# **************************************************************************
# *
# * 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 phenix.protocols.protocol_dock_in_map import PhenixProtRunDockInMap
from pyworkflow.viewer import DESKTOP_TKINTER, Viewer
from pwem.viewers import Chimera
from pwem import Domain
from phenix import Plugin
[docs]class PhenixProtRunDockInMapViewer(Viewer):
""" Visualize the output of protocols superpose pdb """
_environments = [DESKTOP_TKINTER]
_label = 'Dock in map viewer'
_targets = [PhenixProtRunDockInMap]
def _visualize(self, obj, **args):
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
self._getVols()
self._getPdbs()
dim = float()
sampling = float()
if self.vols[0] is not None:
dim, sampling = self._getDimSamplingFromVol(self.vols[0])
else:
# To show pdbs only
dim = 150.
sampling = 1.
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
with open(fnCmd, 'w') as f:
# 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) #1
f.write("cofr 0,0,0\n") # set center of coordinates
if len(self.vols) > 0:
for vol in self.vols:
sampling, volFileName, x, y, z = self._getXYZFromVol(vol)
f.write("open %s\n" % volFileName)
f.write("volume #2 style surface voxelSize %f\n"
"volume #2 origin %0.2f,%0.2f,%0.2f\n"
% (sampling, x, y, z))
for filename in self.pdbList:
f.write("open %s\n" % filename)
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera', 'Plugin', doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(), fnCmd + "&",
cwd=os.getcwd())
return []
def _getVols(self):
self.vols = []
vol1 = self.protocol.inputVolume1.get()
if vol1 is not None:
self.vols.append(vol1)
def _getPdbs(self):
self.pdbList = []
inputPdb = self.protocol.inputStructure.get().getFileName()
self.pdbList.append(inputPdb)
outputPdb = self.protocol.outputPdb.getFileName()
self.pdbList.append(outputPdb)
def _getDimSamplingFromVol(self, vol):
dim = vol.getDim()[0]
sampling = vol.getSamplingRate()
return dim, sampling
def _getXYZFromVol(self, vol):
sampling = vol.getSamplingRate()
volFileName = vol.getFileName()
if vol.hasOrigin():
x, y, z = vol.getOrigin().getShifts()
else:
x, y, z = vol.getOrigin(force=True).getShifts()
return sampling, volFileName, x, y, z