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Read a PDB File
16 min readNov 3, 2020
This program will output a list of coordinates,atoms, bonds, and charges for a given PDB file.
parsePDB(‘1qwt.pdb’,’1qwt.mol2',’1qwt.pqr’)
(array([[ 3.7047e+01, 5.8833e+01, 1.2460e+01],
[ 3.7967e+01, 5.7721e+01, 1.2090e+01],
[ 3.7698e+01, 5.6504e+01, 1.2966e+01],
...,
[ 5.2367e+01, -2.7490e+00, 2.0685e+01],
[ 5.2585e+01, -3.8470e+00, 2.1553e+01],
[ 5.2699e+01, -2.0000e-03, 1.9878e+01]]),
['N',
'C',
'C',
'O',
'C',
'C',
'C',
'O',
'O',
'N',
'C',
'C',
'O',
'C',
'C',
'O',
'N',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'N',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'N',
'C',
'N',
'N',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'O',
'O',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'O',
'O',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'N',
'C',
'C',
'C',
'C',
'C',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'O',
'O',
'N',
'C',
'C',
'O',
'C',
'C',
'C',
'C',
'C',
'C'…