Enabling automatic param/top generation for ligands embedded in a larger system and multiple ligands - #1646

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amjjbonvin wants to merge 13 commits into

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Commits on Aug 1, 2026

Extract ligand(s) before running PRODRG for autotoppar topology

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claude
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7f04028
Enable autotoppar in haddock3-score

amjjbonvin
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claude
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0ee5f06
ruff formatting for cli_score

amjjbonvin
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claude
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2bbfcb9
Fix -k short flag for --keep-all in haddock3-score

amjjbonvin
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claude
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06f7429
Assign unique cofactor-safe CNSSEP letters per ligand in PRODRG

amjjbonvin
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claude
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4388a6c
Apply cofactor-safe CNSSEP separator to single ligands too

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89ed26e

Commits on Aug 2, 2026

Updated changelog
amjjbonvin
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afcbe7b
Use 1AZS_l_u.pdb (GSP ligand) in prodrg complex tests

amjjbonvin
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claude
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815bc12
Ruff formatting
amjjbonvin
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aedb4b6
Update alascan test for autotoppar-enabled scoring

amjjbonvin
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claude
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a657fda
Correct metal-mislabelled ligand atoms before running PRODRG

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dfc0415

Commits on Aug 3, 2026

Use libpdb slice constants and setdefault in libligand

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claude
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19d6f64

Commits on Aug 4, 2026

Merge branch 'main' into prodrg
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