass:
pass
self = dummyClass()
dataFile = chimera.pathFinder().firstExistingFile(
"ResProp", "schemaData.py", 0, 0)
if not dataFile:
raise ImportError, "Could not find schema data file"
execfile(dataFile)
data = self
self = s
for schema in data.schemas:
if schema in self.schemas:
self.deleteSchema(schema)
self.addSchema(schema, data.selections[schema],
data.colorSchemes[schema])
def saveSchemas(self):
if not self.initialized:
return
saveLocs = chimera.pathFinder().pathList("ResProp",
"schemaData.py", 0, 0, 1)
for saveLoc in saveLocs:
if not os.path.exists(saveLoc):
# try to create
dirPath, fileName = os.path.split(saveLoc)
if not os.path.exists(dirPath):
try:
os.makedirs(dirPath)
except:
Pmw.MessageDialog(
title='Save Error',
message_text="Cannot create category save directory '%s'" % (dirPath))
return
try:
saveFile = open(saveLoc, 'w')
except IOError:
print "Cannot write to %s" % saveLoc
continue
saveFile.write("self.schemas = %s\n"
% repr(schemaMgr.schemas))
saveFile.write("self.residues = %s\n"
% repr(schemaMgr.residues))
saveFile.write("self.selections = %s\n"
% repr(schemaMgr.selections))
saveFile.write("self.colorSchemes = {}\n")
for schema in schemaMgr.schemas:
saveFile.write("self.colorSchemes['%s'] = %s\n"
% (schema,
repr(schemaMgr.colorSchemes[schema])))
saveFile.close()
return
Pmw.MessageDialog(message_text="Cannot save schema data.")
def saveSchemas(self):
if not self.initialized:
return
saveLocs = chimera.pathFinder().pathList("ResProp", "schemaData.py", 0,
0, 1)
for saveLoc in saveLocs:
if not os.path.exists(saveLoc):
# try to create
dirPath, fileName = os.path.split(saveLoc)
if not os.path.exists(dirPath):
try:
os.makedirs(dirPath)
except:
Pmw.MessageDialog(
title='Save Error',
message_text=
"Cannot create category save directory '%s'" %
(dirPath))
return
try:
saveFile = open(saveLoc, 'w')
except IOError:
print "Cannot write to %s" % saveLoc
continue
saveFile.write("self.schemas = %s\n" % repr(schemaMgr.schemas))
saveFile.write("self.residues = %s\n" % repr(schemaMgr.residues))
saveFile.write("self.selections = %s\n" %
repr(schemaMgr.selections))
saveFile.write("self.colorSchemes = {}\n")
for schema in schemaMgr.schemas:
saveFile.write("self.colorSchemes['%s'] = %s\n" %
(schema, repr(schemaMgr.colorSchemes[schema])))
saveFile.close()
return
Pmw.MessageDialog(message_text="Cannot save schema data.")
def __init__(self):
self.shown = 0
self.check_for_click = False
import tkgui
import Tkinter
f = Tkinter.Frame(tkgui.app)
self.frame = f
# Create ext widget for displaying messages
msg = Tkinter.Text(f, width = 0, height = 1,
borderwidth = 2, relief = 'ridge',
takefocus = False, cursor = 'left_ptr',
state = 'disabled')
msg.bind('<Map>', self.message_label_mapped_cb)
msg.grid(row = 0, column = 1, sticky = 'ew')
f.columnconfigure(1, weight = 1)
self.message_label = msg
# Read in static icons
import chimage
self.image_info = chimage.get("information_frame.png", f)
self.image_info_bw = chimage.get("information_frame_bw.png", f)
self.image_stop = chimage.get("cross_octagon_frame.png", f)
