def __init__(self, ca_trace):
if isinstance(ca_trace, PDBStructure):
ca_trace = pdb_to_catrace(ca_trace)
assert isinstance(ca_trace, CaTrace)
self.__ca_trace = ca_trace
self.__property_estimator = OneShotPropertyEstimator(ca_trace)
self.__sidechain_handler = BatchSideChainConfigHandler(ca_trace)
self.__signature = {}
self.__placement_matrix = {}
self.__placement_vector = {}
self.__ca_position = {}
self.__logger = logging.getLogger("mutant_model.ResidueLookup")
def get_signatures(pdbfile, amino, property_list, nbrs):
assert os.path.isfile(pdbfile)
assert isinstance(property_list, list)
assert nbrs > 2
assert all([
p in cg.CoarseGrainProperty.supported_properties()
for p in property_list
])
pdblist = sd.read_pdb(pdbfile)
assert len(pdblist) > 0
chain = list(pdblist[0].keys())[0]
pdb = pdblist[0][chain]
try:
ca_trace = sd.pdb_to_catrace(pdb)
except:
return np.array([])
assert isinstance(pdb, sd.PDBStructure)
residue_ids = [r for r in pdb.residue_ids if r > 0][1:-1]
residue_ids = [
r for r in residue_ids if sd.get_amino(pdb.residue_name(r)) == amino
]
residue_ids = cg.filter_complete_residues(pdb, residue_ids)
vol = cg.Volume3D(size=cg.VolumeSignatureGrid.size(),
dim=cg.VolumeSignatureGrid.dim())
if len(residue_ids) > 0:
vol_signature = []
for r in residue_ids:
vol_signature.append(vol.get_signature(pdb, r, reset=True))
nbr_signature = cg.cg_neighbor_signature(ca_trace,
residues=residue_ids,
properties=property_list,
topn=nbrs)
vol_signature, nbr_signature = np.array(vol_signature), np.array(
nbr_signature)
if vol_signature.shape[0] == nbr_signature.shape[0]:
return np.concatenate((nbr_signature, vol_signature), axis=1)
return np.array([])
args = parser.parse_args()
if not os.path.isfile(args.pdb_file):
raise Exception("Can not read pdb file [%s]" % args.pdb_file)
pdb_list = sd.read_pdb(args.pdb_file)
chain = args.chain
assert len(pdb_list) == 1
neigbors = []
r_0, r_1, r_2 = args.residue - 1, args.residue, args.residue + 1
for pdbs in pdb_list:
assert isinstance(pdbs, dict)
assert chain in pdbs
ca_trace = sd.pdb_to_catrace(pdbs[chain])
valid_residues = ca_trace.residue_ids[1:-1]
if args.residue not in valid_residues:
raise Exception("Residue %d not a valid residue!" % args.residue)
neighbors = cg.find_k_neighbors(pdb=ca_trace,
residues=[args.residue],
k=args.topk + 2)
neighbors = [
r for r, d in neighbors[args.residue] if abs(r - args.residue) > 1
]
volumes = [
cg.PropertyCalculator.volume(ca_trace, r) for r in neighbors
]
hydropathy = [
cg.PropertyCalculator.hydropathy(ca_trace, r) for r in neighbors
]
max_coordinate, min_coordinate = read_bounding_box(args.bb_file)
for i in range(len(max_coordinate)):
max_coordinate[i] += args.buffer
min_coordinate[i] -= args.buffer
trajectory = [snap[args.chain] for snap in trajectory]
align_map = None
if args.align_map is not None:
align_map = parse_alignment(args.align_map)
if args.ref_pdb is not None:
ref_pdb = sd.read_pdb(args.ref_pdb)
assert (len(ref_pdb) == 1) and (len(ref_pdb[0]) == 1)
chain = list(ref_pdb[0].keys())[0]
ref_pdb = sd.pdb_to_catrace(ref_pdb[0][chain])
trajectory = mm.align_trajectory(ref_structure=ref_pdb,
tgt_structure=trajectory[0],
trajectory=trajectory,
align_pair=align_map,
ca_trace=True)
signature = mm.Signature(max_coord=max_coordinate,
min_coord=min_coordinate)
res_names = dict()
for trace in trajectory:
for res_id in trace.residue_ids:
if res_id not in res_names:
res_names[res_id] = trace.get_amino(res_id).name(
one_letter_code=False)
import os
import time
from mutant_model import *
from structural_dynamics import read_trajectory_catrace, read_pdb, pdb_to_catrace
if __name__ == "__main__":
pdb_file = os.path.join(os.path.dirname(__file__), 'data',
'structure_1a1v.pdb')
trj_file2 = os.path.join(os.path.dirname(__file__), 'data',
'ex_trajectory_2.pdb')
assert os.path.isfile(pdb_file) and os.path.isfile(trj_file2)
ref_pdb = pdb_to_catrace(read_pdb(pdb_file)[0]['A'])
trj = [pair['A'] for pair in read_trajectory_catrace(trj_file2)]
start = time.time()
aln_trj = align_trajectory(ref_pdb, trj[0], trj, ca_trace=True)
end = time.time()
print("Alignment time: %f" % (end - start))
out_file = os.path.join(os.path.dirname(__file__), 'out',
'aligned_to_1a1v.pdb')
with open(out_file, "w") as fh:
for i, snapshot in enumerate(aln_trj):
fh.write("MODEL %6d\n" % (i + 1))
snapshot.write(fh)
fh.write("ENDMDL\n")