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Incorrect element assignment for 4-character atom names. #4644
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Mar 5, 2024
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Setup
I am reporting a problem with Biopython 1.83, Python 3.11.7, and Linux-6.1.64-09049-g010fe86d9eae-x86_64-with-glibc2.36 as follows:
When running
_assign_element
inPDB/Atom.py
, elements are not correctly assigned for atoms with 4 characters long names such as HNZ1 and HNE2 in the lysine residue.I fixed the code and proposed it as a PR.
Expected behaviour
"H" is assigned for atoms with 4 characters long names such as HNZ1 and HNE2.
Actual behaviour
"X" is assigned for atoms with 4 characters long names such as HNZ1 and HNE2.
Steps to reproduce
To reproduce, construct
Atom
instance without designating elements for atoms using PDB file containing HNX(X = A-Z) group in the lysine residue.(
_assign_element
is automatically run.)The text was updated successfully, but these errors were encountered: