Adding functionality for unconstrained ligand minimization#15

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delalamo wants to merge 29 commits intomainfrom

ligand-minimization

Commits on Jan 13, 2026

Fix CI disk space issue in integration tests

delalamo
and
claude
committed
Merge remote-tracking branch 'origin/claude/detect-chain-gaps-GmW3r' into idealize
delalamo
committed
Add ligand-aware unconstrained minimization support

delalamo
and
claude
committed
Refactor ligand SMILES: use RDKit parsing instead of hardcoded dictionary

delalamo
and
claude
committed
Use try-except imports with helpful error messages for conda deps

delalamo
and
claude
committed
Merge branch 'main' into ligand-minimization
delalamo
committed
Add crystallography artifact removal and mamba installation docs

delalamo
and
claude
committed
Merge main into ligand-minimization

delalamo
and
claude
committed
Simplify --keep-ligand to accept comma-separated values only

delalamo
and
claude
committed
Remove redundant code and update README

delalamo
and
claude
committed
Merge remote-tracking branch 'origin/main' into ligand-minimization
delalamo
committed
Remove requirements.txt and fix integration tests

delalamo
and
claude
committed
Clarify conda-forge dependencies in README

delalamo
and
claude
committed
Make all conda-forge dependencies mandatory

delalamo
and
claude
committed
Enable idealization by default and add missing residue control

delalamo
and
claude
committed
Fix residue numbering after idealization and add resfile warning

delalamo
and
claude
committed
Merge branch 'main' into ligand-minimization
delalamo
authored
Include ligands in unconstrained minimization

delalamo
and
claude
committed
Include ligands in idealization minimization

delalamo
and
claude
committed
Raise error for unparameterizable metallocofactors

delalamo
and
claude
committed
Remove silent error handling for ligand parameterization

delalamo
and
claude
committed
Don't silently skip ligands that fail parameterization

delalamo
and
claude
committed
Simplify ligand handling: use exclusion zones instead of parameterization

delalamo
and
claude
committed

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Adding functionality for unconstrained ligand minimization#15

Adding functionality for unconstrained ligand minimization#15
delalamo wants to merge 29 commits intomainfrom
ligand-minimization

Commits on Jan 12, 2026

Add Docker support with GitHub Container Registry publishing

Adding .DS_Store to .gitignore

Merge branch 'main' of https://github.com/delalamo/GraphRelax into feature/docker-workflow

Add chain gap detection to prevent artificial gap closure during minimization

Fix chain splitting to assign new chain ID once per segment, not per atom

Merge branch 'main' into claude/detect-chain-gaps-GmW3r

Commits on Jan 13, 2026

Fix CI disk space issue in integration tests

Merge remote-tracking branch 'origin/claude/detect-chain-gaps-GmW3r' into idealize

Add ligand-aware unconstrained minimization support

Refactor ligand SMILES: use RDKit parsing instead of hardcoded dictionary

Use try-except imports with helpful error messages for conda deps

Merge branch 'main' into ligand-minimization

Add crystallography artifact removal and mamba installation docs

Merge main into ligand-minimization

Simplify --keep-ligand to accept comma-separated values only

Remove redundant code and update README

Merge remote-tracking branch 'origin/main' into ligand-minimization

Remove requirements.txt and fix integration tests

Clarify conda-forge dependencies in README

Make all conda-forge dependencies mandatory

Enable idealization by default and add missing residue control

Fix residue numbering after idealization and add resfile warning

Merge branch 'main' into ligand-minimization

Include ligands in unconstrained minimization

Include ligands in idealization minimization

Raise error for unparameterizable metallocofactors

Remove silent error handling for ligand parameterization

Don't silently skip ligands that fail parameterization

Simplify ligand handling: use exclusion zones instead of parameterization