Source code for continuousflex.protocols.protocol_nma

# **************************************************************************
# *
# * Authors:  Carlos Oscar Sanchez Sorzano (, May 2013
# *           Slavica Jonic                (
# * Ported to Scipion:
# *           J.M. De la Rosa Trevin (, 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
# * 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 ''
# *
# **************************************************************************

import os
import math
from os.path import basename, exists, join

from pwem.convert.atom_struct import cifToPdb
from pwem.emlib import MetaData, MDL_NMA_ATOMSHIFT, MDL_NMA_MODEFILE
from pyworkflow.utils import redStr, replaceBaseExt
from pyworkflow.utils.path import copyFile, createLink, makePath, cleanPath, moveFile
from pyworkflow.protocol.params import (PointerParam, IntParam, FloatParam, 
from pwem.objects import SetOfNormalModes

from xmipp3.base import XmippMdRow
from .protocol_nma_base import FlexProtNMABase, NMA_CUTOFF_REL
from .convert import rowToMode, getNMAEnviron

[docs]class FlexProtNMA(FlexProtNMABase): """ Flexible angular alignment using normal modes """ _label = 'nma analysis' def _defineParams(self, form): form.addSection(label='Normal Mode Analysis') form.addParam('inputStructure', PointerParam, label="Input structure", important=True, pointerClass='AtomStruct', help='The input structure can be an atomic model ' '(true PDB) or a pseudoatomic model\n' '(an EM volume converted into pseudoatoms)') FlexProtNMABase._defineParamsCommon(self,form) form.addParam('rtbBlockSize', IntParam, default=10, expertLevel=LEVEL_ADVANCED, label='Number of residues per RTB block (for atomic structures)', help='Used only with atoms. Normal modes of atomic structures are computed with the RTB method. \n' 'This is the RTB block size. In the RTB method, aminoacids are grouped into blocks of this size ' 'that are moved translationally and rotationally together.') form.addSection(label='Animation') form.addParam('amplitude', FloatParam, default=50, label='Amplitude', help='Used only for animations of computed normal modes. ' 'This is the amplitude with which atoms or pseudoatoms are moved ' 'along normal modes in the animations. \n' 'Normal-mode amplitudes corresponding to given images are computed by image analysis.') form.addParam('nframes', IntParam, default=10, expertLevel=LEVEL_ADVANCED, label='Number of frames', help='Number of frames used in animations.') form.addParam('downsample', FloatParam, default=1, expertLevel=LEVEL_ADVANCED, # condition=isEm label='Downsample pseudoatoms (for visualization)', help='Used only with pseudoatoms and only for visualization purposes. \n' 'A downsample factor of 2 means removing one half of the pseudoatoms.') form.addParam('pseudoAtomThreshold', FloatParam, default=0, expertLevel=LEVEL_ADVANCED, # condition=isEm label='Pseudoatom mass threshold (for visualization)', help='Used only with pseudoatoms and only for visualization purposes. \n ' 'Pseudoatoms whose mass is below this threshold are removed. \n' 'The threshold value should be between 0 and 1. ' 'A threshold of 0 implies no pseudoatom removal.') def _insertAllSteps(self): # Some steps will differ if the input is a volume or a pdb file self.structureEM = self.inputStructure.get().getPseudoAtoms() n = self.numberOfModes.get() # Link the input inputFn = self.inputStructure.get().getFileName() localFn = self._getPath(replaceBaseExt(basename(inputFn),'pdb')) self._insertFunctionStep('copyPdbStep', inputFn, localFn, self.structureEM) # Construct string for relative-absolute cutoff # This is used to detect when to reexecute a step or not cutoffStr='' if self.cutoffMode == NMA_CUTOFF_REL: cutoffStr = 'Relative %f'%self.rcPercentage.get() else: cutoffStr = 'Absolute %f'%self.rc.get() # Compute modes self.pseudoAtomRadius=1 if self.structureEM: with open(inputFn, 'r') as fh: first_line = fh.readline() second_line = fh.readline() self.pseudoAtomRadius = float(second_line.split()[2]) if self.cutoffMode == NMA_CUTOFF_REL: params = '-i %s --operation distance_histogram %s' \ % (localFn, self._getExtraPath('pseudoatoms_distance.hist')) self._insertRunJobStep("xmipp_pdb_analysis", params) self._insertFunctionStep('computeModesStep', localFn, n, cutoffStr) self._insertFunctionStep('reformatOutputStep',"pseudoatoms.pdb") else: if self.cutoffMode == NMA_CUTOFF_REL: params = '-i %s --operation distance_histogram %s' % (localFn, self._getExtraPath('atoms_distance.hist')) self._insertRunJobStep("xmipp_pdb_analysis", params) self._insertFunctionStep('computePdbModesStep', n, self.rtbBlockSize.get(), cutoffStr) self._insertFunctionStep('reformatPdbOutputStep', n) self._insertFunctionStep('qualifyModesStep', n, self.collectivityThreshold.get(), self.structureEM) self._insertFunctionStep('animateModesStep', n, self.amplitude.get(), self.nframes.get(), self.downsample.get(), self.pseudoAtomThreshold.get(), self.pseudoAtomRadius) self._insertFunctionStep('computeAtomShiftsStep', n) self._insertFunctionStep('createOutputStep')
[docs] def copyPdbStep(self, inputFn, localFn, isEM): """ Copy the input pdb file and also create a link 'atoms.pdb' """ if inputFn.endswith(".cif") or inputFn.endswith(".mmcif"): cifToPdb(inputFn, localFn) else: copyFile(inputFn, localFn) if isEM: fnOut = self._getPath('pseudoatoms.pdb') else: fnOut = self._getPath('atoms.pdb') if not os.path.exists(fnOut): createLink(localFn, fnOut) # Keeping only the lines that start with ATOM newlines = [] with open(localFn) as f: lines = f.readlines() for line in lines: if line.startswith("ATOM ") or line.startswith("TER ") or line.startswith("END "): newlines.append(line) with open(localFn, mode='w') as f: f.writelines(newlines) # Shifting the atom numbers after line 100000 one step to the left: newlines = [] with open(localFn) as f: lines = f.readlines() for line in lines: if line.startswith("ATOM ") or line.startswith("TER "): # print(int(line.split()[1])) if int(line.split()[1])>99999: if line.startswith("ATOM "): newline = line.replace("ATOM 1", "ATOM 1") else: newline = line.replace("TER 1", "TER 1") newlines.append(newline) else: newlines.append(line) with open(localFn, mode='w') as f: f.writelines(newlines)
[docs] def computePdbModesStep(self, numberOfModes, RTBblockSize, cutoffStr): rc = self._getRc(self._getExtraPath('atoms_distance.hist')) self._enterWorkingDir() # For atoms, the interaction force constant was set to 10 as ElNemo RTB code may ask for its value \ # (the RTBForceConstant entry was removed from gui as the value does not change the ENM computed normal modes). self.runJob('', "%d %d atoms.pdb %f %f" % (numberOfModes, RTBblockSize, rc, 10.0), env=getNMAEnviron()) self.runJob("nma_elnemo_pdbmat","",env=getNMAEnviron()) self.runJob("nma_diagrtb","",env=getNMAEnviron()) if not exists("diagrtb.eigenfacs"): msg = "Modes cannot be computed. Check the number of modes you " \ "asked to compute and/or consider " msg += "increasing cut-off distance. The maximum number of " \ "modes allowed by the method for atomic " msg += "normal mode analysis is 6 times the number of RTB blocks " \ "but the protocol allows only up " msg += "to 200 modes as 20-100 modes are usually enough. If the " \ "number of modes is below the minimum " msg += "between 200 and 6 times the number of RTB blocks, consider " \ "increasing cut-off distance." self._printWarnings(redStr(msg) + '\n') self.runJob("rm","-f *.dat_run diagrtb.dat pdbmat.xyzm pdbmat.sdijf " "pdbmat.dat") self._leaveWorkingDir()
