Source code for atomstructutils.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.emlib.image import ImageHandler

from atomstructutils.protocols import ProtAtomStrucOperate, ProtAverageSubunits
from atomstructutils.protocols.protocol_convertsymmetry import \
    ProtAtomStrucConvertSymmetry
from pwem.viewers import Chimera
from pyworkflow.viewer import DESKTOP_TKINTER, Viewer
from pwem import Domain


[docs]class ProtAtomStrucOperateViewer(Viewer): """ Visualize the output of protocol protocol_convertsymmetry """ _environments = [DESKTOP_TKINTER] _label = 'atomStruct Operate viewer' _targets = [ProtAtomStrucOperate, ProtAverageSubunits] def _visualize(self, obj, **args): # run in the background fnCmd = self.protocol._getExtraPath("chimera_output.cxc") chimeraPlugin = Domain.importFromPlugin('chimera', 'Plugin', doRaise=True) chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(), fnCmd + "&") return []
[docs]class ProtAtomStrucConvertSymmetryViewer(Viewer): """ Visualize the output of protocol protocol_convertsymmetry """ _environments = [DESKTOP_TKINTER] _label = 'convertsymmetry viewer' _targets = [ProtAtomStrucConvertSymmetry] def _visualize(self, obj, **args): # The input pdb is a parameter from the protocol # and from the parent protocol. inputAtomStruct = self.protocol.pdbFileToBeRefined.get() # To show pdbs only dim = 150. sampling = 1. bildFileName = os.path.abspath(self.protocol._getTmpPath( "axis_output.bild")) Chimera.createCoordinateAxisFile(dim, bildFileName=bildFileName, sampling=sampling) fnCmd = self.protocol._getTmpPath("chimera_output.cxc") f = open(fnCmd, 'w') f.write("open %s\n" % bildFileName) f.write("cofr 0,0,0\n") # set center of coordinates f.write("open %s\n" % os.path.abspath(inputAtomStruct.getFileName())) f.write("style stick\n") if self.protocol.hasAttribute('rotatedAtomStruct'): outputAtomStruct = self.protocol.rotatedAtomStruct.getFileName() f.write("open %s\n" % os.path.abspath(outputAtomStruct)) f.write("view\n") f.close() # run in the background chimeraPlugin = Domain.importFromPlugin('chimera', 'Plugin', doRaise=True) chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(), fnCmd + "&") return []