# Read in the selection icon, which is only in b/w because
# we want to tint it with the user selected highlight color.
# To do so, we need to have a PIL image to play with, so we
# cannot use chimage.
from CGLtk import textForeground
icon_name = "magnifier_left_%s.png" % textForeground(f["background"])
import chimera, os.path
filename = chimera.pathFinder().firstExistingFile("chimera",
os.path.join("images", icon_name),
False, False)
if not filename:
import errno, os
raise IOError(errno.ENOENT, os.strerror(errno.ENOENT), icon_name)
from PIL import Image
self.pil_selection = image = Image.open(filename)
self.image_selection_bw = remove_alpha(self.pil_selection, f)
self.image_selection = None # to be constructed later
# Create selection button
self.selections_button = Tkinter.Button(f, image=self.image_selection_bw,
command=self._sel_cb,
**button_opts)
self.selections_button.grid(row=0, column=3, **grid_opts)
self.selection_handler_ID = None
self.first_selection = True
# Create task buttons
self.task_info_button = Tkinter.Button(f, image=self.image_info_bw,
command=self._task_info_cb,
**button_opts)
self.task_info_button.grid(row=0, column=2, **grid_opts)
self.task_stop_button = Tkinter.Button(f, image=self.image_stop,
command=self._task_stop_cb,
**button_opts)
# Stop button is created here but grid'ed in only when needed
self.task_event_queue = []
self.task_stop_button.bind("<Key>", self._task_stop_key_handler)
self.task_stop_button.bind("<Button-1>", self._task_stop_button_handler)
# Create resize handle
import Ttk
sg = Ttk.Sizegrip(f)
sg.grid(row=0, column=4, sticky='se')
# Add help balloons to buttons
import help
help.register(self.selections_button, balloon="selection inspector")
help.register(self.task_info_button, balloon="task panel")
help.register(self.task_stop_button, balloon="cancel current task")
#
# Find a preferences file and load it
#
if chimera.preferencesFile is not None:
pf = None
if os.access(chimera.preferencesFile, os.R_OK):
filename = chimera.preferencesFile
preferences.load(filename)
else:
from chimera import replyobj
replyobj.error("File \"%s\" is not readable\n" %
chimera.preferencesFile)
filename = None
else:
pf = chimera.pathFinder()
files = pf.allExistingFiles("", PreferenceFile)
if files:
for filename in files:
try:
preferences.load(filename)
except IOError:
continue
except Exception, e:
from chimera import replyobj
replyobj.error(
'%s: %s.\n'
'Using factory default preference '
'settings.\n'
'The settings in the current '
'preferences file cannot be\n'
except ImportError:
pass
try:
# attempt to get main/side chain selectors registered
import chain
except ImportError:
pass
try:
# attempt to get surface category selectors registered
import Categorizer
except ImportError:
pass
# restore saved selectors
saveLoc = chimera.pathFinder().firstExistingFile(
"selectionGUI", "selectors", 0, 1)
if saveLoc:
try:
saveFile = open(saveLoc, 'r')
except:
replyobj.error("Cannot read existing selector save file '%s'\n"
% (saveLoc))
saveFile = None
if saveFile:
selMgr.integrateSelDict(eval(saveFile.read()))
del saveFile
del saveLoc
#
# Find a preferences file and load it
#
if chimera.preferencesFile is not None:
pf = None
if os.access(chimera.preferencesFile, os.R_OK):
filename = chimera.preferencesFile
preferences.load(filename)
else:
from chimera import replyobj
replyobj.error("File \"%s\" is not readable\n" %
chimera.preferencesFile)
filename = None
else:
pf = chimera.pathFinder()
files = pf.allExistingFiles("", PreferenceFile)
if files:
for filename in files:
try:
preferences.load(filename)
except IOError:
continue
except Exception, e:
from chimera import replyobj
replyobj.error('%s: %s.\n'
'Using factory default preference '
'settings.\n'
'The settings in the current '
'preferences file cannot be\n'
'applied until the file has been '
raise ValueError, "Line %d of %s is %s, " \
"expected %s" % (chars.index(char)+1,
fileName, fields[0], char)
for i in range(len(chars)):
matrix[(fields[0], chars[i])] = float(
fields[i+1])
mfile.close()
break
return matrix
import chimera
import os
matrices = {}
matrixFiles = {}
for dir in chimera.pathFinder().allExistingDirs("SmithWaterman", "matrices"):
for matrixFile in os.listdir(dir):
if matrixFile.endswith(".matrix"):
ftype = "protein"
name = matrixFile[:-7]
elif matrixFile.endswith(".dnamatrix"):
ftype = "dna"
name = matrixFile[:-10]
else:
continue
path = os.path.join(dir, matrixFile)
try:
matrices[name] = readMatrixFile(path, style=ftype)
except ValueError:
chimera.replyobj.reportException()
matrixFiles[name] = path
def __init__(self):
self.shown = 0
self.check_for_click = False
import tkgui
import Tkinter
f = Tkinter.Frame(tkgui.app)
self.frame = f
# Create ext widget for displaying messages
msg = Tkinter.Text(f,
width=0,
height=1,
borderwidth=2,
relief='ridge',
takefocus=False,
cursor='left_ptr',
state='disabled')
msg.bind('<Map>', self.message_label_mapped_cb)
msg.grid(row=0, column=1, sticky='ew')
f.columnconfigure(1, weight=1)
self.message_label = msg
# Read in static icons
import chimage
self.image_info = chimage.get("information_frame.png", f)
self.image_info_bw = chimage.get("information_frame_bw.png", f)
self.image_stop = chimage.get("cross_octagon_frame.png", f)
