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ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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`database.thermo.getThermoData` clears molecule's labeled atoms #725

Closed connie closed 1 year ago

connie commented 8 years ago

This behavior works when running an RMG job because getThermoData is used mostly in rmgpy.rmg.model as shown by the history of the function: https://github.com/ReactionMechanismGenerator/RMG-Py/commit/29cf8dc85222d0fd37459a7329f218904394ad1d

But can lead to erratic behavior if using outside of a normal RMG run because it erases all labeled atoms.

It is also called in database.thermo.getThermoDataFromGroups and whenever radical count > 1. BUT the atom labels are not erased when the thermo is directly retrieved from libraries or QM and radical count = 0, so it can definitely lead to unexpected issues in the future with these inconsistencies.

nyee commented 8 years ago

When does an inputted molecule start with labels/What was the application for this?

github-actions[bot] commented 1 year ago

This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.