def transpSurf(amount):
if amount != -1:
aopacity = opacity = min(1.0, 1 - amount)
else:
opacity = 1
aopacity = -1
atoms = selAtoms()
import Midas
surfatoms = Midas.atomMSMSModels(atoms)
for s,atoms in surfatoms.items():
adjustMSMSTransparency(s, atoms, opacity, aopacity)
splist = selectedSurfacePieces(implied = True)
from chimera import MSMSModel
for p in splist:
s = p.model
if isinstance(s, MSMSModel) and s.molecule:
adjustMSMSTransparency(s, s.atoms, opacity, aopacity)
else:
adjustSurfacePieceTransparency(p, opacity)
if (len(atoms) > 0 and not selection.currentEmpty()
and len(surfatoms) == 0 and len(splist) == 0):
from replyobj import warning
warning('No surfaces shown for selected atoms.\n')
def transpSurf(amount):
if amount != -1:
aopacity = opacity = min(1.0, 1 - amount)
else:
opacity = 1
aopacity = -1
atoms = selAtoms()
import Midas
surfatoms = Midas.atomMSMSModels(atoms)
for s, atoms in surfatoms.items():
adjustMSMSTransparency(s, atoms, opacity, aopacity)
splist = selectedSurfacePieces(implied=True)
from chimera import MSMSModel
for p in splist:
s = p.model
if isinstance(s, MSMSModel) and s.molecule:
adjustMSMSTransparency(s, s.atoms, opacity, aopacity)
else:
adjustSurfacePieceTransparency(p, opacity)
if (len(atoms) > 0 and not selection.currentEmpty() and len(surfatoms) == 0
and len(splist) == 0):
from replyobj import warning
warning('No surfaces shown for selected atoms.\n')
def reregister(name, function):
"""Reregister dialog creation/display function
Same function variations allowed as in register.
"""
global _allDialogs
try:
dialog = _allDialogs[name]
_allDialogs[name] = function
except KeyError:
replyobj.warning("error dialog %s missing\n" % name)
def contextCB(app):
"""Display help for selected widget.
contextCB(app) => None
"""
rootX, rootY = chimera.viewer.trackingXY("help")
if rootX != -1:
# find widget that was under cursor
widget = app.winfo_containing(rootX, rootY)
if widget:
widget.event_generate('<<Help>>', rootx=rootX, rooty=rootY)
return
replyobj.warning('pick part of application to get context help\n')
def register(name, function, replace=0):
"""Register dialog creation/display function
The function is called with no arguments. The function
can also be a class, or an instance of a class. If it
is an instance, then the enter method is called.
"""
global _allDialogs
if not replace and _allDialogs.has_key(name):
replyobj.warning("error dialog %s already registered\n" % name)
return
_allDialogs[name] = function
def contextCB(app):
"""Display help for selected widget.
contextCB(app) => None
"""
rootX, rootY = chimera.viewer.trackingXY("help")
if rootX != -1:
# find widget that was under cursor
widget = app.winfo_containing(rootX, rootY)
if widget:
widget.event_generate('<<Help>>', rootx=rootX,
rooty=rootY)
return
replyobj.warning('pick part of application to get context help\n')
def display(name, wait=False):
"""Display the dialog with the given name.
The registered dialog display function is called.
If wait is true, then this function doesn't return
until the dialog is displayed.
The dialog instance is returned if available.
"""
if not _allDialogs.has_key(name):
replyobj.warning("no known dialog named: %s\n" % name)
return None
dialog = find(name, create=1)
if not callable(dialog) and hasattr(dialog, 'enter'):
dialog.enter()
if wait:
import _tkinter
import chimera.tkgui
chimera.tkgui.update_windows()
return dialog
def getSequences(molecule, asDict=False):
"""return all non-trivial sequences in a molecule
This function is also available as molecule.sequences(...)
returns a list of sequences for the given molecule, one sequence per
multi-residue chain. The sequence name is "Chain X" where X is
the chain ID, or "Principal chain" if there is no chain ID.
The 'residues' attribute of each sequence is a list of the
residues for that sequence, and the attribute 'resmap' is a
dictionary that maps residue to sequence position (zero-based).
The 'residues' attribute will self-delete if the corresponding
model is closed.
If 'asDict' is true, return a dictionary of Sequences keyed on
chain ID (can throw AssertionError if multiple chains have same ID),
otherwise return a list.
"""
from chimera import bondsBetween, openModels, triggers
from copy import copy
def connected(res1, res2):
if res1.id.chainId != ' ' \
and res1.id.chainId == res2.id.chainId \
and not res1.isHet and not res2.isHet:
return True
return bondsBetween(res1, res2, onlyOne=True)
if hasattr(molecule, '_SequenceSequences'):
seqList, seqDict, trigIDs = molecule._SequenceSequences
if asDict:
if seqDict is not None:
return copy(seqDict)
else:
return copy(seqList)
chain = None
prevRes = None
seqs = []
# don't start a sequence until we've seen two residues in the chain
for res in molecule.residues:
# if a residue has only one heavy atom, and that is connected
# to only one other heavy atom, then don't put the residue
# in the sequence
#
# if heavy is connected to no other heavy atom (presumably
# metal or ion), end the chain
atomLists = res.atomsMap.values()
# take only one atom in each list, to avoid counting
# alternate locations as multiple atoms
atoms = map(lambda l: l[0], atomLists)
heavys = filter(lambda a: a.element.number > 1, atoms)
chainBreak = prevRes == None
if len(heavys) == 0:
continue
# heavys more reliably connected than hydrogens
if prevRes and not connected(prevRes, res):
didMod = 0
if seq:
for sr in seq.residues:
if connected(sr, res):
didMod = 1
if didMod:
continue
chainBreak = 1
elif prevRes and prevRes.id == res.id and len(heavys) == 1:
continue
elif chain is not None:
# HET residues in named chains get the chain name,
# but in blank chains they get 'het' -- allow for this
truePrevID = chain
trueResID = res.id.chainId
if truePrevID != trueResID:
if truePrevID in (" ", "het"):
prevID = " "
else:
prevID = truePrevID
if trueResID in (" ", "het"):
resID = " "
else:
resID = trueResID
if resID != prevID:
chainBreak = 1
if chainBreak:
# if chain ID changes in middle of connected chain
# need to remember new chain ID...
chain = res.id.chainId
startRes = res
prevRes = res
seq = None
continue # to avoid starting single-residues chains
if not seq:
if not chain or chain == " ":
name = PRINCIPAL
chain = " "
else:
name = CHAIN_FMT % chain
seq = StructureSequence(startRes.molecule, name)
seq.chain = chain
seqs.append(seq)
seq.append(startRes)
seq.append(res)
prevRes = res
sd = {}
for seq in seqs[:]:
# set 'fromSeqres' in this loop so that all sequences have it
seq.fromSeqres = None
if seq.chain in sd:
# a sequence of all 'X' residues or all het loses
if str(seq).replace('X', ' ').isspace() \
or len([r for r in seq.residues if not r.isHet]) == 0:
seqs.remove(seq)
continue
elif str(sd[seq.chain]).replace('X', ' ').isspace() \
or len([r for r in sd[seq.chain].residues
if not r.isHet]) == 0:
seqs.remove(sd[seq.chain])
sd[seq.chain] = seq
continue
if asDict:
raise AssertionError("Multiple chains with"
" same ID: '%s'" % seq.chain)
sd = None
break
sd[seq.chain] = seq
# use full sequence if available...
seqresSeqs = seqresSequences(molecule, asDict=True)
for chain, seq in sd.items():
try:
srSeq = seqresSeqs[chain]
except (KeyError, TypeError):
continue
seq.fromSeqres = True
if len(srSeq) == len(seq):
# no adjustment needed
continue
if len(srSeq) < len(seq):
seq.fromSeqres = False
import replyobj
replyobj.warning("SEQRES record for chain %s of %s is incomplete.\n"
"Ignoring record as basis for sequence." % (chain, molecule))
continue
from MultAlignViewer.structAssoc import estimateAssocParams, tryAssoc
estLen, segments, gaps = estimateAssocParams(seq)
# if a jump in numbering is in an unresolved part of the
# structure, the estimated length can be too long...
estLen = min(estLen, len(srSeq))
try:
# since gapping a structure sequence is considered an
# "error", need to allow a lot more errors than normal...
matchMap, numErrors = tryAssoc(srSeq, seq, segments, gaps, estLen,
maxErrors=int(len(seq)/2))
except ValueError:
seq.fromSeqres = False
continue
for i in range(len(srSeq)):
if i in matchMap:
del matchMap[i]
else:
seq.residues.insert(i, None)
seq.resMap = matchMap
seq[:] = srSeq[:]
# try to avoid identical names
baseNames = {}
for seq in seqs:
baseNames.setdefault(seq.name, []).append(seq)
for baseName, sameNamedSeqs in baseNames.items():
if len(sameNamedSeqs) > 1:
for i, seq in enumerate(sameNamedSeqs):
seq.name += " [%d]" % (i+1)
if hasattr(molecule, '_SequenceSequences'):
