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bioexcel / biobb_chemistry

Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
https://mmb.irbbarcelona.org/biobb/
Apache License 2.0
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Include the ability for acpype to determine the charge of ligand #2

Closed DomFijan closed 3 years ago

DomFijan commented 3 years ago

Current implementation does not allow any of the acpype utilities to leave out the charge option (-n ) thus it is not possible to have acpype determine the charge.

In this implementation charge key in properties dictionary can be provided None as an argument which will then start acpype without charge argument which in turn then makes acpype determine the charge of the system (often with decent results). The documentation has been updated accordingly.

Default charge of 0 was left as is, although it might make sense at some point to change it to None, as such option could be slightly more intuitive.

gbayarri commented 3 years ago

Added to master, thanks for your contribution, @DomFijan