Vina preparation fabricates zero charges and name-based atom types
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Active
- Tech stack
- python
- Domain
- bioinformatics
Research direction
Start with devguide/pending_bugs/vina_preparation_fabricates_zero_charges_and_name_based_atom_types.md, then review the preparation path and the linked MolSysMT issues #221 and #222. The work is complete when validated charges and atom types drive a documented PDBQT projection, or incomplete inputs are rejected with actionable diagnostics without dropping polar hydrogens by name.
Written by the indexing model from the issue text.
Description
What — Current preparation writes zero partial charges, guesses AutoDock types from names, and drops hydrogens by name, including polar receptor hydrogens.
How — Replace these assumptions with validated MolSysMT parameters and a documented PDBQT projection; until available, reject incomplete inputs with actionable diagnostics.
Why — The generated PDBQT can be syntactically accepted while misrepresenting the prepared receptor or ligand chemistry.
Record — devguide/pending_bugs/vina_preparation_fabricates_zero_charges_and_name_based_atom_types.md
Related — uibcdf/dockingmt#3. DockingMT needs MolSysMT charge and atom-typing capabilities tracked in uibcdf/molsysmt#221 and uibcdf/molsysmt#222; the local Vina opt-in is provisional while those provider issues remain open.
- Dominant language
- Python
- Stars
- 1
- Forks
- 0
- Avg merge
- 30m
- Merged PRs (30d)
- 1
Getting set up
This project ships no dev container, Dockerfile or contributing guide, so setting up is up to you: start from its README, and see our first-contribution guide for the general steps.
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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