fu / p3d

p3d - python module for structural bioinformatics

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I am Christian Fufezan, excited about tec, programming, CNC, data viz, diving and coffee.

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p3d's Issues

Fails to parse .pdb file of a single amino acid.

The file contains atoms as lines:
ATOM 1 CA ACE 1 -2.184 0.591 0.910 1.00 7.00 MAIN
ATOM 2 C ACE 1 -0.665 0.627 0.966 1.00 0.00 MAIN
ATOM 3 O ACE 1 -0.069 1.213 1.868 1.00 0.00 MAIN
ATOM 4 N ALA 2 0.000 0.000 0.000 1.00 3.00 MAIN
ATOM 5 H ALA 2 -0.490 -0.462 -0.712 1.00 0.00 MAIN
.
.
.
(http://wbiomed.curtin.edu.au/biochem/tutorials/pdb/ala.pdb)

and since there is the word "MAIN" at the end of each line rather than the initial letter of the atom name, it fails to parse.
In my case it was Alanine, which it failed to read, it says:

The following atom was missed by the reg-ex.
ATOM 1 CA ALA 1 -0.208 -0.536 0.032 1.00 0.00
This branch is for debugging purpose ...,
adapted pattern matches line now ...