if (to_recompute):
extractPDB(u_pdb_filepath, u_chain_filepath, u_chain_name)
# construct unbound the mesh.
u_regular_mesh, u_vertex_normals, u_vertices, u_names = \
ext_and_trg.msms_wrap(u_chain_filepath, to_recompute=to_recompute)
u_vertex_hbond, u_vertex_hphobicity, u_vertex_charges = \
ext_and_trg.compute_features(u_chain_filepath_base, u_vertices, u_names, u_regular_mesh, to_recompute=to_recompute)
# construct Complex the mesh.
C_regular_mesh, C_vertex_normals, C_vertices, C_names = \
ext_and_trg.msms_wrap(C_pdb_filepath, to_recompute=to_recompute)
# identify groundtruth
iface = ext_and_trg.find_iface(C_regular_mesh, u_regular_mesh,
ground_truth_cut_dist)
# save results
save_ply(ply_filepath, u_regular_mesh.vertices,\
u_regular_mesh.faces, normals=u_vertex_normals, charges=u_vertex_charges,\
normalize_charges=True, hbond=u_vertex_hbond, hphob=u_vertex_hphobicity,\
iface=iface)
ext_and_trg.copy_tmp2dst(ply_filepath, masif_opts['ply_chain_dir'])
#ext_and_trg.copy_tmp2dst(u_chain_filepath, masif_opts['pdb_chain_dir'])
# clean the /tmp dir
my.run_it(r'rm ' + os.path.dirname(u_chain_filepath_base) + r'/*' +
u_pdb_name + r'*')
my.run_it(r'rm ' + os.path.dirname(u_chain_filepath_base) + r'/*' +
C_pdb_name + r'*')
mesh = pymesh.form_mesh(v3, f3)
# I believe It is not necessary to regularize the full mesh. This can speed up things by a lot.
full_regular_mesh = mesh
# Find the vertices that are in the iface.
v3 = full_regular_mesh.vertices
# Find the distance between every vertex in regular_mesh.vertices and those in the full complex.
kdt = KDTree(v3)
d, r = kdt.query(regular_mesh.vertices)
d = np.square(
d) # Square d, because this is how it was in the pyflann version.
assert (len(d) == len(regular_mesh.vertices))
iface_v = np.where(d >= 2.0)[0]
iface[iface_v] = 1.0
# Convert to ply and save.
save_ply(out_filename1+".ply", regular_mesh.vertices,\
regular_mesh.faces, normals=vertex_normal, charges=vertex_charges,\
normalize_charges=True, hbond=vertex_hbond, hphob=vertex_hphobicity,\
iface=iface)
else:
# Convert to ply and save.
save_ply(out_filename1+".ply", regular_mesh.vertices,\
regular_mesh.faces, normals=vertex_normal, charges=vertex_charges,\
normalize_charges=True, hbond=vertex_hbond, hphob=vertex_hphobicity)
if not os.path.exists(masif_opts['ply_chain_dir']):
os.makedirs(masif_opts['ply_chain_dir'])
if not os.path.exists(masif_opts['pdb_chain_dir']):
os.makedirs(masif_opts['pdb_chain_dir'])
shutil.copy(out_filename1 + '.ply', masif_opts['ply_chain_dir'])
shutil.copy(out_filename1 + '.pdb', masif_opts['pdb_chain_dir'])