# Read in the selection icon, which is only in b/w because
# we want to tint it with the user selected highlight color.
# To do so, we need to have a PIL image to play with, so we
# cannot use chimage.
from CGLtk import textForeground
icon_name = "magnifier_left_%s.png" % textForeground(f["background"])
import chimera, os.path
filename = chimera.pathFinder().firstExistingFile(
"chimera", os.path.join("images", icon_name), False, False)
if not filename:
import errno, os
raise IOError(errno.ENOENT, os.strerror(errno.ENOENT), icon_name)
from PIL import Image
self.pil_selection = image = Image.open(filename)
self.image_selection_bw = remove_alpha(self.pil_selection, f)
self.image_selection = None # to be constructed later
# Create selection button
self.selections_button = Tkinter.Button(f,
image=self.image_selection_bw,
command=self._sel_cb,
**button_opts)
self.selections_button.grid(row=0, column=3, **grid_opts)
self.selection_handler_ID = None
self.first_selection = True
# Create task buttons
self.task_info_button = Tkinter.Button(f,
image=self.image_info_bw,
command=self._task_info_cb,
**button_opts)
self.task_info_button.grid(row=0, column=2, **grid_opts)
self.task_stop_button = Tkinter.Button(f,
image=self.image_stop,
command=self._task_stop_cb,
**button_opts)
# Stop button is created here but grid'ed in only when needed
self.task_event_queue = []
self.task_stop_button.bind("<Key>", self._task_stop_key_handler)
self.task_stop_button.bind("<Button-1>",
self._task_stop_button_handler)
# Create resize handle
import Ttk
sg = Ttk.Sizegrip(f)
sg.grid(row=0, column=4, sticky='se')
# Add help balloons to buttons
import help
help.register(self.selections_button, balloon="selection inspector")
help.register(self.task_info_button, balloon="task panel")
help.register(self.task_stop_button, balloon="cancel current task")
import residues
except ImportError:
pass
try:
# attempt to get main/side chain selectors registered
import chain
except ImportError:
pass
try:
# attempt to get surface category selectors registered
import Categorizer
except ImportError:
pass
# restore saved selectors
saveLoc = chimera.pathFinder().firstExistingFile("selectionGUI", "selectors",
0, 1)
if saveLoc:
try:
saveFile = open(saveLoc, 'r')
except:
replyobj.error("Cannot read existing selector save file '%s'\n" %
(saveLoc))
saveFile = None
if saveFile:
selMgr.integrateSelDict(eval(saveFile.read()))
del saveFile
del saveLoc
raise ValueError, "Line %d of %s is %s, " \
"expected %s" % (chars.index(char)+1,
fileName, fields[0], char)
for i in range(len(chars)):
matrix[(fields[0], chars[i])] = float(fields[i + 1])
mfile.close()
break
return matrix
import chimera
import os
matrices = {}
matrixFiles = {}
for dir in chimera.pathFinder().allExistingDirs("SmithWaterman", "matrices"):
for matrixFile in os.listdir(dir):
if matrixFile.endswith(".matrix"):
ftype = "protein"
name = matrixFile[:-7]
elif matrixFile.endswith(".dnamatrix"):
ftype = "dna"
name = matrixFile[:-10]
else:
continue
path = os.path.join(dir, matrixFile)
try:
matrices[name] = readMatrixFile(path, style=ftype)
except ValueError:
chimera.replyobj.reportException()
matrixFiles[name] = path