# deregister from previous sequence's triggers...
# (don't destroy the old sequences, may be in use elsewhere)
seqList, seqDict, trigIDs = molecule._SequenceSequences
for i, seq in enumerate(seqList):
seq.triggers.deleteHandler(seq.TRIG_DELETE, trigIDs[i])
else:
# invalidate the sequences cache if residues added/deleted
molecule.__cacheHandlerID = triggers.addHandler('Residue',
_invalidateCacheCB, molecule)
# register for current sequence's triggers
trigIDs = []
for seq in seqs:
trigIDs.append(
seq.triggers.addHandler(seq.TRIG_DELETE, _delSeq, None))
molecule._SequenceSequences = (seqs, sd, trigIDs)
if asDict:
return copy(sd)
return copy(seqs)
def display(widgetOrURL, package=chimera, newWindow=False):
"""Display given html help file.
display(widgetOrURL, package=chimera, newWindow=False) => None
The url may be either a string, or a "widget" that has been
registered. In the latter case it is mapped according to
how it was registered.
"""
try:
# compensate for Pmw megawidgets not being Tk widgets
widgetOrURL = widgetOrURL.component('hull')
except:
pass
if isinstance(widgetOrURL, basestring):
url = widgetOrURL
elif hasattr(widgetOrURL, 'winfo_parent'):
# show help associated with widget or parent widget
while widgetOrURL:
if _helpMap.has_key(widgetOrURL):
url, package = _helpMap[widgetOrURL]
break
parent = widgetOrURL.winfo_parent()
if not isinstance(parent, str):
widgetOrURL = parent
elif parent == "":
widgetOrURL = None
else:
widgetOrURL = widgetOrURL._nametowidget(parent)
if not widgetOrURL:
replyobj.warning('internal error -- no help found for widget\n')
return
elif isinstance(widgetOrURL, tuple):
url, package = widgetOrURL
if isinstance(package, basestring):
package = __import__(package)
else:
replyobj.warning("internal error -- no help avaiable for: %s\n" %
widgetOrURL)
return
protocol, location, path, parameters, query, fragment = \
urlparse.urlparse(url, allow_fragments=True)
path = urllib.quote(path)
parameters = urllib.quote(parameters)
query = urllib.quote(query)
fragment = urllib.quote(fragment)
if path and path[0] != '/':
file = os.path.join(package.__path__[0], "helpdir", path)
if os.path.exists(file):
protocol = 'file'
if sys.platform == 'darwin':
#
# Setting location to localhost is needed on
# Mac OS X with Internet Explorer because
# urlunparse() produces urls like
# file:/index.blah instead of
# file:///index.html or
# file://localhost/index.html
# required by the browser.
#
location = 'localhost'
path = urllib.pathname2url(file)
if path[0:3] == '///':
path = path[2:]
url = urlparse.urlunparse(
(protocol, location, path, parameters, query, fragment))
else:
# Fetch development version of docs -- a released
# version would have the help files included.
protocol = 'http'
url = urlparse.urljoin('http://www.cgl.ucsf.edu/chimera/docs/',
url)
replyobj.status("See web browser for %s\n" % url, blankAfter=10)
import webbrowser
try:
webbrowser.open(url, newWindow)
except webbrowser.Error:
from chimera import NonChimeraError
raise NonChimeraError(
"Could not locate a web browser to use.\n"
"\nTry setting your BROWSER environment variable to\n"
"the command-line name of the web browser you want\n"
"to use and restart Chimera.")
except OSError, e:
from chimera import NonChimeraError
import errno
if e.errno == errno.ENOENT:
if protocol == 'file' \
and not os.path.exists(urllib.url2pathname(path)):
raise
# Bug starting webbrowser (firefox, bug 1512),
# Windows usually opens it eventually
raise NonChimeraError(
"Error or delay starting default web browser.\n"
"\n"
"Wait a little and if the default web browser\n"
"doesn't start up, start it by hand, and try\n"
"again.")
