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Fix PDBQT parser for wrong H elements interpolation #957

Merged
merged 2 commits into from Jan 24, 2023
Merged

Fix PDBQT parser for wrong H elements interpolation #957

merged 2 commits into from Jan 24, 2023

Commits on Jan 8, 2023

  1. fix unrecognized H element in PDBQT files 

    Some protonated PDBQT files have H atom names starting with numbers.
e.g. in Arginines `2HH2`.
Previous code was infering element name from the first 2 letters of
the atom name in PDBQT files. This resulted in having these atoms default
to unknown elements, with a default vdw radius far greater than H's value
and buggy connectivity after autobonding.
This trick was probably used as a workaround due to special atom
types being written in the elements columns.
In this commit , the atom types are used instead
with a mapping to element names taken from Meeko, a utility
library for conversions to PDBQT.
    @papillot
    papillot committed Jan 8, 2023
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  2. add tests for PDBQT

    @papillot
    papillot committed Jan 8, 2023
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