Source code for atsas.protocols.protocol_pdb_to_saxs

# **************************************************************************
# *
# * Authors:  Carlos Oscar Sanchez Sorzano (, May 2013
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * 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 3 of the License, or
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# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
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import numpy

from pwem.protocols import ProtPreprocessVolumes, PointerParam
from pyworkflow.protocol import IntParam, FloatParam, FileParam, StringParam
from pyworkflow.utils import *
from pyworkflow.protocol.constants import LEVEL_ADVANCED
from pyworkflow.utils.path import createLink

from atsas import Plugin

# TODO: Move to 3D Tools

[docs]class AtsasProtConvertPdbToSAXS(ProtPreprocessVolumes): """ Protocol for converting a PDB file (true atoms or pseudoatoms) into a SAXS curve. This is actually a wrapper to the program Crysol from Atsas. See documentation at: """ _label = 'convert PDB to SAXS curve' # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputStructure', PointerParam, pointerClass='AtomStruct', label="Input structure", important=True) form.addParam('numberOfSamples', IntParam, default=256, expertLevel=LEVEL_ADVANCED, label='Number of samples', help='Number of samples of the curve (parameter ns)') form.addParam('maximumFrequency', FloatParam, default=0.3, expertLevel=LEVEL_ADVANCED, label='Maximum frequency (1/A)', help='Maximum frequency of the curve (parameter sm)') form.addParam('numberOfHarmonics', IntParam, default=18, expertLevel=LEVEL_ADVANCED, label='Number of harmonics', help='Number of harmonics to generate the curve ' '(parameter lm)') form.addParam('experimentalSAXS', FileParam, filter="*.dat", default='', label='Experimental SAXS curve (optional)', help="This parameter is optional. If it is given the " "simulated SAXS curve will be compared to the " "experimental one") form.addParam('otherCrysol', StringParam, default='', label='Other parameters for Crysol', help='See') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep('crysolWrapper') # --------------------------- STEPS functions -----------------------------
[docs] def crysolWrapper(self): experimentalSAXS = "" if self.experimentalSAXS.get() != "": experimentalSAXS = os.path.abspath(self.experimentalSAXS.get()) inputStructure = os.path.abspath( self.inputStructure.get().getFileName()) self._enterWorkingDir() if experimentalSAXS != "": createLink(experimentalSAXS, 'experimental_SAXS_curve.dat') experimentalSAXS = 'experimental_SAXS_curve.dat' createLink(inputStructure, 'pseudoatoms.pdb') self.runJob(Plugin.getProgram('crysol'), "pseudoatoms.pdb %s -lm %d -sm %f -ns %d %s" % (experimentalSAXS, self.numberOfHarmonics, self.maximumFrequency, self.numberOfSamples, self.otherCrysol)) self.runJob("mv", "*log *txt extra") if experimentalSAXS == "": self.runJob("mv", "*alm extra") self._leaveWorkingDir()
# --------------------------- INFO functions ------------------------------ def _summary(self): summary = [] summary.append('Number of samples: %d' % self.numberOfSamples) summary.append('Maximum frequency: %f' % self.maximumFrequency) summary.append('Number of Harmonics: %d' % self.numberOfHarmonics) if not self.experimentalSAXS.empty(): summary.append( 'Experimental SAXS curve: %s' % self.experimentalSAXS) if not self.otherCrysol.empty(): summary.append('Other crysol parameters: %s' % self.otherCrysol) # Goodness of fit fnInt = self._getPath("") if exists(fnInt): x = numpy.loadtxt(fnInt, skiprows=1) diff = numpy.log(x[:, 1]) - numpy.log(x[:, 3]) idx = numpy.isfinite(diff) RMS = math.sqrt( 1.0 / numpy.sum(idx) *[idx], diff[idx])) summary.append("RMS=%f" % RMS) return summary def _methods(self): summary = [] summary.append('We computed the SAXS curve of the model %s.' % self.inputStructure.get().getNameId()) summary.append('We simulated the SAXS curve using the method described ' 'in [Svergun1995] up to a frequency of %f (1/Angstroms),' ' with %d harmonics and %d samples.' % (self.maximumFrequency, self.numberOfHarmonics, self.numberOfSamples)) return summary def _citations(self): return ['Svergun1995'] def _validate(self): errors = [] return errors