Source code for atomstructutils.protocols.protocol_operate

# **************************************************************************
# *
# * Authors:     Marta Martinez (mmmtnez@cnb.csic.es)
# *              Roberto Marabini (roberto@cnb.csic.es)
# *
# * 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'
# *
# **************************************************************************
import sys
from pwem.protocols import EMProtocol
from pwem.objects import AtomStruct
from pwem.viewers import Chimera
from pyworkflow.protocol.params import (EnumParam,
                                        IntParam,
                                        MultiPointerParam,
                                        PointerParam,
                                        StringParam)
from pwem.convert.atom_struct import AtomicStructHandler, fromCIFTommCIF
import os


[docs]class ProtAtomStrucOperate(EMProtocol): """Utilities for handling PDB/mmcif atomic structure files. Current plugin utilities: (A) extract a chain from an atom structure (pdb/cif file), (B) perform union of several atomic structures""" operationsDict = {0: 'addChain', 1: 'extractChain', 2: 'reNumberChain', 3: 'reNameChain', 4: 'extractAllChains'} operationsDictInv = {value:key for key, value in operationsDict.items()} # operationsDictInv = {value:key for key, value in list(operationsDict.items())} _label = 'operator' _program = "" def _defineParams(self, form): form.addSection(label='Input') form.addParam('pdbFileToBeRefined', PointerParam, pointerClass="AtomStruct", label='Atomic Structure 1:', allowsNull=True, important=True, help="Input the reference atomic structure.") form.addParam('Operation', EnumParam, choices=[val for key, val in sorted(self.operationsDict.items())], label="Operation:", default=0, help="Select operation to be performed") form.addParam('InputAtomStruct2', MultiPointerParam, pointerClass="AtomStruct", label='Atomic Structure 2:', allowsNull=True, condition="Operation == %d" % self.operationsDictInv['addChain'], important=True, help="Input the atomic structures to be added.") form.addParam('inputStructureChain', StringParam, condition="Operation == %d or Operation == %d" % (self.operationsDictInv['extractChain'], self.operationsDictInv['reNameChain']), label="Chain ", allowsNull=True, help="Select a particular chain of the atomic " "structure.") form.addParam('start', IntParam, condition="Operation == %d" % (self.operationsDictInv['extractChain']), label="Start at residue #", allowsNull=True, default=-1, help="Extract Chain starting at this number of residue. " "-1 = first residue") form.addParam('offset', IntParam, condition="Operation == %d" % (self.operationsDictInv['reNumberChain']), label="Offset residue by", allowsNull=True, default=-1, help="renumber residues by adding offset value") form.addParam('end', IntParam, condition="Operation == %d" % self.operationsDictInv['extractChain'], label="End at residue #", allowsNull=True, default=-1, help="Extract Chain ending at this number of residue." " -1 -> last residue") form.addParam('chainName', StringParam, condition="Operation == %d " % (self.operationsDictInv['reNameChain']), label="New Chain name", allowsNull=True, default=-1, help="Give Chain this new name") # --------------------------- INSERT steps functions -------------------- def _insertAllSteps(self): dim = 150. sampling = 1. bildFileName = os.path.abspath(self._getExtraPath( "axis_output.bild")) Chimera.createCoordinateAxisFile(dim, bildFileName=bildFileName, sampling=sampling) fnCmd = self._getExtraPath("chimera_output.cxc") f = open(fnCmd, 'w') f.write("open %s\n" % bildFileName) f.write("cofr 0,0,0\n") # set center of coordinates f.close() if self.Operation == self.operationsDictInv['addChain']: listStructFileName = [] for aStruct in self.InputAtomStruct2: listStructFileName.append(aStruct.get().getFileName()) self._insertFunctionStep('addChainStep', self.pdbFileToBeRefined.get().getFileName(), listStructFileName ) elif self.Operation == self.operationsDictInv['extractChain']: self._insertFunctionStep('extractChainStep', self.pdbFileToBeRefined.get().getFileName()) elif self.Operation == self.operationsDictInv['extractAllChains']: self._insertFunctionStep('extractAllChainsStep', self.pdbFileToBeRefined.get().getFileName()) elif self.Operation == self.operationsDictInv['reNumberChain']: self._insertFunctionStep('reNumberChainStep', self.pdbFileToBeRefined.get().getFileName()) elif self.Operation == self.operationsDictInv['reNameChain']: self._insertFunctionStep('reNameChainStep', self.pdbFileToBeRefined.get().getFileName() ) else: raise Exception("ERROR: Invalid operation *%s* I quit" % self.Operation)
[docs] def reNumberChainStep(self, structFileName): import json outFileName = self._getExtraPath("atomStruct_reNumberedChain.cif") aStruct1 = AtomicStructHandler(structFileName) chainIdDict = json.loads(self.inputStructureChain.get()) aStruct1.renumberChain(chainID=chainIdDict['chain'], offset=self.offset.get(), modelID=chainIdDict['model'], filename=outFileName) #aStruct1.write(outFileName) self.createOutputStep(outFileName)
[docs] def reNameChainStep(self, structFileName): import json outFileName = self._getExtraPath("atomStruct_reNamedChain.cif") aStruct1 = AtomicStructHandler(structFileName) chainIdDict = json.loads(self.inputStructureChain.get()) aStruct1.renameChain(chainID=chainIdDict['chain'], newChainName=self.chainName.get(), modelID=chainIdDict['model'], filename=outFileName) #aStruct1.write(outFileName) self.createOutputStep(outFileName)
[docs] def addChainStep(self, structFileName, listStructFileName): outFileName = self._getExtraPath("atomStruct_addChain.cif") aStruct1 = AtomicStructHandler(structFileName) print("Adding to Atomic Struct {}".format(structFileName)) for fileName in listStructFileName: print("AddingStruct {}".format(fileName)) sys.stdout.flush() aStruct1.addStruct(fileName, outFileName) #aStruct1.write(outFileName) self.createOutputStep(outFileName, twoRelations=True)
[docs] def extractChainStep(self, structFileName): import json outFileName = self._getExtraPath("atomStruct_extractChain.cif") aStruct1 = AtomicStructHandler(structFileName) chainIdDict = json.loads(self.inputStructureChain.get()) end = self.end.get() if end == -1: end = sys.maxsize aStruct1.extractChain(chainID=chainIdDict['chain'], start=self.start.get(), end=end, modelID=chainIdDict['model'], filename=outFileName) self.createOutputStep(outFileName)
[docs] def extractAllChainsStep(self, structFileName): import json outFileName = self._getExtraPath("atomStruct_extractChain_%s.cif") aStruct1 = AtomicStructHandler(structFileName) listOfChains, _ = aStruct1.getModelsChains() for model, chainDic in listOfChains.items(): for chainID, lenResidues in chainDic.items(): chainIdDict = json.loads('{"model": %d, "chain": "%s", "residues": %d}' % (model, str(chainID), lenResidues)) chainIDStr=chainIdDict['chain'] aStruct1.extractChain(modelID=chainIdDict['model'], chainID=chainIDStr, start=-1, end=sys.maxsize, filename=outFileName%chainIDStr) self.createOutputStep(outFileName%chainIDStr,suffix=chainIDStr)
[docs] def createOutputStep(self, outFileName, twoRelations=False, suffix=''): outFileName = os.path.abspath(outFileName) fnCmd = self._getExtraPath("chimera_output.cxc") f = open(fnCmd, 'a+') f.write("open %s\n" % outFileName) f.close() pdb = AtomStruct() pdb.setFileName(outFileName) # MM: to get appropriate cif files to be visualize with Chimera # Transform the output cif file in mmcif log = self._log fromCIFTommCIF(outFileName, outFileName, log) if suffix=="": self._defineOutputs(outputPdb=pdb) else: outputDict = {'outputPdb_chain%s'%suffix: pdb} self._defineOutputs(**outputDict) self._defineSourceRelation(self.pdbFileToBeRefined, pdb) if twoRelations: self._defineSourceRelation(self.InputAtomStruct2, pdb)
# --------------------------- UTILS functions ------------------ def _validate(self): errors = [] return errors def _summary(self): summary = [] return summary def _citations(self): return ['Cock2009']