log to TS
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
Research direction
Start by locating the log-to-TS method and the ASE Gaussian calculator code that writes the input title block. Review how TS metadata is currently recovered from atom sorting labels. Done means Gaussian inputs preserve ts.reaction_label, ts.reaction_family, ts.direction, and labeled atoms so log-to-TS generation remains reliable across ASE versions.
Written by the indexing model from the issue text.
Description
To update the TS database, we need to work backwards: generate a TS from a log file. We currently rely on the atom sorting labels to identify the atoms in the reaction center. However, sometimes the sorting labels in the log file don't match up with the TS sorting labels (if using a different version of ase for example). We could make the log to TS method more robust if we include key information in the gaussian log file needed to generate the TS, such as ts.reaction_label, ts.reaction_family, ts.direction, and ts.rmg_molecule.get_all_labeled_atoms(). We could do this by adding these attributes to the title block of the gaussian input file (unfortunately Gaussian doesn't print comments in output). However, ase's gaussian calculator does not have a title parameter (it just writes Gaussian input prepared by ASE), so we would need to change ase Gaussian code
- Dominant language
- Python
- Stars
- 51
- Forks
- 19
- PR merge metrics
- No merged PRs in 30d
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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