Extracting fields from a Protein Data Bank file (PDB) using python
Sometime, for large pdb files, one cannot use the split command from python.
Below is the python line to extract fields from a pdb file:
with open('min.pdb') as pdbfile:
for line in pdbfile:
if line[:4] == 'ATOM' or line[:6] == "HETATM":
print line
splitted_line = [line[:6], line[6:11], line[12:16], line[17:20], line[21], line[22:26], line[30:38], line[38:46], line[46:54]]
print splitted_line
print "%-6s%5s %4s %3s %s%4s %8s%8s%8s\n"%tuple(splitted_line)Sample output:
# Original line
HETATM10000 O HOH B3257 2.509 40.006 -4.097 1.00 0.00 O
# Splitted line
['HETATM', '10000', ' O ', 'HOH', 'B', '3257', ' 2.509', ' 40.006', ' -4.097']
# Go back to pdb formatted line
HETATM10000 O HOH B3257 2.509 40.006 -4.097