adding hydrogens ignores the pH option

[amjjbonvin]

Describe the bug

When running the ligand parametrisation example and part adding the hydrogens, obabel reports that it will ignore the defined pH because both the -p and -p options are given. Extract from a log file:

*** Open Babel Warning  in DoTransformations
  Both -p and -h options are set. All implicit hydrogens (-h) will be added without considering pH.

To Reproduce

Run the ligand parametrisation notebook, and check the log file generated by the Add Hydrogens step

Expected behavior

the -h and -p options should be exclusive, allowing to control the pH to define the protonation state.

Desktop (please complete the following information):

• OS: OSX 13.6.2
• Python version: 3.12.0 (installed via miniconda)
• BioBB version 4.1.0

[amjjbonvin]

Tested manually with obabel that when using only the -p options hydrogens are added considering the defined pH. With both -h and -p all hydrogens are added by default, irrespective of the defined pH

[gbayarri]

Fixed in PR https://github.com/bioexcel/biobb_chemistry/pull/7, it will be available in the next release.

Thanks!

[github-actions[bot]]

This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.

[amjjbonvin]

This strange to close an issue as completed when nothing has happened… it is not because it was stale that it is completed.

[gbayarri]

Hi, @amjjbonvin , it's an automatic action. It's reopened until next release.

Best.

[amjjbonvin]

Hi Genis

Thanks. Then you could close it as “not planned” or something else, but not as “completed” (might be easier to extract stats of what has been done) :-)

Cheers Alexandre

[gbayarri]

Fixed in the new 4.2.0 version