# **************************************************************************
# *
# * Authors: Roberto Marabini (roberto@cnb.csic.es)
# * Marta Martinez (mmmtnez@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import os
import pyworkflow.utils as pwutils
import pyworkflow.viewer as pwviewer
import pwem.constants as emcts
import pwem.emlib.metadata as md
import pwem.objects as emobj
from pwem import emlib
from pwem import Config as emConfig
from pwem.objects import SetOfAtomStructs
from pyworkflow.utils import OS
chimeraPdbTemplateFileName = "Atom_struct__%06d.cif"
chimeraMapTemplateFileName = "Map__%06d.mrc"
chimeraPythonFileName = "chimeraScript.py"
chimeraScriptFileName = "chimeraScript.cxc"
chimeraConfigFileName = "chimera.ini"
sessionFile = "SESSION.cxs"
symMapperScipionchimera = {}
symMapperScipionchimera[emcts.SYM_CYCLIC] = "Cn"
symMapperScipionchimera[emcts.SYM_DIHEDRAL] = "Dn"
symMapperScipionchimera[emcts.SYM_TETRAHEDRAL] = "T"
symMapperScipionchimera[emcts.SYM_OCTAHEDRAL] = "O"
symMapperScipionchimera[emcts.SYM_I222] = "222"
symMapperScipionchimera[emcts.SYM_I222r] = "222r"
symMapperScipionchimera[emcts.SYM_In25] = "n25"
symMapperScipionchimera[emcts.SYM_In25r] = "n25r"
symMapperScipionchimera[emcts.SYM_I2n3] = "2n3"
symMapperScipionchimera[emcts.SYM_I2n3r] = "2n3r"
symMapperScipionchimera[emcts.SYM_I2n5] = "2n5"
symMapperScipionchimera[emcts.SYM_I2n5r] = "2n5r"
[docs]class Chimera:
""" Helper class to execute chimera and handle its environment. """
# Map symmetries from Scipion convention to Chimera convention
_symmetryMap = {
emcts.SYM_CYCLIC: 'Cn',
emcts.SYM_DIHEDRAL: 'Dn',
emcts.SYM_TETRAHEDRAL: 'T',
emcts.SYM_OCTAHEDRAL: 'O',
emcts.SYM_I222: '222',
emcts.SYM_I222r: '222r',
emcts.SYM_In25: 'n25',
emcts.SYM_In25r: 'n25r',
emcts.SYM_I2n3: '2n3',
emcts.SYM_I2n3r: '2n3r',
emcts.SYM_I2n5: '2n5',
emcts.SYM_I2n5r: '2n5r'
}
[docs] @classmethod
def getSymmetry(cls, scipionSym):
""" Return the equivalent Chimera symmetry from Scipion one. """
return cls._symmetryMap[scipionSym]
[docs] @classmethod
def getHome(cls):
""" Returns chimera home, trying first to take it from chimera plugin. If it fails it will return, the default value in the config"""
with pwutils.weakImport("chimera"):
from chimera import Plugin as chimeraPlugin
return chimeraPlugin.getHome()
return os.path.join(emConfig.EM_ROOT, 'chimerax-1.2.5')
[docs] @classmethod
def getEnviron(cls):
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = pwutils.Environ(os.environ)
environ.set('PATH', os.path.join(cls.getHome(), 'bin'),
position=pwutils.Environ.BEGIN)
if "REMOTE_MESA_LIB" in os.environ:
environ.set('LD_LIBRARY_PATH', os.environ['REMOTE_MESA_LIB'],
position=pwutils.Environ.BEGIN)
return environ
[docs] @classmethod
def getProgram(cls, progName="ChimeraX"):
""" Return the program binary that will be used. """
home = cls.getHome()
if home is None:
return None
path = os.path.join(home, 'bin', os.path.basename(progName))
if OS.isWSL():
path +=".exe"
return path
[docs] @classmethod
def runProgram(cls, program=None, args="", cwd=None):
""" Internal shortcut function to launch chimera program. """
prog = program or cls.getProgram()
pwutils.runJob(None, prog, args, env=cls.getEnviron(),
cwd=cwd)
[docs] @classmethod
def createCoordinateAxisFile(cls, dim, bildFileName="/tmp/axis.bild",
sampling=1, r1=0.1):
""" Create a coordinate system, Along each dimension
we place a small sphere in the negative axis. In this way
chimera shows the system of coordinates origin in the
window center"""
ff = open(bildFileName, "w")
arrowDict = {}
arrowDict["x"] = arrowDict["y"] = arrowDict["z"] = \
sampling * dim * 1. / 2.
arrowDict["r1"] = r1 * dim / 50.
