Using ARIA Python 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')