Source code for chimera.viewers.viewer

# **************************************************************************
# *
# * Authors:  Roberto Marabini (roberto@cnb.csic.es), May 2013
# *           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 2 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

from pwem.convert import Ccp4Header
from pwem.emlib.image import ImageHandler
from pwem.objects import Volume
from pwem.objects import Transform

from ..protocols import ChimeraSubtractionMaps
from ..protocols.protocol_fit import ChimeraProtRigidFit
from ..protocols.protocol_operate import ChimeraProtOperate
from ..protocols.protocol_restore import ChimeraProtRestore
from ..protocols.protocol_modeller_search import ChimeraModelFromTemplate

from pwem.viewers.viewer_chimera import (Chimera,
                                         sessionFile)
from pyworkflow.viewer import DESKTOP_TKINTER, Viewer


[docs]class ChimeraViewerBase(Viewer): """ Visualize the output of protocols protocol_fit and protocol_operate """ _environments = [DESKTOP_TKINTER] def _visualize(self, obj, **args): # THe input map or pdb may be a parameter from the protocol # or from the parent protocol. dim = 150. sampling = 1. _inputVol = None directory = self.protocol._getExtraPath() try: try: if self.protocol.inputVolume.get() is not None: _inputVol = self.protocol.inputVolume.get() elif self.protocol.pdbFileToBeRefined.get().getVolume() is not None: _inputVol = self.protocol.pdbFileToBeRefined.get().getVolume() elif self.protocol.inputVolumes[0] is not None: _inputVol = self.protocol.inputVolumes[0].get() except: output3DMapList = [] for filename in sorted(os.listdir(directory)): if filename.endswith(".mrc"): output3DMapList.append(filename.split('.')[0]) output3DMap = str(output3DMapList[0]) if len(output3DMap) > 0: _inputVol = self.protocol.output3DMap except: # TODO: I do not know if we still need this part # Remark that inputProtocol does not longer exist, it has been replaced by inputProtocolDict # Compare with the previous code, specially the alternative directory for item in list(self.protocol.inputProtocolDict().values()): if item.hasAttribute('inputVolume') and item.inputVolume.get() is not None: _inputVol = item.inputVolume.get() break elif item.hasAttribute('pdbFileToBeRefined') and \ item.pdbFileToBeRefined.get().getVolume() is not None: _inputVol = item.pdbFileToBeRefined.get().getVolume() break # directory = item._getExtraPath() if _inputVol is not None: dim = _inputVol.getDim()[0] sampling = _inputVol.getSamplingRate() bildFileName = self.protocol._getExtraPath("axis_output.bild") Chimera.createCoordinateAxisFile(dim, bildFileName=bildFileName, sampling=sampling) fnCmd = self.protocol._getExtraPath("chimera_output.cxc") f = open(fnCmd, 'w') # change to workingDir # If we do not use cd and the project name has an space # the protocol fails even if we pass absolute paths f.write('cd %s\n' % os.getcwd()) f.write("open %s\n" % bildFileName) f.write("cofr 0,0,0\n") # set center of coordinates inputVolFileName = '' counter = 2 if _inputVol is not None: # In case we have PDBs only, _inputVol is None: self.visInputVolume(f, _inputVol, counter) else: counter = 1 if (self.protocol.hasAttribute("inputVolume2") and\ self.protocol.inputVolume2.get() is not None): counter += 1 _inputVol2 = self.protocol.inputVolume2.get() self.visInputVolume(f, _inputVol2, counter) for filename in sorted(os.listdir(directory)): if filename.endswith(".mrc") and filename != inputVolFileName: counter += 1 volFileName = os.path.join(directory, filename) vol = Volume() vol.setFileName(volFileName) # fix mrc header ccp4header = Ccp4Header(volFileName, readHeader=True) sampling = ccp4header.computeSampling() origin = Transform() shifts = ccp4header.getOrigin() origin.setShiftsTuple(shifts) f.write("open %s\n" % volFileName) f.write("volume #%d style surface voxelSize %f\n" "volume #%d origin %0.2f,%0.2f,%0.2f\n" % (counter, sampling, counter, shifts[0], shifts[1], shifts[2])) f.write("volume #%d level %0.3f\n" % (counter, 0.001)) for filename in os.listdir(directory): if filename.endswith(".pdb") or filename.endswith(".cif"): if not (filename.startswith("Atom_struct_out_") or filename.startswith("tmp_")): path = os.path.join(directory, filename) # f.write("open %s\n" % os.path.abspath(path)) f.write("open %s\n" % path) f.write("view\n") f.close() # run in the background Chimera.runProgram(Chimera.getProgram(), fnCmd + "&") return []
[docs] def visInputVolume(self, f, vol, counter): inputVolFileName = ImageHandler.removeFileType(vol.getFileName()) f.write("open %s\n" % inputVolFileName) if vol.hasOrigin(): x, y, z = vol.getOrigin().getShifts() else: x, y, z = vol.getOrigin(force=True).getShifts() f.write("volume #%d style surface voxelSize %f\n" "volume #%d origin %0.2f,%0.2f,%0.2f\n" % (counter, vol.getSamplingRate(), counter, x, y, z))
[docs]class ChimeraRestoreViewer(Viewer): """ Visualize the output of protocols protocol_fit and protocol_operate """ _label = 'viewer restore' _targets = [ChimeraProtRestore] def _visualize(self, obj, **args): fnCmd = self.protocol._getExtraPath("chimera_restore_session.cxc") f = open(fnCmd, 'w') # change to workingDir # If we do not use cd and the project name has an space # the protocol fails even if we pass absolute paths f.write('cd %s\n' % os.getcwd()) path1 = os.path.join(self.protocol._getExtraPath(), sessionFile) if os.path.exists(path1): # restored SESSION path = path1 else: # SESSION from inputProtocol path2 = os.path.join( self.protocol.inputProtocol.get()._getExtraPath(), sessionFile) path = path2 f.write("open %s\n" % path) Chimera.runProgram(Chimera.getProgram(), fnCmd + "&") return []
[docs]class ChimeraProtRigidFitViewer(ChimeraViewerBase): _label = 'viewer fit' _targets = [ChimeraProtRigidFit]
[docs]class ChimeraProtOperateViewer(ChimeraViewerBase): _label = 'viewer operate' _targets = [ChimeraProtOperate]
[docs]class ChimeraModelFromTemplateViewer(ChimeraViewerBase): _label = 'viewer model from template' _targets = [ChimeraModelFromTemplate]
[docs]class ChimeraSubtractionMapsViewer(ChimeraViewerBase): _label = 'viewer subtract maps' _targets = [ChimeraSubtractionMaps]