Ejemplo n.º 1
0
def extract_acc(pdb_id):

    atoms = prody.performDSSP(pdb_id)
    map_atom_group(atoms)
    uid2acc = {}

    for uid, uresnum, acc in izip(atoms.getData('uids'),
                                  atoms.getData('uresnums'),
                                  atoms.getData('dssp_acc')):
        if uid is None:
            continue
        if uid not in uid2acc:
            uid2acc[uid] = []
        if uresnum-1 >= len(uid2acc[uid]):
            uid2acc[uid] += [-1]*(uresnum-len(uid2acc[uid]))
        uid2acc[uid][uresnum-1] = acc

    return uid2acc
Ejemplo n.º 2
0
def extract_secondary_structures(pdb_id, uid2data):

    atoms = prody.performDSSP(pdb_id)
    map_atom_group(atoms)
    uid2structure = {}
    for uid in uid2data:
        uid2structure[uid] = ["_"] * len(uid2data[uid]['sequence'])

    for uid, uresnum, secstr in izip(atoms.getData('uids'), atoms.getData('uresnums'), atoms.getSecstrs()):
        if uid is None:
            continue
        if secstr == "":
            secstr = "-"
        uid2structure[uid][uresnum-1] = secstr

    uid2structure = dict((uid, "".join(seq)) for uid, seq in uid2structure.iteritems())

    return uid2structure
Ejemplo n.º 3
0
def extract_acc(pdb_id):

    atoms = prody.performDSSP(pdb_id)
    map_atom_group(atoms)
    uid2acc = {}

    for uid, uresnum, acc in izip(atoms.getData('uids'),
                                  atoms.getData('uresnums'),
                                  atoms.getData('dssp_acc')):
        if uid is None:
            continue
        if uid not in uid2acc:
            uid2acc[uid] = []
        if uresnum - 1 >= len(uid2acc[uid]):
            uid2acc[uid] += [-1] * (uresnum - len(uid2acc[uid]))
        uid2acc[uid][uresnum - 1] = acc

    return uid2acc
Ejemplo n.º 4
0
def extract_secondary_structures(pdb_id, uid2data):

    atoms = prody.performDSSP(pdb_id)
    map_atom_group(atoms)
    uid2structure = {}
    for uid in uid2data:
        uid2structure[uid] = ["_"] * len(uid2data[uid]['sequence'])

    for uid, uresnum, secstr in izip(atoms.getData('uids'),
                                     atoms.getData('uresnums'),
                                     atoms.getSecstrs()):
        if uid is None:
            continue
        if secstr == "":
            secstr = "-"
        uid2structure[uid][uresnum - 1] = secstr

    uid2structure = dict(
        (uid, "".join(seq)) for uid, seq in uid2structure.iteritems())

    return uid2structure
Ejemplo n.º 5
0
    atoms = prody.performDSSP(pdb_id)
    map_atom_group(atoms)
    uid2acc = {}

    for uid, uresnum, acc in izip(atoms.getData('uids'),
                                  atoms.getData('uresnums'),
                                  atoms.getData('dssp_acc')):
        if uid is None:
            continue
        if uid not in uid2acc:
            uid2acc[uid] = []
        if uresnum-1 >= len(uid2acc[uid]):
            uid2acc[uid] += [-1]*(uresnum-len(uid2acc[uid]))
        uid2acc[uid][uresnum-1] = acc

    return uid2acc



if __name__ == "__main__":

    atoms = prody.performDSSP('104l')

    uids, uresnums = map_atom_group(atoms)

    for res in atoms.iterResidues():
        print(res.getResname(), res.getData('uids')[0], res.getData('uresnums')[0], res.getSecstrs()[0])

    structures = extract_secondary_structures('104l')
    print(structures)
Ejemplo n.º 6
0
    uid2acc = {}

    for uid, uresnum, acc in izip(atoms.getData('uids'),
                                  atoms.getData('uresnums'),
                                  atoms.getData('dssp_acc')):
        if uid is None:
            continue
        if uid not in uid2acc:
            uid2acc[uid] = []
        if uresnum - 1 >= len(uid2acc[uid]):
            uid2acc[uid] += [-1] * (uresnum - len(uid2acc[uid]))
        uid2acc[uid][uresnum - 1] = acc

    return uid2acc


if __name__ == "__main__":

    atoms = prody.performDSSP('104l')

    uids, uresnums = map_atom_group(atoms)

    for res in atoms.iterResidues():
        print(res.getResname(),
              res.getData('uids')[0],
              res.getData('uresnums')[0],
              res.getSecstrs()[0])

    structures = extract_secondary_structures('104l')
    print(structures)