[docs] def reformatPdbOutputStep(self, numberOfModes): self._enterWorkingDir() makePath('modes') Natoms = self._countAtoms("atoms.pdb") fhIn = open('diagrtb.eigenfacs') fhAni = open('vec_ani.txt','w') for n in range(numberOfModes): # Skip two lines fhIn.readline() fhIn.readline() fhOut=open('modes/vec.%d'%(n+1),'w') for i in range(Natoms): line=fhIn.readline() fhOut.write(line) fhAni.write(line.rstrip().lstrip()+" ") fhOut.close() if n!=(numberOfModes-1): fhAni.write("\n") fhIn.close() fhAni.close() self.runJob("","",env=getNMAEnviron()) cleanPath("vec_ani.txt") moveFile('vec_ani.pkl', 'extra/vec_ani.pkl') self._leaveWorkingDir()
[docs] def animateModesStep(self, numberOfModes,amplitude,nFrames,downsample, pseudoAtomThreshold,pseudoAtomRadius): makePath(self._getExtraPath('animations')) self._enterWorkingDir() if self.structureEM: fn = "pseudoatoms.pdb" self.runJob("","%s extra/vec_ani.pkl 7 %d " "%f extra/animations/" "animated_mode %d %d %f"%\ (fn,numberOfModes,amplitude,nFrames,downsample, pseudoAtomThreshold),env=getNMAEnviron()) else: fn="atoms.pdb" self.runJob("","%s extra/vec_ani.pkl 7 %d %f " "extra/animations/animated_mode " "%d"%\ (fn,numberOfModes,amplitude,nFrames),env=getNMAEnviron()) for mode in range(7,numberOfModes+1): fnAnimation = join("extra", "animations", "animated_mode_%03d" % mode) fhCmd=open(fnAnimation+".vmd",'w') fhCmd.write("mol new %s.pdb\n" % self._getPath(fnAnimation)) fhCmd.write("animate style Loop\n") fhCmd.write("display projection Orthographic\n") if self.structureEM: fhCmd.write("mol modcolor 0 0 Beta\n") fhCmd.write("mol modstyle 0 0 Beads %f 8.000000\n" %(pseudoAtomRadius)) else: fhCmd.write("mol modcolor 0 0 Index\n") if self._checkPDB_CA(fn): fhCmd.write("mol modstyle 0 0 Beads 1.000000 8.000000\n") # fhCmd.write("mol modstyle 0 0 Beads 1.800000 6.000000 " # "2.600000 0\n") else: fhCmd.write("mol modstyle 0 0 NewRibbons 1.800000 6.000000 " "2.600000 0\n") fhCmd.write("animate speed 0.5\n") fhCmd.write("animate forward\n") fhCmd.close(); self._leaveWorkingDir()
[docs] def computeAtomShiftsStep(self, numberOfModes): fnOutDir = self._getExtraPath("distanceProfiles") makePath(fnOutDir) maxShift=[] maxShiftMode=[] for n in range(7, numberOfModes+1): fnVec = self._getPath("modes", "vec.%d" % n) if exists(fnVec): fhIn = open(fnVec) md = MetaData() atomCounter = 0 for line in fhIn: x, y, z = map(float, line.split()) d = math.sqrt(x*x+y*y+z*z) if n==7: maxShift.append(d) maxShiftMode.append(7) else: if d>maxShift[atomCounter]: maxShift[atomCounter]=d maxShiftMode[atomCounter]=n atomCounter+=1 md.setValue(MDL_NMA_ATOMSHIFT,d,md.addObject()) md.write(join(fnOutDir,"vec%d.xmd" % n)) fhIn.close() md = MetaData() for i, _ in enumerate(maxShift): fnVec = self._getPath("modes", "vec.%d" % (maxShiftMode[i]+1)) if exists(fnVec): objId = md.addObject() md.setValue(MDL_NMA_ATOMSHIFT, maxShift[i],objId) md.setValue(MDL_NMA_MODEFILE, fnVec, objId) md.write(self._getExtraPath('maxAtomShifts.xmd'))
[docs] def createOutputStep(self): fnSqlite = self._getPath('modes.sqlite') nmSet = SetOfNormalModes(filename=fnSqlite) md = MetaData(self._getPath('modes.xmd')) row = XmippMdRow() for objId in md: row.readFromMd(md, objId) nmSet.append(rowToMode(row)) inputPdb = self.inputStructure.get() nmSet.setPdb(inputPdb) self._defineOutputs(outputModes=nmSet) self._defineSourceRelation(self.inputStructure, nmSet)
def _checkPDB_CA(self, fnPDB): # This function returns true if all the atoms are CA and P, otherwise false from continuousflex.protocols.utilities.pdb_parser import m_inout_read_pdb pdb_read = m_inout_read_pdb(fnPDB) for atom in pdb_read: if atom.type != " C" or atom.loc != "A ": if atom.type != " P": return False return True