arrowDict["r2"] = 2 * arrowDict["r1"]
arrowDict["rho"] = 0.75 # axis thickness
ff.write(".color red\n" # red
".arrow 0 0 0 %(x)f 0 0 %(r1)f %(r2)f %(rho)f\n"
".color 0 0 0\n.sphere -%(x)f 0 0 0.00001\n"
".color yellow\n" # yellow
".arrow 0 0 0 0 %(y)f 0 %(r1)f %(r2)f %(rho)f\n"
".color 0 0 0\n.sphere 0 -%(y)f 0 0.00001\n"
".color blue\n"
".arrow 0 0 0 0 0 %(z)f %(r1)f %(r2)f %(rho)f\n"
".color 0 0 0\n.sphere 0 0 -%(z)f 0.00001\n" %
arrowDict)
ff.close()
[docs]class ChimeraAngDist(pwviewer.CommandView):
def __init__(self, volFile, tmpFilesPath, **kwargs):
self.kwargs = kwargs
self.volfile = os.path.abspath(os.path.join(volFile))
self.cmdFile = os.path.join(tmpFilesPath,
"chimera_angular_distribution.cxc")
self.axis = os.path.abspath(os.path.join(tmpFilesPath, "axis.bild"))
self.spheres = os.path.abspath(os.path.join(tmpFilesPath,
"spheres.bild"))
self.angularDistributionList = []
self.angularDistFile = kwargs.get('angularDistFile', None)
if self.angularDistFile:
fileName = self.angularDistFile
if '@' in self.angularDistFile:
fileName = self.angularDistFile.split("@")[1]
if not (os.path.exists(fileName)): # check blockname:
raise Exception("Path %s does not exists" %
self.angularDistFile)
self.volOrigin = kwargs.get('volOrigin', None)
self.spheresColor = kwargs.get('spheresColor', 'orange')
spheresDistance = kwargs.get('spheresDistance', -1)
spheresMaxRadius = kwargs.get('spheresMaxRadius', None)
self.initVolumeData(self.volfile)
self.spheresDistance = (float(spheresDistance) if spheresDistance != -1
else (0.75 * self.voxelSize * max(self.xdim,
self.ydim,
self.zdim)) / 2)
self.spheresMaxRadius = (float(spheresMaxRadius) if spheresMaxRadius
else 0.02 * self.spheresDistance)
self.readAngularDistFile()
format = kwargs.get('format', None)
self._createChimeraScript(self.cmdFile, format)
program = Chimera.getProgram()
pwviewer.CommandView.__init__(self, '%s "%s" &' % (program,
self.cmdFile),
env=Chimera.getEnviron(), **kwargs)
def _createChimeraScript(self, scriptFile, format):
Chimera.createCoordinateAxisFile(self.xdim,
bildFileName=self.axis,
sampling=self.voxelSize)
self.createAngularDistributionFile(bildFileName=self.spheres)
fhCmd = open(scriptFile, 'w')
fhCmd.write("open %s\n" % self.axis)
fhCmd.write("open %s\n" % self.spheres)
fhCmd.write("cofr 0,0,0\n")
if format is not None:
fhCmd.write("open %s format %s\n" % (self.volfile.replace(":mrc", ""),
format))
else:
fhCmd.write("open %s\n" % self.volfile.replace(":mrc", ""))
fhCmd.write("volume #3 voxelSize %s\n" % self.voxelSize)
x, y, z = self.volOrigin
fhCmd.write("volume #3 origin %s,%s,%s\n" % (x, y, z))
fhCmd.write("view\n")
fhCmd.close()
[docs] def createAngularDistributionFile(self, bildFileName="/tmp/spheres.bild"):
ff = open(bildFileName, "w")
for angulardist in self.angularDistributionList:
ff.write("%s\n" % angulardist)
ff.close()
[docs] def initVolumeData(self, volfile):
if volfile.endswith('.mrc'):
volfile += ':mrc'
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@')
else:
file = volfile
if ':' in file:
file = file[0: file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists" % file)
self.voxelSize = self.kwargs.get('voxelSize', 1.0)
self.image = emlib.Image(self.volfile)
self.image.convert2DataType(md.DT_DOUBLE)
self.xdim, self.ydim, self.zdim, self.n = self.image.getDimensions()
self.vol = self.image.getData()
[docs] def readAngularDistFile(self):
angleRotLabel = md.MDL_ANGLE_ROT
angleTiltLabel = md.MDL_ANGLE_TILT
anglePsiLabel = md.MDL_ANGLE_PSI
mdAngDist = md.MetaData(self.angularDistFile)
if not mdAngDist.containsLabel(md.MDL_ANGLE_PSI):
anglePsiLabel = None
if mdAngDist.containsLabel(md.RLN_ORIENT_PSI):
angleRotLabel = md.RLN_ORIENT_ROT
angleTiltLabel = md.RLN_ORIENT_TILT
anglePsiLabel = md.RLN_ORIENT_PSI
if not mdAngDist.containsLabel(md.MDL_WEIGHT):
mdAngDist.fillConstant(md.MDL_WEIGHT, 1.)
