Source code for xmipp3.protocols.protocol_convert_pdb

# -*- coding: utf-8 -*-
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# *
# * Authors:  Jesus Cuenca (
# *           Roberto Marabini (
# *           Ignacio Foche
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import os

import pyworkflow.protocol.params as params
import pyworkflow.protocol.constants as const
from pyworkflow.utils import replaceBaseExt, removeExt, getExt, createLink

from pwem.convert import cifToPdb, downloadPdb, headers
from pwem.objects import Volume, Transform
from pwem.protocols import ProtInitialVolume

[docs]class XmippProtConvertPdb(ProtInitialVolume): """ Convert a PDB file into a volume. """ _label = 'convert a PDB' IMPORT_FROM_ID = 0 IMPORT_OBJ = 1 IMPORT_FROM_FILES = 2 # --------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): """ Define the parameters that will be input for the Protocol. This definition is also used to generate automatically the GUI. """ form.addSection(label='Input') form.addParam('inputPdbData', params.EnumParam, choices=['id', 'object', 'file'], label="Retrieve PDB from", default=self.IMPORT_FROM_ID, display=params.EnumParam.DISPLAY_HLIST, help='Retrieve PDB data from server, use a pdb Object, or a local file') form.addParam('pdbId', params.StringParam, condition='inputPdbData == IMPORT_FROM_ID', label="Pdb Id ", allowsNull=True, help='Type a pdb Id (four alphanumeric characters).') form.addParam('pdbObj', params.PointerParam, pointerClass='AtomStruct', label="Input pdb ", condition='inputPdbData == IMPORT_OBJ', allowsNull=True, help='Specify a pdb object.') form.addParam('pdbFile', params.FileParam, label="File path", condition='inputPdbData == IMPORT_FROM_FILES', allowsNull=True, help='Specify a path to desired PDB structure.') form.addParam('sampling', params.FloatParam, default=1.0, label="Sampling rate (Å/px)", help='Sampling rate (Angstroms/pixel)') form.addParam('vol', params.BooleanParam, label='Use a volume as an empty template?', default=False, help='Use an existing volume to define the size and origin for the output volume. If this option' 'is selected, make sure that "Center PDB" in advanced parameters is set to *No*.') form.addParam('volObj', params.PointerParam, pointerClass='Volume', label="Input volume ", condition='vol', allowsNull=True, help='The origin and the final size of the output volume will be taken from this volume.') form.addParam('setSize', params.BooleanParam, label='Set final size?', default=False, condition='vol == False') form.addParam('size_z', params.IntParam, condition='setSize and not vol', allowsNull=True, label="Final size (px) Z", help='Final size in Z in pixels. If no value is provided, protocol will estimate it.') form.addParam('size_y', params.IntParam, condition='setSize and not vol', allowsNull=True, label="Final size (px) Y", help='Final size in Y in pixels. If no value is provided, protocol will estimate it.') form.addParam('size_x', params.IntParam, condition='setSize and not vol', allowsNull=True, label="Final size (px) X", help='Final size in X in pixels. If desired output size is x = y = z you can only fill this ' 'field. If no value is provided, protocol will estimate it.') form.addParam('centerPdb', params.BooleanParam, default=True, expertLevel=const.LEVEL_ADVANCED, label="Center PDB", help='Center PDB with the center of mass') form.addParam('outPdb', params.BooleanParam, default=False, expertLevel=const.LEVEL_ADVANCED, label="Store centered PDB", help='Set to \'Yes\' if you want to save centered PDB. ' 'It will be stored in the output directory of this protocol') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): """ In this function the steps that are going to be executed should be defined. Two of the most used functions are: _insertFunctionStep or _insertRunJobStep """ if self.inputPdbData == self.IMPORT_FROM_ID: self._insertFunctionStep('pdbDownloadStep') self._insertFunctionStep('convertPdbStep') self._insertFunctionStep('createOutput') # --------------------------- STEPS functions --------------------------------------------
[docs] def pdbDownloadStep(self): """Download all pdb files in file_list and unzip them.""" downloadPdb(self.pdbId.get(), self._getPdbFileName(), self._log)
[docs] def convertPdbStep(self): """ Although is not mandatory, usually is used by the protocol to register the resulting outputs in the database. """ pdbFn = self._getPdbFileName() outFile = removeExt(self._getVolName()) if getExt(pdbFn)==".cif": pdbFn2=replaceBaseExt(pdbFn, 'pdb') cifToPdb(pdbFn, pdbFn2) pdbFn = pdbFn2 if " " in pdbFn: pdbFn_extra = self._getExtraPath(os.path.basename(pdbFn.replace(" ", "_"))) else: pdbFn_extra = self._getExtraPath(os.path.basename(pdbFn)) createLink(pdbFn, pdbFn_extra) samplingR = self.sampling.get() args = '-i %s --sampling %f -o %s' % (pdbFn_extra, samplingR, outFile) if self.centerPdb: args += ' --centerPDB' if self.outPdb: args += ' --oPDB' if self.vol: vol = self.volObj.get() size = vol.getDim() ccp4header = headers.Ccp4Header(vol.getFileName(), readHeader=True) self.shifts = ccp4header.getOrigin() args += ' --size %d %d %d --orig %d %d %d' % (size[2], size[1], size[0], self.shifts[0]/samplingR, self.shifts[1]/samplingR, self.shifts[2]/samplingR) if self.setSize and not self.vol: args += ' --size' if self.size_x.hasValue(): args += ' %d' % self.size_x.get() if self.size_y.hasValue() and self.size_z.hasValue(): args += ' %d %d' % (self.size_y.get(), self.size_z.get())"Input file: " + pdbFn)"Output file: " + outFile) program = "xmipp_volume_from_pdb" self.runJob(program, args)
[docs] def createOutput(self): volume = Volume() volume.setSamplingRate(self.sampling.get()) volume.setFileName(self._getVolName()) if self.vol: origin = Transform() origin.setShiftsTuple(self.shifts) volume.setOrigin(origin) self._defineOutputs(outputVolume=volume) if self.inputPdbData == self.IMPORT_OBJ: self._defineSourceRelation(self.pdbObj, volume)
# --------------------------- INFO functions -------------------------------------------- def _summary(self): """ Even if the full set of parameters is available, this function provides summary information about an specific run. """ summary = [] # Add some lines of summary information if not hasattr(self, 'outputVolume'): summary.append("outputVolume not ready yet.") else: if self.inputPdbData == self.IMPORT_FROM_ID: summary.append("Input PDB ID: %s" % self.pdbId.get()) elif self.inputPdbData == self.IMPORT_OBJ: summary.append("Input PDB File: %s" % self.pdbObj.get().getFileName()) else: summary.append("Input PDB File: %s" % self.pdbFile.get()) return summary def _validate(self): """ The function of this hook is to add some validation before the protocol is launched to be executed. It should return a list of errors. If the list is empty the protocol can be executed. """ errors = [] if self.inputPdbData == self.IMPORT_FROM_ID: lenStr = len(self.pdbId.get()) if lenStr != 4: errors = ["Pdb id is composed only by four alphanumeric characters"] return errors # --------------------------- UTLIS functions -------------------------------------------- def _getPdbFileName(self): if self.inputPdbData == self.IMPORT_FROM_ID: return self._getExtraPath('%s.cif' % self.pdbId.get()) elif self.inputPdbData == self.IMPORT_OBJ: return self.pdbObj.get().getFileName() else: return self.pdbFile.get() def _getVolName(self): return self._getExtraPath(replaceBaseExt(self._getPdbFileName().replace(" ", "_"), "vol"))