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Define ligand torsion policy across RDKit and Vina reference differences

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Active
Tech stack
python
Domain
backend

Research direction

Start with the pinned 1IEP, 1S63, ethyl acetate, and 5X72 cases in the issue, comparing exact bond identity, fragment partitions, atom mapping, hydrogens, RDKit version and mode, and Vina parser acceptance. Review uibcdf/molsysmt#224, uibcdf/molsysmt#214, and uibcdf/dockingmt#6 for scope boundaries; done means a minimal differential matrix and an explicit policy for allowed choices, warnings, rejection, and automatic selection.

Written by the indexing model from the issue text.

Description

component:molsysmt enhancement

What

Document and decide DockingMT's ligand torsion-selection policy when RDKit rotatable-bond descriptors and published AutoDock Vina ligand PDBQT branch trees disagree. The current explicit-bond bridge validates a bounded set of structural conditions but does not implement a general automatic classifier.

Reproduction and evidence

  • Pinned Vina 1IEP: seven published PDBQT branches; RDKit 2025.09.5 CalcNumRotatableBonds(Strict) counts seven on the hydrogen-suppressed source. This agreement alone does not validate automatic perception because DockingMT currently selects the seven reference bonds explicitly.
  • Pinned Vina 1S63: six published PDBQT branches; RDKit Strict counts five. The extra published branch is the aryl–C≡N bond (source indices 26–27). DockingMT currently accepts that bond when explicitly requested. The source SDF has 29 atoms, while the PDBQT has 30, so hydrogen placement must be compared separately.
  • Ethyl acetate CC(=O)OCC: RDKit Strict counts one rotatable bond; DockingMT currently accepts both nonterminal single-bond requests, including the ester acyl C–O bond (indices 1–3).
  • The official Vina 5X72 P59/P69 stereoisomer pair has two branches each and provides a smaller positive structural control.

Outcome

Build a pinned, minimal differential case matrix with exact bond identity, fragment partition, source atom mapping, hydrogen handling, RDKit version and descriptor mode, and Vina parser acceptance. Define which differences are allowed explicit choices, which require warnings or rejection, and whether any automatic selection policy is scientifically supported. Do not silently identify RDKit Strict with Vina's branch choices.

DockingMT owns the docking protocol choice and user-facing policy. General chemical classification and reusable fragment output belong to uibcdf/molsysmt#224; the temporary PDBQT writer belongs ultimately to uibcdf/molsysmt#214. Related consumer work: uibcdf/dockingmt#6. No Meeko runtime dependency is proposed.

Record: devguide/pending_proposals/define_ligand_torsion_policy_across_rdkit_and_vina_references.md (partial). Pinned matrix and current evidence: devguide/validation/vina_torsion_matrix.md and commit 2fe344d.

Dominant language
Python
Stars
1
Forks
0
Avg merge
30m
Merged PRs (30d)
1

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First steps

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