code stringlengths 3 6.57k |
|---|
chain.get_residues() |
len(chain) |
at_i.get_name() |
at_j.get_name() |
np.linalg.norm(at_i.get_coord() |
at_j.get_coord() |
range(len(chain) |
range(len(chain) |
np.linalg.norm(at_i.get_coord() |
at_j.get_coord() |
compute_ave_atom_contact(structure, threshold, excluded=[]) |
len(chain) |
np.zeros((res_count,res_count) |
compute_atom_contact(model, threshold, excluded) |
len(structure) |
compute_max_residue(structure, ave_struct_contact_matrix) |
np.sum(ave_struct_contact_matrix[i]) |
res.get_resname() |
res.get_resname() |
res.get_resname() |
res.get_resname() |
compute_normalization_factor(pdb_dir, threshold, output) |
PDBParser() |
glob.iglob(pdb_dir + "/*.pdb") |
filename.split('/') |
split('.') |
parser.get_structure(label,filename) |
compute_ave_atom_contact(structure, 2) |
compute_max_residue(structure, ave_struct_contact_matrix) |
open(output, "w") |
csv.writer(outfile) |
csvfile.writerow([key,res_dir_dict[key]]) |
read_normalization(norm_fact) |
open(norm_fact) |
csv.reader(normfile) |
float(row[1]) |
compute_interaction(res_1, res_2, inter_atoms, norm_dict) |
return (inter_atoms*100.0) |
sqrt(norm_1*norm_2) |
compute_atom_contact(model, contact_thresh, excluded) |
np.zeros(model_contact.shape) |
range(len(residues) |
range(len(residues) |
get_residues() |
residues.append(res.get_resname() |
np.zeros((len(residues) |
len(residues) |
np.zeros((len(residues) |
len(residues) |
len(structure) |
range(len(residues) |
range(len(residues) |
structure.get_id() |
np.savetxt(filename,PSN,fmt='%d') |
PDBParser() |
glob.iglob(pdb_dir + "/*.pdb") |
filename.split('/') |
split('.') |
parser.get_structure(label,filename) |
main(argv) |
sys.exit(2) |
sys.exit() |
in ("-p", "--pdb_dir") |
in ("-f", "--norm_fact") |
in ("-e", "--edge_prct") |
string_to_float(arg) |
in ("-c", "--contact_thresh") |
string_to_float(arg) |
in ("-i", "--interaction_thresh") |
arg.split(",") |
interaction_thresh.append(string_to_float(i) |
in ("-o", "--output") |
in ("-n","--normalize") |
PDBParser() |
parser.get_structure('1akg','../native/1acw.pdb') |
compute_normalization_factor(pdb_dir, contact_thresh, output) |
compute_normalization_factor(pdb_dir, contact_thresh, outdir) |
read_normalization(norm_fact) |
main(sys.argv[1:]) |
and (lambda x:x) |
or (lambda x:x.encode('latin1') |
protoc_insertion_point(imports) |
_symbol_database.Default() |
_b('\n\x11\x61\x64\x64ressbook.proto\"1\n\x06Person\x12\x0c\n\x04name\x18\x01 \x01(\t\x12\n\n\x02id\x18\x02 \x01(\x05\x12\r\n\x05\x65mail\x18\x03 \x01(\tb\x06proto3') |
_b("") |
decode('utf-8') |
_b("") |
decode('utf-8') |
_sym_db.RegisterFileDescriptor(DESCRIPTOR) |
_reflection.GeneratedProtocolMessageType('Person', (_message.Message,) |
protoc_insertion_point(class_scope:Person) |
_sym_db.RegisterMessage(Person) |
protoc_insertion_point(module_scope) |
ListedColormap(['#FFAAAA', '#AAFFAA', '#AAAAFF']) |
ListedColormap(['#FF0000', '#00FF00', '#0000FF']) |
plot_iris_knn() |
datasets.load_iris() |
neighbors.KNeighborsClassifier(n_neighbors=3) |
knn.fit(X, y) |
min() |
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