Source code for phenix.protocols.protocol_validation_cryoem

# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *              Marta Martinez (mmmtnez@cnb.csic.es)
# *
# *
# * 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.
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# * 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.constants import MOLPROBITY, VALIDATION_CRYOEM, PHENIXVERSION
from phenix import Plugin
from pwem.convert.atom_struct import retry
from .protocol_refinement_base import PhenixProtRunRefinementBase

[docs]class PhenixProtRunValidationCryoEM(PhenixProtRunRefinementBase): """MolProbity is a Phenix application to validate the geometry of an atomic structure inferred from an electron density map. """ _label = 'validation_cryoem' _program = "" #_version = VERSION_1_2 VALIDATIONCRYOEMFILE = 'validation_cryoem.mrc' VALIDATIONCRYOEMPKLFILE = 'validation_cryoem.pkl' # --------------------------- DEFINE param functions ------------------- def _defineParams(self, form): super(PhenixProtRunValidationCryoEM, self)._defineParams(form) param = form.getParam('inputVolume') param.help.set("\nSet the starting volume.\nPhenix will calculate " "real-space correlation between map and atomic structure.\n" "If the volume and atomic structure are not correctly " "fitted, values of real-space correlation will indicate " "not correlation at all.\n") # --------------------------- INSERT steps functions -------------------- def _insertAllSteps(self): if self.inputVolume.get() is not None: self.vol = self.inputVolume.get() elif self.inputStructure.get().getVolume() is not None: self.vol = self.inputStructure.get().getVolume() if self.vol is not None: self._insertFunctionStep('convertInputStep', self.VALIDATIONCRYOEMFILE) self._insertFunctionStep('runValidationCryoEMStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------
[docs] def runValidationCryoEMStep(self): version = Plugin.getPhenixVersion() if version == '1.13': print("PHENIX version: 1.13") else: print("PHENIX version: ", version) fileName = self.inputStructure.get().getFileName() atomStruct = os.path.abspath(fileName) # starting volume (.mrc) if self.vol is not None: tmpMapFile = self.VALIDATIONCRYOEMFILE volume = os.path.abspath(self._getExtraPath(tmpMapFile)) else: volume = None # MolProbity is run to get the file molprobity.out # (necessary to get geometry outliers) numberOfThreads = self.numberOfThreads.get() args = self._writeArgsMolProbity(atomStruct, vol=volume) cwd = os.getcwd() + "/" + self._getExtraPath() # script with auxiliary files retry(Plugin.runPhenixProgram, Plugin.getProgram(MOLPROBITY), args, cwd=cwd, listAtomStruct=[atomStruct], log=self._log) args = self._writeArgsValCryoEM(atomStruct, volume, self.vol) if Plugin.getPhenixVersion() != PHENIXVERSION and self.vol is not None: retry(Plugin.runPhenixProgram, Plugin.getProgram(VALIDATION_CRYOEM), args, cwd=cwd, listAtomStruct=[atomStruct], log=self._log)
[docs] def createOutputStep(self): VALIDATIONCRYOEMPKLFILENAME = self._getExtraPath( self.VALIDATIONCRYOEMPKLFILE) self._readValidationPklFile(VALIDATIONCRYOEMPKLFILENAME) self._store()
# --------------------------- INFO functions --------------------------- def _validate(self): errors = self.validateBase(VALIDATION_CRYOEM, 'VALIDATION_CRYOEM') # Check that the input volume exist if (self.inputVolume.get() or self.inputStructure.get().getVolume()) \ is None: errors.append("Error: You should provide a volume.\n") return errors def _summary(self): summary = PhenixProtRunRefinementBase._summary(self) summary.append("https://www.phenix-online.org/documentation/" "reference/validation_cryo_em.html") return summary def _methods(self): methodsMsgs = [] methodsMsgs.append("TODO") return methodsMsgs def _citations(self): return ['Afonine_2018']