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Using ARIA Python API

Some tips for using ARIA python sources as an API

add aria sources to python:

  • on the fly
    import os, sys
    aria_path = os.path.join(os.environ['ARIA2'], 'src/py')
    sys.path.insert(0, aria_path)
    • PYTHONPATH
    # bash
    export PYTHONPATH=$PYTHONPATH:$ARIA2/src/py

    # csh
    setenv PYTHONPATH ${PYTHONPATH}:${ARIA2}/src/py

    # zsh
    export PYTHONPATH=$PYTHONPATH:$ARIA2/src/py

    aria data manipulation

    • read an aria project

    from aria import *
    import AriaXML

    pickler = AriaXML.AriaXMLPickler()

    project = pickler.load(project_file)

    • read sequence in aria XML format

    molecule =  pickler.load(molecule_file)
    • navigating in the molecule
    for chain in molecule.get_chains():
        for residue in c.getResidues():
            for atom in r.getAtoms():
                print a


    • reading shifts assignments

    shift_list = pickler.load(shifts_file)
    assignments = shift_list.getShiftAssignments()

    • reading spectra

    spectrum = pickler.load(spectrum_file)
    crosspeaks = spectrum.getPeaks()

    • reading noe_restraints.pickle

    from tools import Load

    aria_peaks = Load(pickle_file)
    • navigating in the peaks
    for p in aria_peaks:
        for c in p.getContributions():
            for sp in c.getSpinPairs():
                a, b = sp.getAtoms()
                print a, b, p.getDistance() 

    • reading an cns structure ensemble created by aria

    import StructureEnsemble as SE

    from glob import glob
    list_of_pdb = glob(os.path.join(iteration_path, '*.pdb'))

    se_settings = SE.StructureEnsembleSettings()
    ensemble = SE.StructureEnsemble(se_settings)
    ensemble.read(list_of_pdb, molecule, format='cns')



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