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
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
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
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
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)
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)