source: trunk/mzcms/models.py @ 24

"""Models for mzcms.

"""
from persistent import Persistent
from repoze.folder import Folder

from parsers import parse_dats

class Experiment(Folder):
    __parent__ = __name__ = None
    def __init__(self, proteins, peptides, spectra, psms):
        super(Experiment, self).__init__()
        self['proteins'] = Proteins(proteins)
        self['peptides'] = Peptides(peptides)
        self['spectra'] = Spectra(spectra)
        self['psms'] = Psms(psms)

class Proteins(Folder):
    """Proteins folder factory"""
    def __init__(self, proteins):
        self.name = 'proteins'

class Protein(Persistent):
    """A Protein"""
    def __init__(self, native_id, sequence, pep_refs):
        self.sequence = str(native_id)
        self.sequence = str(sequence)
        self.pep_refs = tuple(pep_refs)

class Peptides(Folder):
    """Peptides folder factory"""
    def __init__(self):
        self.name = 'peptides'

class Peptide(Persistent):
    """A peptide"""
    def __init__(self, sequence, mass):
        self.sequence = str(sequence)
        self.mass = float(mass)
        self.length = len(sequence)

class Spectra(Folder):
    """Spectra folder factory"""
    def __init__(self):
        self.name = 'spectra'


class Spectrum(Persistent):
    """A Spectrum"""
    def __init__(self, scan, run, peaks, prec_mz, prec_charge):
        self.scan = int(scan)
        self.run = str(scan)
        self.peaks = tuple(peaks)
        self.prec_mz = float(prec_mz)
        self.prec_charge = int(prec_charge)

class Psms(Folder):
    """Psms folder factory"""
    def __init__(self):
        self.name = 'psms'

class Psm(Persistent):
    """A Peptide to Spectrum Match"""
    def __init__(self, score, rank, delta_mass, delta_score,
                 sequence_rank2, pep_ref, spec_ref):
        self.score = float(score)
        self.rank = int(rank)
        self.delta_mass = float(delta_mass)
        self.delta_score = float(delta_score)
        self.sequence_rank2 = str(sequence_rank2)
        self.pep_ref = str(pep_ref)
        self.spec_ref = str(spec_ref)

def appmaker(zodb_root):
    if not 'app_root' in zodb_root:
        data = parse_dats('./dats')
        app_root = Experiment(data)
        zodb_root['app_root'] = app_root
        import transaction
        transaction.commit()

    return zodb_root['app_root']