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Select active ligand torsions for Vina preparation

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
48/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Active
Tech stack
python
Domain
backend

Research direction

Read devguide/pending_proposals/select_active_ligand_torsions_for_vina_preparation.md and inspect dockingmt/preparation/_temporary_torsions.py at aba7849. Review related uibcdf/molsysmt#224 before deciding how the temporary bridge should be replaced. Done means explicit ligand bonds are validated, PDBQT ROOT/BRANCH records and rigid fragments are derived, and source atom/bond mapping survives Vina poses using the same tests and behavior.

Written by the indexing model from the issue text.

Description

component:molsysmt enhancement

What — Allow the docking protocol to choose which candidate ligand bonds are active torsions.
How — Select explicit bonds from a MolSysMT ligand, validate them, derive a rigid-fragment tree, write PDBQT ROOT/BRANCH records, and preserve the source atom map through Vina poses. The general graph operation is temporarily implemented in DockingMT until MolSysMT provides it.
Why — A flexible-ligand Vina input requires a valid torsion tree and an inspectable selection, rather than only a TORSDOF count.
Record — devguide/pending_proposals/select_active_ligand_torsions_for_vina_preparation.md
Related — uibcdf/dockingmt#3; uibcdf/molsysmt#224 owns reusable rotatable-bond classification and rigid-fragment derivation. Temporary bridge: dockingmt/preparation/_temporary_torsions.py at aba7849. Remove that bridge and consume the MolSysMT operation when it passes the same tests and preserves source atom/bond mapping.

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

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