Source code for continuousflex.protocols.protocol_nma_alignment

# **************************************************************************
# *
# * Authors:  Carlos Oscar Sanchez Sorzano (coss@cnb.csic.es), May 2013
# *           Qiyu Jin
# *           Slavica Jonic                (slavica.jonic@upmc.fr)
# * Ported to Scipion:
# *           J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es), Jan 2014
# *
# * 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 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 basename

from pwem.convert.atom_struct import cifToPdb
from pyworkflow.utils import replaceBaseExt

from pyworkflow.utils import isPower2, getListFromRangeString
from pyworkflow.utils.path import copyFile, cleanPath 
import pyworkflow.protocol.params as params
from pwem.protocols import ProtAnalysis3D

from pyworkflow.protocol.params import NumericRangeParam
import pwem as em
import pwem.emlib.metadata as md

from xmipp3.base import XmippMdRow
from xmipp3.convert import (writeSetOfParticles, xmippToLocation,
                            getImageLocation, createItemMatrix,
                            setXmippAttributes)
from .convert import modeToRow


NMA_ALIGNMENT_WAV = 0
NMA_ALIGNMENT_PROJ = 1    

        
[docs]class FlexProtAlignmentNMA(ProtAnalysis3D): """ Protocol for flexible angular alignment. """ _label = 'nma alignment' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputModes', params.PointerParam, pointerClass='SetOfNormalModes', label="Normal modes", help='Set of modes computed by normal mode analysis.') form.addParam('modeList', NumericRangeParam, expertLevel=params.LEVEL_ADVANCED, label="Modes selection", help='Select the normal modes that will be used for image analysis. \n' 'If you leave this field empty, all computed modes will be selected for image analysis.\n' 'You have several ways to specify the modes.\n' ' Examples:\n' ' "7,8-10" -> [7,8,9,10]\n' ' "8, 10, 12" -> [8,10,12]\n' ' "8 9, 10-12" -> [8,9,10,11,12])\n') form.addParam('inputParticles', params.PointerParam, label="Input particles", pointerClass='SetOfParticles', help='Select the set of particles that will be analyzed using normal modes.') form.addParam('copyDeformations', params.PathParam, expertLevel=params.LEVEL_ADVANCED, label='Precomputed results (for development)', help='Only for tests during development. Enter a metadata file with precomputed elastic ' 'and rigid-body alignment parameters and perform ' 'all remaining steps using this file.') form.addSection(label='Combined elastic and rigid-body alignment') form.addParam('trustRegionScale', params.IntParam, default=1, expertLevel=params.LEVEL_ADVANCED, label='Elastic-alignment trust region scale', help='For elastic alignment, this parameter scales the initial ' 'value of the trust region radius of Powell optimization. ' 'The default value of 1 works in majority of cases. \n' 'This value should not be changed except by expert users. ' 'Larger values (e.g., between 1 and 2) can be tried ' 'for larger expected amplitudes of conformational change.') form.addParam('alignmentMethod', params.EnumParam, default=NMA_ALIGNMENT_WAV, choices=['wavelets & splines', 'projection matching'], label='Rigid-body alignment method', help='For rigid-body alignment, Projection Matching method (faster) or ' 'Wavelets and Splines method (more accurate) can be used. In the case of Wavelets and Splines, ' 'the size of images should be a power of 2.') form.addParam('discreteAngularSampling', params.FloatParam, default=10, label="Discrete angular sampling (deg)", help='This is the angular step (in degrees) with which a library of reference projections ' 'is computed for rigid-body alignment in Projection Matching and Wavelets methods. \n' 'This alignment is refined with Splines method when Wavelets and Splines alignment is chosen.') form.addParallelSection(threads=0, mpi=8) #--------------------------- INSERT steps functions --------------------------------------------
[docs] def getInputPdb(self): """ Return the Pdb object associated with the normal modes. """ return self.inputModes.get().getPdb()
def _insertAllSteps(self): atomsFn = self.getInputPdb().getFileName() # Define some outputs filenames self.imgsFn = self._getExtraPath('images.xmd') self.modesFn = self._getExtraPath('modes.xmd') self.structureEM = self.inputModes.get().getPdb().getPseudoAtoms() if self.structureEM: self.atomsFn = self._getExtraPath(basename(atomsFn)) copyFile(atomsFn, self.atomsFn) else: localFn = self._getExtraPath(replaceBaseExt(basename(atomsFn),'pdb')) cifToPdb(atomsFn, localFn) self.atomsFn = self._getExtraPath(basename(localFn)) self._insertFunctionStep('convertInputStep', atomsFn) if self.copyDeformations.empty(): #ONLY FOR DEBUGGING self._insertFunctionStep("performNmaStep", self.atomsFn, self.modesFn) else: # TODO: for debugging and testing it will be useful to copy the deformations # metadata file, not just the deformation.txt file self._insertFunctionStep('copyDeformationsStep', self.copyDeformations.get()) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def convertInputStep(self, atomsFn): # Write the modes metadata taking into account the selection self.writeModesMetaData() # Write a metadata with the normal modes information # to launch the nma alignment programs writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
