def experimental_method(pdb_path):
"""
Get String representation of Experimental method used file of interest.
Use header for this information.
:param pdb_path: Path to PDB file
:return:
"""
parser = PDBParser(get_header=True)
parser.get_structure('', pdb_path)
return parser.get_header()['structure_method']
def load_from_file(self, path):
"""
Load a file from PDB or mmCIF. .gz is supported.
:param path: Path to PDB or mmCIF file
:rtype: tuple(bio.PDB.Structure.Structure, dict)
"""
structure = None
if re.search(".pdb", path):
parser = PDBParser()
else:
parser = MMCIFParser()
path = path.strip()
model_id = os.path.basename(path)
#if os.path.basename(path).split('.')[-1] == 'gz':
# GZ = gzip.open(path, 'rb')
# GZ.close()
#else :
structure = parser.get_structure(model_id, open_file(path))
header = parser.get_header()
return structure, header
if len(coords) != 3:
break
lines.append(
"ATOM {0} {5} {1} A {6} {2:5.2f} {3:5.2f} {4:5.2f} 0 0 {7}\n"
.format(3 * idx + i + 1, name, coords[i][0], coords[i][1],
coords[i][2], atoms[i], idx + 1, atoms[i][0]))
fp.write("END\n")
fp.writelines(lines)
fp.close()
if __name__ == '__main__':
pn_test = os.curdir + '/../rgn_pytorch/data/text_sample'
data = load_data(pn_test)
for d in data:
id = str(d[0][0]).replace('#', '')
pdb_file_name = pn_test + '_' + id + '.pdb'
proteinnet_to_pdb_file(d, pdb_file_name, id)
p = PDBParser(PERMISSIVE=0)
# pdb_file_name = os.curdir + '/../rgn_pytorch/data/1mbs'
structure = p.get_structure("1", pdb_file_name)
header = p.get_header()
print(header)
model = structure[0]
dssp = DSSP(model, pdb_file_name)
# DSSP data is accessed by a tuple (chain_id, res_id)
a_key = list(dssp.keys())[2]
# (dssp index, amino acid, secondary structure, relative ASA, phi, psi,
# NH_O_1_relidx, NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy,
# NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx, O_NH_2_energy)
