Source code for continuousflex.protocols.protocol_batch_cluster

# **************************************************************************
# *
# * Authors:
# * J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# * Slavica Jonic (slavica.jonic@upmc.fr)
# * Mohamad Harastani (mohamad.harastani@upmc.fr)
# *
# * 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 os.path import isfile
from pyworkflow.protocol.params import PointerParam, FileParam
from pwem.protocols import BatchProtocol
from pwem.objects import SetOfParticles, Volume, AtomStruct
from xmipp3.convert import writeSetOfParticles
from pwem.utils import runProgram
import pwem.emlib.metadata as md
import numpy as np


[docs]class FlexBatchProtNMACluster(BatchProtocol): """ Protocol executed when a cluster is created from NMA images and theirs deformations. """ _label = 'nma cluster' def _defineParams(self, form): form.addHidden('inputNmaDimred', PointerParam, pointerClass='EMObject') form.addHidden('sqliteFile', FileParam) #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): imagesMd = self._getExtraPath('images.xmd') outputVol = self._getExtraPath('reconstruction.vol') self._insertFunctionStep('convertInputStep', imagesMd) params = '-i %(imagesMd)s -o %(outputVol)s --fast' % locals() self._insertFunctionStep('reconstructStep', params) self._insertFunctionStep('centroidPdbStep') self._insertFunctionStep('createOutputStep', outputVol) #--------------------------- STEPS functions --------------------------------------------
[docs] def convertInputStep(self, imagesMd): # It is unusual to create the output in the convertInputStep, # but just to avoid reading twice the sqlite with particles inputSet = self.inputNmaDimred.get().getInputParticles() partSet = self._createSetOfParticles() partSet.copyInfo(inputSet) tmpSet = SetOfParticles(filename=self.sqliteFile.get()) partSet.appendFromImages(tmpSet) # Register outputs partSet.setAlignmentProj() self._defineOutputs(outputParticles=partSet) self._defineTransformRelation(inputSet, partSet) writeSetOfParticles(partSet, imagesMd) # Add the NMA displacement to clusters XMD files md_file_nma = md.MetaData(self.inputNmaDimred.get().getParticlesMD()) md_file_org = md.MetaData(imagesMd) for objID in md_file_org: # if image name is the same, we add the nma displacement from nma to org id_org = md_file_org.getValue(md.MDL_ITEM_ID, objID) for j in md_file_nma: id_nma = md_file_nma.getValue(md.MDL_ITEM_ID, j) print(id_nma) if id_org == id_nma: displacements = md_file_nma.getValue(md.MDL_NMA, j) md_file_org.setValue(md.MDL_NMA, displacements, objID) break md_file_org.write(imagesMd)
[docs] def reconstructStep(self, params): runProgram('xmipp_reconstruct_fourier_accel', params)
[docs] def centroidPdbStep(self): imagesMd = self._getExtraPath('images.xmd') md_file = md.MetaData(imagesMd) deformations = [] for j in md_file: deformations.append(md_file.getValue(md.MDL_NMA, j)) ampl = np.mean(np.array(deformations), axis= 0) print(self.getFnPDB()) fnPDB, pseudo = self.getFnPDB() fnModeList = self.getFnModes() fnOutPDB = self._getExtraPath('centroid.pdb') params = " --pdb " + fnPDB params += " --nma " + fnModeList params += " -o " + fnOutPDB params += " --deformations " + ' '.join(str(i) for i in ampl) runProgram('xmipp_pdb_nma_deform', params)
[docs] def createOutputStep(self, outputVol): vol = Volume() vol.setFileName(outputVol) vol.setSamplingRate(self.outputParticles.getSamplingRate()) atm = AtomStruct() fnPDB, pseudo = self.getFnPDB() fnOutPDB = self._getExtraPath('centroid.pdb') atm.setPseudoAtoms(pseudo) atm.setFileName(fnOutPDB) atm.setVolume(vol) self._defineOutputs(centroidPDB=atm) self._defineOutputs(outputVol=vol)
#--------------------------- Utility functions -----------------------------------------
[docs] def getFnPDB(self): # This functions returns the path of the structure, false if is atomic, true if pseudoatomic path = self.inputNmaDimred.get().inputNMA.get()._getExtraPath('atoms.pdb') if isfile(path): return path, False else: path = self.inputNmaDimred.get().inputNMA.get()._getExtraPath('pseudoatoms.pdb') return path, True
[docs] def getFnModes(self): return self.inputNmaDimred.get().inputNMA.get()._getExtraPath('modes.xmd')
#--------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] return summary def _validate(self): errors = [] return errors def _citations(self): return [] def _methods(self): return []