# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (coss@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'
# *
# **************************************************************************
from pyworkflow.viewer import (DESKTOP_TKINTER, WEB_DJANGO, Viewer)
from pyworkflow.gui.plotter import Plotter
from ..protocols.protocol_pdb_to_saxs import AtsasProtConvertPdbToSAXS
[docs]class AtsasViewer(Viewer):
""" Wrapper to visualize Pdb to SAXS. """
_targets = [AtsasProtConvertPdbToSAXS]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def __init__(self, **args):
Viewer.__init__(self, **args)
[docs] def visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, AtsasProtConvertPdbToSAXS):
if obj.experimentalSAXS.empty():
fnInt = obj._getPath("pseudoatoms00.int")
else:
fnInt = obj._getPath("pseudoatoms00.fit")
import numpy
x = numpy.loadtxt(fnInt, skiprows=1)
xplotter = Plotter(windowTitle="SAXS Curves")
a = xplotter.createSubPlot('SAXS curves', 'Angstroms^-1',
'log(SAXS)', yformat=False)
a.plot(x[:, 0], numpy.log(x[:, 1]))
a.plot(x[:, 0], numpy.log(x[:, 3]))
if obj.experimentalSAXS.empty():
xplotter.showLegend(['SAXS in solution', 'SAXS in vacuo'])
else:
xplotter.showLegend(['Experimental SAXS', 'SAXS from volume'])
xplotter.show()