maxweight = mdAngDist.aggregateSingle(md.AGGR_MAX, md.MDL_WEIGHT)
minweight = mdAngDist.aggregateSingle(md.AGGR_MIN, md.MDL_WEIGHT)
interval = maxweight - minweight
x2 = self.xdim / 2
y2 = self.ydim / 2
z2 = self.zdim / 2
self.angularDistributionList.append('.color %s\n' % self.spheresColor)
for id in mdAngDist:
rot = mdAngDist.getValue(angleRotLabel, id)
tilt = mdAngDist.getValue(angleTiltLabel, id)
psi = mdAngDist.getValue(anglePsiLabel, id) if anglePsiLabel else 0
weight = mdAngDist.getValue(md.MDL_WEIGHT, id)
# Avoid zero division
weight = 0 if interval == 0 else (weight - minweight) / interval
weight = weight + 0.5 # add 0.5 to avoid zero weight
x, y, z = emlib.Euler_direction(rot, tilt, psi)
radius = weight * self.spheresMaxRadius
x = x * self.spheresDistance # + x2
y = y * self.spheresDistance # + y2
z = z * self.spheresDistance # + z2
command = ('.sphere %.1f %.1f %.1f %.1f' %
(x, y, z, radius))
self.angularDistributionList.append(command)
[docs]class ChimeraView(pwviewer.CommandView):
""" View for calling an external command. """
[docs] def getProgram(self):
return Chimera.getProgram()
[docs] def getEnviron(self):
return Chimera.getEnviron()
def __init__(self, inputFiles, **kwargs):
if isinstance(inputFiles,str):
inputFiles = [inputFiles]
# If WLS we need to adapt the paths to windows style
if OS.isWSL():
for i, file in enumerate(inputFiles):
inputFiles[i] =OS.WLSfile2Windows(file)
# Join files
filesStr = '" "'.join(inputFiles)
filesStr = filesStr.replace(":mrc", "")
program = self.getProgram()
pwviewer.CommandView.__init__(self, '%s "%s" &' % (program, filesStr),
env=self.getEnviron(), **kwargs)
[docs]class ChimeraViewer(pwviewer.Viewer):
""" Wrapper to visualize PDB object with Chimera. """
_environments = [pwviewer.DESKTOP_TKINTER]
_targets = [emobj.AtomStruct, emobj.PdbFile, emobj.SetOfAtomStructs,
emobj.Volume, emobj.SetOfVolumes, emobj.SetOfClasses3D]
_name = "ChimeraX"
def __init__(self, **kwargs):
pwviewer.Viewer.__init__(self, **kwargs)
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, emobj.AtomStruct):
objSet = SetOfAtomStructs.create(outputPath='/tmp', suffix=self.protocol.getObjId())
objSet.append(obj)
if hasattr(obj, '_chimeraScript'):
objSet.copyAttributes(obj, '_chimeraScript')
obj, cls = objSet, type(objSet)
if issubclass(cls, emobj.SetOfAtomStructs):
if hasattr(obj, '_chimeraScript'):
fn = obj._chimeraScript.get()
view = ChimeraView(fn)
return [view]
else:
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'w')
f.write('cd %s\n' % os.getcwd())
f.write("cofr 0,0,0\n") # set center of coordinates
f.write("style stick\n")
_inputVol = obj.getFirstItem().getVolume()
if _inputVol is not None:
volID = 1
dim, sampling = _inputVol.getDim()[0], _inputVol.getSamplingRate()
f.write("open %s\n" % _inputVol.getFileName())
x, y, z = _inputVol.getOrigin(force=True).getShifts()
f.write("volume #%d style surface voxelSize %f\nvolume #%d origin "
"%0.2f,%0.2f,%0.2f\n"
% (volID, sampling, volID, x, y, z))
else:
dim, sampling = 150., 1.
