Source code for chimera.protocols.protocol_fit

# **************************************************************************
# *
# * Authors:     Grigory Sharov (sharov@igbmc.fr)
# *              Marta Martinez (mmmtnez@cnb.csic.es)
# *              Roberto Marabini (roberto@cnb.csic.es)
# *
# * L'Institut de genetique et de biologie moleculaire et cellulaire (IGBMC)
# *
# * 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'
# *
# **************************************************************************

from .protocol_base import ChimeraProtBase


[docs]class ChimeraProtRigidFit(ChimeraProtBase): # """Protocol to perform rigid fit using Chimera. # Execute command *scipionwrite [model #n] [refmodel #p] # [saverefmodel 0|1]* from command line in order to transferm fitted # pdb to scipion. Default values are model=#0, # refmodel =#1 and saverefmodel 0 (false). # model refers to the pdb file. refmodel to a 3Dmap""" """Protocol to perform rigid fit using Chimera. Execute command *scipionwrite #n [prefix stringAddedToFilename] model refers to the pdb file""" _label = 'rigid fit' def _defineParams(self, form): super(ChimeraProtRigidFit, self)._defineParams(form) param = form.getParam('pdbFileToBeRefined') param.label.set('Atomic structure to be fitted') param.help.set('PDBx/mmCIF file to be fitted. ') param = form.getParam('inputPdbFiles') param.label.set('Other reference atomic structures') param.help.set('Other PDBx/mmCIF files used as reference.') param.allowsNull.set('True') # --------------------------- INSERT steps functions --------------------
[docs] def prerequisitesStep(self): """ """ if self.inputVolume.get() is None: fnVol = self.pdbFileToBeRefined.get().getVolume() index, fn = fnVol.getLocation() print("Volume: Volume associated to atomic structure %s(%d)\n" % (fn, index)) else: fnVol = self.inputVolume.get() print("Volume: Input volume %s\n" % fnVol)
def _validate(self): errors = super(ChimeraProtRigidFit, self)._validate() # Check that the input volume exist if (not self.pdbFileToBeRefined.get().hasVolume()) and ( self.inputVolume.get() is None): errors.append("Error: You should provide a volume.\n") return errors