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Vina preparation fabricates zero charges and name-based atom types

Aperta
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#5 45 commenti 0 reazioni 0 assegnatari Vedi su GitHub

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Valutazione

Difficoltà
5/5
Tempo stimato
Più di una settimana
Idoneità per principianti
25/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Attiva
Stack tecnologico
python
Ambito
bioinformatics

Direzione di ricerca

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.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

bug component:molsysmt

Original report — 2026-09-22

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.

Current partial status — 2026-10-10

Corrected exact-head checkpoint: 2466b8f; CI 38044401501, attempt 1.

All four required lanes executed ordinary sibling/consumer installation, immutable SDK/dependency preflight, isolated installed import/Requires-Python checks and the complete source suite successfully:

Python Passed / skipped Suite seconds Retained warnings Job
3.11 1095 / 0 496.17 848 114190895556
3.12 1095 / 0 465.40 848 114190895458
3.13 1095 / 0 337.01 848 114190895455
3.14 1095 / 0 480.86 848 114190895507

Quality passes. Distribution/reporting passes 24 tests in 1.18 s. MolSysSuite policy and Conda publication governance pass. All six executed CI jobs succeed. Python 3.14 produced and retained dockingmt-python-coverage-38044401501-1 successfully.

Pending external completion: coverage publisher job 114192761648 is queued without executed steps. Native CI status is queued, conclusion absent, so this is not a globally terminal green run. Owning recovery: #49 (cross-linked #5), inspect the same publisher when allocated, verify download/upload results, and append terminal evidence without changing/rebuilding the scientific candidate. No workflow cancellation, policy waiver or repeated suite is used to hide this missing publisher evidence. Local native logs and the separate pending checkpoint receipt are retained.

Both preparation roles require complete finite supplied charges or explicit MolSysMT assignment; supplied zeros remain valid, provider failures propagate, and current automatic Vina cannot bypass absent values with provisional opt-in. The receptor delegates the explicitly chosen charge stage before typing and performs no H addition/repair. Maintained contract, guard; unit-policy feedback remains MolSysMT #381.

The initial 77c1c5c hosted candidate has 1,080 passed / 15 failed in each of four lanes, identical to the local diagnostic causes; its tests do not qualify. The test-only correction is independently qualified above. Original scientific archives, producer bytes, source/reference digests and unintegrated 5X72 displacement work remain unchanged. Sibling worktrees and shared dependency/environment state are preserved.

Keep #5/#49 partial: MolSysMT #223 still owns the native H/charge projection object and maps; broader molecular export/pose/snapshot retirement and chemical/scoring acceptance remain separate. These source/isolated-installed checkpoints are not an installed-whole-suite artifact or scientific/public admission claim.

Lingua principale
Python
Stelle
1
Fork
0
Merge medio
30m
PR unite (30g)
1

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