# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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.objects as emobj
[docs]class Vmd:
""" Help class to run VMD and manage its environment. """
[docs] @classmethod
def getEnviron(cls):
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = pwutils.Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['VMD_HOME'], 'bin'),
position=pwutils.Environ.BEGIN)
return environ
[docs]class VmdView(pwviewer.CommandView):
""" View for calling an external command. """
def __init__(self, vmdCommand, **kwargs):
pwviewer.CommandView.__init__(self, 'vmd %s' % vmdCommand,
env=Vmd.getEnviron(), **kwargs)
[docs] def show(self):
pwutils.runJob(None, '', self._cmd, env=Vmd.getEnviron())
[docs]class VmdViewer(pwviewer.Viewer):
""" Wrapper to visualize PDB objects with VMD viewer. """
_environments = [pwviewer.DESKTOP_TKINTER]
# _targets = [AtomStruct]
def __init__(self, **args):
pwviewer.Viewer.__init__(self, **args)
[docs] def visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, emobj.AtomStruct):
VmdView(obj.getFileName()).show()
# FIXME: there is an asymmetry between ProtocolViewer and Viewer.
# For the first, the visualize method return a list of View's,
# while for the second, the visualize method directly shows
# the objects. (the first approach is preferable)
else:
raise Exception('VmdViewer.visualize: can not visualize class: %s'
% obj.getClassName())