raise NonChimeraError("Unable to start web browswer.\n"
"Open <%s> in your web browswer.\n"
"(%s)" % (path, e))
def saveImage(filename=None, width=None, height=None, format=None,
units="pixels", description=None, supersample=None,
master=None, printMode=None, raytrace=False,
raytracePreview=None, raytraceWait=None,
raytraceKeepInput=None,
hideDialogs=True, statusMessages=True, raiseWindow=True,
task=None):
if chimera.nogui and chimera.opengl_platform() != 'OSMESA':
raise chimera.UserError, "Need graphics to save images (or use headless Linux version)"
if statusMessages:
from replyobj import status
else:
def status(*args, **kw):
pass
if printMode is None:
printMode = chimera.viewer.camera.mode()
horizPixels, vertPixels, supersample = \
imageArgs(units, width, height, supersample)
savedSD = None # saved screen distance
if units != 'pixels':
adjustFOV = preferences.get(IMAGE_SETUP, ADJUST_FOV)
if adjustFOV == 1 or (adjustFOV == ONLY_STEREO_CAMERAS
and printMode != 'mono'):
# if image is twice as wide as screen,
# screenDistance is half as much
savedSD = chimera.viewer.camera.screenDistance
adjust = convert[units] / convert['millimeters']
image_width = width * adjust
adjust = chimera.viewer.camera.windowWidth / image_width
chimera.viewer.camera.screenDistance *= adjust
if raytrace:
if not checkPovrayLicense():
return
# TODO: make default an argument or preference
if raytraceWait is None:
raytraceWait = preferences.get(POVRAY_SETUP, WAIT_POVRAY)
if raytraceKeepInput is None:
raytraceKeepInput = preferences.get(POVRAY_SETUP, KEEP_INPUT)
if raytracePreview is None:
raytracePreview = preferences.get(POVRAY_SETUP, SHOW_PREVIEW)
quality = DEFAULT_JPEG_QUALITY
format = 'PNG'
if not chimera.nogui and not filename:
if not master:
master = tkgui.app
chooseDialog = _ChooseFileDialog(filterSet='povray',
format=format)
result = chooseDialog.run(master)
if result is None:
status("Image save cancelled.")
return
filename, format = result[0]
quality = chooseDialog.quality.get()
if not filename:
replyobj.error("Need filename for POV-Ray output")
return
if filename.endswith('.png') or filename.endswith('.jpg'):
povfilename = filename[:-4] + '.pov'
inifilename = filename[:-4] + '.ini'
else:
povfilename = filename + '.pov'
inifilename = filename + '.ini'
if task is None:
from chimera.tasks import Task
task = Task("raytrace image", None)
task.updateStatus("Generating POV-Ray data file")
import exports
exports.doExportCommand('POV-Ray', povfilename)
task.updateStatus("Generating POV-Ray parameter file")
if savedSD is not None:
chimera.viewer.camera.screenDistance = savedSD
import SubprocessMonitor as SM
cmd = [
preferences.get(POVRAY_SETUP, POVRAY_EXE),
inifilename,
"+I%s" % povfilename,
"+O%s" % filename,
"+V" # need verbose to monitor progress
]
inifile = open(inifilename, 'w')
print >> inifile, (
"Width=%d\n"
"Height=%d\n"
# add font path, CHIMERA/share/fonts
"Library_Path=\"%s\"\n"
"Bounding=On\n"
"Bounding_Threshold=1\n"
"Split_Unions=On\n"
"Remove_Bounds=On\n"
"Quality=%d"
) % (
horizPixels,
vertPixels,
os.path.join(os.environ['CHIMERA'], 'share', 'fonts'),
preferences.get(POVRAY_SETUP, POV_QUALITY)
)
if not preferences.get(POVRAY_SETUP, ANTIALIAS):
print >> inifile, "Antialias=Off"
else:
print >> inifile, (
"Antialias=On\n"
"Antialias_Threshold=%f\n"
"Antialias_Depth=%d\n"
"Sampling_Method=%d"
) % (
preferences.get(POVRAY_SETUP, ANTIALIAS_THRESHOLD),
preferences.get(POVRAY_SETUP, ANTIALIAS_DEPTH),
preferences.get(POVRAY_SETUP, ANTIALIAS_METHOD)
)
if not preferences.get(POVRAY_SETUP, JITTER):
print >> inifile, "Jitter=Off"
else:
print >> inifile, (
"Jitter=On\n"
"Jitter_Amount=%f\n"
) % (
preferences.get(POVRAY_SETUP, JITTER_AMOUNT),
)
oa = preferences.get(POVRAY_SETUP, OUTPUT_ALPHA)
if oa == 1 or (oa == 2 and chimera.bgopacity):
if chimera.viewer.depthCue:
replyobj.warning("Depth-cueing disables transparent background")
print >> inifile, "Output_Alpha=On"
if format in ('PNG', 'Stereo PNG'):
print >> inifile, ("; output PNG\n"
"Output_File_Type=N8")
elif format in ('JPEG', 'Stereo JPEG'):
print >> inifile, ("; output JPEG\n"
"Output_File_Type=J%d") % quality
elif format in ('PPM'):
print >> inifile, ("; output PPM\n"
