Ligand PDBQT writer shifts columns for four-character atom names
Nobody has claimed this yet.
Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 86/100
Research direction
Start at PreparedLigand.to_pdbqt() and reproduce with the pinned 1S63 ligand SDF and published branch bonds. Check the emitted chlorine record against the stated PDBQT column positions, add a regression for four-character atom names and explicit rejection of longer names, and verify that Vina accepts the generated ligand.
Written by the indexing model from the issue text.
Description
What
DockingMT's temporary ligand PDBQT writer shifts fixed-width fields when an atom name has four characters. Vina's official 1S63 ligand source contains a chlorine atom that DockingMT names Cl23; the generated record places 3 in the alternate-location column and shifts the residue and coordinates. Parsing the Y field from columns 39-46 then fails (4 131.71).
Reproduction
Convert the pinned AutoDock Vina 1S63 ligand SDF to MolSysMT, request the six published ligand branch bonds, and call PreparedLigand.to_pdbqt(). The emitted chlorine line starts ATOM 29 Cl23 LIG and has a malformed coordinate field. Source: ccsb-scripps/AutoDock-Vina commit 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645, example/docking_with_zinc_metalloproteins/data/1s63_ligand.sdf.
Expected
PDBQT atom-name field occupies exactly columns 13-16 for one- through four-character names, coordinates stay in columns 31-54, and Vina accepts the generated ligand. Names longer than four characters fail explicitly rather than shifting fields.
DockingMT owns this temporary writer fix. General PDBQT serialization belongs to uibcdf/molsysmt#214; the 1S63 regression should inform its eventual implementation. Related matrix: uibcdf/dockingmt#17.
- Dominant language
- Python
- Stars
- 1
- Forks
- 0
- Avg merge
- 30m
- Merged PRs (30d)
- 1
Getting set up
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First steps
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