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim, bildFileName=bildFileName, sampling=sampling)
f.write("open %s\n" % bildFileName)
for AS in obj:
f.write("open %s\n" % AS.getFileName())
#f.write("style stick\n")
f.close()
view = ChimeraView(fnCmd)
return [view]
elif issubclass(cls,emobj.Volume):
view = ChimeraView(obj.getFileName())
return [view]
elif issubclass(cls,emobj.EMSet):
files = obj.getFiles()
view = ChimeraView(files)
return [view]
else:
raise Exception('ChimeraViewer.visualize: '
'can not visualize class: %s' % obj.getClassName())
[docs]class ChimeraOldView(ChimeraView):
""" View for calling an external command. """
[docs] def getProgram(self):
return emConfig.CHIMERA_OLD_BINARY_PATH
[docs] def getEnviron(self):
return None
[docs]class ChimeraOldViewer(ChimeraViewer):
""" Wrapper to visualize Chimera OLD (1.10 , 1.13, ..) compatible objects . """
_name = "Chimera"
def __init__(self, **kwargs):
pwviewer.Viewer.__init__(self, **kwargs)
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, emobj.EMSet):
files = obj.getFiles()
view = ChimeraOldView(files)
return [view]
elif issubclass(cls, (emobj.Volume, emobj.AtomStruct)):
view = ChimeraOldView(obj.getFileName())
return [view]
else:
raise Exception('ChimeraOldViewer.visualize: '
'can not visualize class: %s' % obj.getClassName())
[docs]def mapVolsWithColorkey(displayVolFileName,
mapVolFileName,
stepColors, # List with resolution values
colorList, # List with colors
voldim, # pixels
volOrigin=None, # in A.
step=-1, # chimera volume step (display resolution)
sampling=1.,
scriptFileName='/tmp/chimeraColor.py',
bgColorImage='white', # background color
showAxis=True,
fontSize=12): # default chimera font size
""" colors surface of volume 'displayVolFileName' using values from
'mapVolFikeName'. A colorkey is created using the values in stepColors
and the color in colorList. """
scriptFile = scriptFileName
fhCmd = open(scriptFile, 'w')
fhCmd.write("from chimerax.core.commands import run\n")
fhCmd.write("run(session, 'set bgColor %s')\n" % bgColorImage)
chimeraVolId = 1
bildFileName = scriptFile.replace(".py", ".bild")
Chimera.createCoordinateAxisFile(voldim[0],
bildFileName=bildFileName,
sampling=sampling)
# axis
fhCmd.write("run(session, 'open %s')\n" % bildFileName)
if not showAxis:
fhCmd.write("run(session, 'hide #1')\n")
fhCmd.write("run(session, 'cofr 0,0,0')\n") # set center of coordinates
chimeraVolId += 1
# first volume
if volOrigin is None:
x = -voldim[0] * sampling // 2
y = -voldim[1] * sampling // 2
z = -voldim[2] * sampling // 2
else:
# TODO, not sure about sign
x = volOrigin[0]
y = volOrigin[1]
z = volOrigin[2]
fhCmd.write("run(session, 'open %s')\n" % displayVolFileName)
if step == -1:
fhCmd.write("run(session, 'volume #%d voxelSize %s')\n" %
(chimeraVolId, str(sampling)))
else:
fhCmd.write("run(session, 'volume #%d voxelSize %s step %d')\n" %
(chimeraVolId, str(sampling), step))
fhCmd.write("run(session, 'volume #%d origin %0.2f,%0.2f,%0.2f')\n"
% (chimeraVolId, x, y, z))
# second volume
chimeraVolId += 1
fhCmd.write("run(session, 'open %s')\n" % mapVolFileName)
# TODO: Why no step here?
fhCmd.write("run(session, 'volume #%d voxelSize %f')\n" % (chimeraVolId, sampling))
fhCmd.write("run(session, 'volume #%d origin %0.2f,%0.2f,%0.2f')\n"
% (chimeraVolId, x, y, z))
fhCmd.write("run(session, 'vol #%d hide')\n" % chimeraVolId)
# replace scolor + colorkey which has been discontinued in chimerax
scolorStr = ''
for step, color in zip(stepColors, colorList):
scolorStr += '%s,%s:' % (step, color)
scolorStr = scolorStr[:-1]
fhCmd.write("run(session, 'color sample #%d map #%d "
"palette " % (chimeraVolId - 1, chimeraVolId) +
scolorStr + "')\n"
)
fhCmd.write(generateColorLegend(stepColors, colorList, threeLabelsOnly=False))
fhCmd.write("run(session, 'view')\n")
fhCmd.close()
[docs]def generateColorLegend(stepColors, colorList, threeLabelsOnly=True):
"""Return a string to write in a chimera script file a color legend - key command
:param stepColors: list with the values for the colors
:param colorList: list with the colors
:param threeLabelsOnly: True, with ignore stepColors and show just 3 values: min, max and medium."""
colorStr = 'run(session, "key{} fontSize 15 size 0.025,0.4 pos 0.01,0.3")\n'
labelCount, keyStr = 0, ''
stepColors.reverse(), colorList.reverse()
if threeLabelsOnly:
labelsIndex = [0, len(colorList) - 1, (len(colorList) - 1) // 2]
for step, color in zip(stepColors, colorList):
if not threeLabelsOnly or labelCount in labelsIndex:
keyStr += ' {}:{}'.format(color, step)
else:
keyStr += ' {}:'.format(color)
labelCount += 1
return colorStr.format(keyStr)