"Output_File_Type=P")
if chimera.nogui or not raytracePreview:
print >> inifile, "Display=Off"
else:
print >> inifile, "Display=On"
if not raytraceWait:
print >> inifile, "Pause_when_Done=On"
inifile.close()
if raytraceKeepInput:
inputs = []
else:
inputs = [ povfilename, inifilename ]
def afterCB(aborted, inputs=inputs, outputs=[filename]):
import os
for fn in inputs:
try:
os.remove(fn)
except OSError:
pass
if aborted:
for fn in outputs:
try:
os.remove(fn)
except OSError:
pass
task.updateStatus("Starting POV-Ray")
try:
subproc = SM.Popen(cmd, stdin=None, stdout=None,
stderr=SM.PIPE, daemon=True)
except OSError, e:
raise chimera.UserError, "Unable run POV-Ray executable: %s" % e
progress = povrayProgress(subproc)
progress.start()
subproc.setProgress(progress)
info = 'running "%s"' % '" "'.join(cmd)
if not chimera.nogui and statusMessages:
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
replyobj.info(info + '\n')
task.updateStatus(info)
subprog = SM.monitor('running POV-Ray', subproc,
title="POV-Ray progress",
task=task,
afterCB=afterCB)
if raytraceWait:
subprog.wait()
return
def display(widgetOrURL, package=chimera, newWindow=False):
"""Display given html help file.
display(widgetOrURL, package=chimera, newWindow=False) => None
The url may be either a string, or a "widget" that has been
registered. In the latter case it is mapped according to
how it was registered.
"""
try:
# compensate for Pmw megawidgets not being Tk widgets
widgetOrURL = widgetOrURL.component('hull')
except:
pass
if isinstance(widgetOrURL, basestring):
url = widgetOrURL
elif hasattr(widgetOrURL, 'winfo_parent'):
# show help associated with widget or parent widget
while widgetOrURL:
if _helpMap.has_key(widgetOrURL):
url, package = _helpMap[widgetOrURL]
break
parent = widgetOrURL.winfo_parent()
if not isinstance(parent, str):
widgetOrURL = parent
elif parent == "":
widgetOrURL = None
else:
widgetOrURL = widgetOrURL._nametowidget(parent)
if not widgetOrURL:
replyobj.warning('internal error -- no help found for widget\n')
return
elif isinstance(widgetOrURL, tuple):
url, package = widgetOrURL
if isinstance(package, basestring):
package = __import__(package)
else:
replyobj.warning("internal error -- no help avaiable for: %s\n" % widgetOrURL)
return
protocol, location, path, parameters, query, fragment = \
urlparse.urlparse(url, allow_fragments=True)
path = urllib.quote(path)
parameters = urllib.quote(parameters)
query = urllib.quote(query)
fragment = urllib.quote(fragment)
if path and path[0] != '/':
file = os.path.join(package.__path__[0], "helpdir", path)
if os.path.exists(file):
protocol = 'file'
if sys.platform == 'darwin':
#
# Setting location to localhost is needed on
# Mac OS X with Internet Explorer because
# urlunparse() produces urls like
# file:/index.blah instead of
# file:///index.html or
# file://localhost/index.html
# required by the browser.
#
location = 'localhost'
path = urllib.pathname2url(file)
if path[0:3] == '///':
path = path[2:]
url = urlparse.urlunparse((protocol, location,
path, parameters,
query, fragment))
else:
# Fetch development version of docs -- a released
# version would have the help files included.
protocol = 'http'
url = urlparse.urljoin(
'http://www.cgl.ucsf.edu/chimera/docs/', url)
replyobj.status("See web browser for %s\n" % url, blankAfter=10)
import webbrowser
try:
webbrowser.open(url, newWindow)
except webbrowser.Error:
from chimera import NonChimeraError
raise NonChimeraError("Could not locate a web browser to use.\n"
"\nTry setting your BROWSER environment variable to\n"
"the command-line name of the web browser you want\n"
"to use and restart Chimera.")
except OSError, e:
from chimera import NonChimeraError
import errno
if e.errno == errno.ENOENT:
if protocol == 'file' \
and not os.path.exists(urllib.url2pathname(path)):
raise
# Bug starting webbrowser (firefox, bug 1512),
# Windows usually opens it eventually
raise NonChimeraError(
"Error or delay starting default web browser.\n"
"\n"
"Wait a little and if the default web browser\n"
"doesn't start up, start it by hand, and try\n"
"again.")
raise NonChimeraError("Unable to start web browswer.\n"
"Open <%s> in your web browswer.\n"
"(%s)" % (path, e))