Examples » PDB files

There are many flavours of PDB managed differently by different programs. By default pyxmolpp2 uses AMBER-compatible convention. For example, reading tleap-like .pdb file as a standard one results to an error:

import os
from pyxmolpp2 import PdbFile

pdb_filename = os.path.join(os.environ["TEST_DATA_PATH"], "trjtool/GB1/run00001.pdb")
pdb_file = PdbFile(pdb_filename, PdbFile.STANDARD_V3)

Traceback (most recent call last):
  File "<string>", line 5, in <module>
RuntimeError: PDB line: can't read int
at line 1:6-10
ATOM       1 N   MET A   1       5.303 -17.908 -11.078  1.00  0.00              
~~~~~~^^^^^

To write multiple frames to a single pdb you can use next snippet:

pdb_file = PdbFile(pdb_filename)
frames = pdb_file.frames()

with open("/dev/null", "w") as output:
    for i, frame in enumerate(frames):
        output.write("MODEL    {i:4d}\n")
        frame.to_pdb(output)
        output.write("ENDMDL\n")