def get_npdb_dicts(self):
mplanes = np.array(self.opm.get_planes())
dist = abs(point_plane_dist(mplanes[1][0], mplanes[0]))
npdb_dict = {}
npdb_tm_dict = {}
npdb_sol_dict = {}
for suffix, pdb_file in self.water_variants:
npdb = NumPdb(pdb_file, features=self.npdb_features)
npdb_dict[suffix] = npdb
sele = npdb.sele()
i = 0
# create transmembrane region selection
for numa in npdb.iter_resno(incomplete=True):
flag = True
for c in numa._coords:
d1 = abs(point_plane_dist(c, mplanes[0]))
d2 = abs(point_plane_dist(c, mplanes[1]))
if d1 < dist and d2 < dist:
flag = False
break
for a in numa._atoms:
sele[i] = flag
i += 1
npdb_sol_dict[suffix] = npdb.copy(sele=sele)
npdb.copy(sele=sele).write(self.outpath("sol_region.pdb"))
np.logical_not(sele, sele)
npdb_tm_dict[suffix] = npdb.copy(sele=sele)
npdb.copy(sele=sele).write(self.outpath("tm_region.pdb"))
return npdb_dict, npdb_tm_dict, npdb_sol_dict
def make_processed_pdb(self):
npdb = NumPdb(self.opm.processed_file, features=self.npdb_features)
sele = npdb.sele()
coords_dict = {}
i = 0
tree = scipy.spatial.KDTree(npdb['xyz'])
for numa in npdb._iter_resno():
for c in numa._coords:
c = tuple(c)
# remove atoms with identical coords
if c in coords_dict:
print npdb._atoms[i]
sele[i] = False
else:
coords_dict[c] = True
sele[i] = True
# remove atoms with almost identical coords
rslt = tree.query(c, k=10, distance_upper_bound=0.2)
rslt[1].sort()
if rslt[1][0] != i and rslt[0][1] != np.inf:
print i, npdb._atoms[i]
sele[i] = False
i += 1
npdb.copy(sele=sele).write2(self.processed_pdb)
def get_npdb_dicts(self):
npdb_dict = {}
npdb_tm_dict = {}
npdb_sol_dict = {}
for suffix, pdb_file in self.water_variants:
npdb = NumPdb(pdb_file, features=self.npdb_features)
npdb_dict[suffix] = npdb
sele = npdb.sele()
i = 0
# create transmembrane region selection
for numa in npdb.iter_resno(incomplete=True):
flag = True
for a in numa._atoms:
sele[i] = flag
i += 1
npdb_sol_dict[suffix] = npdb.copy(sele=sele)
npdb.copy(sele=sele).write(self.outpath("sol_region.pdb"))
np.logical_not(sele, sele)
npdb_tm_dict[suffix] = npdb.copy(sele=sele)
npdb.copy(sele=sele).write(self.outpath("tm_region.pdb"))
return npdb_dict, npdb_tm_dict, npdb_sol_dict