# This is now done differently (see _insertAllSteps) and this line must be removed now # Copy the atoms file to current working dir #copyFile(atomsFn, self.atomsFn)
[docs] def writeModesMetaData(self): """ Iterate over the input SetOfNormalModes and write the proper Xmipp metadata. Take into account a possible selection of modes (This option is just a shortcut for testing. The recommended way is just create a subset from the GUI and use that as input) """ modeSelection = [] if self.modeList.empty(): modeSelection = [] else: modeSelection = getListFromRangeString(self.modeList.get()) mdModes = md.MetaData() inputModes = self.inputModes.get() for mode in inputModes: # If there is a mode selection, only # take into account those selected if not modeSelection or mode.getObjId() in modeSelection: row = XmippMdRow() modeToRow(mode, row) row.writeToMd(mdModes, mdModes.addObject()) mdModes.write(self.modesFn)
[docs] def copyDeformationsStep(self, deformationMd): copyFile(deformationMd, self.imgsFn) # We need to update the image name with the good ones # and the same with the ids. inputSet = self.inputParticles.get() mdImgs = md.MetaData(self.imgsFn) for objId in mdImgs: imgPath = mdImgs.getValue(md.MDL_IMAGE, objId) index, fn = xmippToLocation(imgPath) # Conside the index is the id in the input set particle = inputSet[index] mdImgs.setValue(md.MDL_IMAGE, getImageLocation(particle), objId) mdImgs.setValue(md.MDL_ITEM_ID, int(particle.getObjId()), objId) mdImgs.write(self.imgsFn)
[docs] def performNmaStep(self, atomsFn, modesFn): sampling = self.inputParticles.get().getSamplingRate() discreteAngularSampling = self.discreteAngularSampling.get() trustRegionScale = self.trustRegionScale.get() odir = self._getTmpPath() imgFn = self.imgsFn args = "-i %(imgFn)s --pdb %(atomsFn)s --modes %(modesFn)s --sampling_rate %(sampling)f " args += "--discrAngStep %(discreteAngularSampling)f --odir %(odir)s --centerPDB " args += "--trustradius_scale %(trustRegionScale)d --resume " if self.getInputPdb().getPseudoAtoms(): args += "--fixed_Gaussian " if self.alignmentMethod == NMA_ALIGNMENT_PROJ: args += "--projMatch " self.runJob("xmipp_nma_alignment", args % locals()) cleanPath(self._getPath('nmaTodo.xmd')) inputSet = self.inputParticles.get() mdImgs = md.MetaData(self.imgsFn) for objId in mdImgs: imgPath = mdImgs.getValue(md.MDL_IMAGE, objId) index, fn = xmippToLocation(imgPath) # Conside the index is the id in the input set particle = inputSet[index] mdImgs.setValue(md.MDL_IMAGE, getImageLocation(particle), objId) mdImgs.setValue(md.MDL_ITEM_ID, int(particle.getObjId()), objId) mdImgs.write(self.imgsFn)
[docs] def createOutputStep(self): inputSet = self.inputParticles.get() partSet = self._createSetOfParticles() pdbPointer = self.inputModes.get()._pdbPointer partSet.copyInfo(inputSet) partSet.setAlignmentProj() partSet.copyItems(inputSet, updateItemCallback=self._updateParticle, itemDataIterator=md.iterRows(self.imgsFn, sortByLabel=md.MDL_ITEM_ID)) self._defineOutputs(outputParticles=partSet) self._defineSourceRelation(pdbPointer, partSet) self._defineTransformRelation(self.inputParticles, partSet)
#--------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] return summary def _validate(self): errors = [] xdim = self.inputParticles.get().getDim()[0] if not isPower2(xdim): errors.append("Image dimension (%s) is not a power of two, consider resize them" % xdim) return errors def _citations(self): return ['Jonic2005', 'Sorzano2004b','Jin2014'] def _methods(self): pass #--------------------------- UTILS functions -------------------------------------------- def _printWarnings(self, *lines): """ Print some warning lines to 'warnings.xmd', the function should be called inside the working dir.""" fWarn = open("warnings.xmd",'w') for l in lines: print >> fWarn, l fWarn.close() def _getLocalModesFn(self): modesFn = self.inputModes.get().getFileName() return self._getBasePath(modesFn) def _updateParticle(self, item, row): setXmippAttributes(item, row, md.MDL_ANGLE_ROT, md.MDL_ANGLE_TILT, md.MDL_ANGLE_PSI, md.MDL_SHIFT_X, md.MDL_SHIFT_Y, md.MDL_FLIP, md.MDL_NMA, md.MDL_COST) createItemMatrix(item, row, align=em.ALIGN_PROJ)