Fix HBond conflict and stabilize tempdir usage#231
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Chen-Jie7 wants to merge 4 commits intoRosettaCommons:productionfrom
Open
Fix HBond conflict and stabilize tempdir usage#231Chen-Jie7 wants to merge 4 commits intoRosettaCommons:productionfrom
Chen-Jie7 wants to merge 4 commits intoRosettaCommons:productionfrom
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When a user specifies select_fixed_atoms for a ligand with only a subset of its atoms, the unfixed atoms were ending up physically disconnected from the fixed ones (e.g., C11-C12 bond at 5-11A instead of ~1.5A). Three root causes were addressed: 1. _set_origin() zeroed coordinates for ALL unfixed atoms including ligand atoms, placing them at the origin. Now excludes ligand atoms (identified via atom_array.hetero) from zeroing. 2. centre_random_augment_around_motif() applied centering asymmetrically when centering_affects_motif=False, pulling unfixed ligand atoms away from fixed ones. Now accepts an is_ligand_atom mask and excludes ligand atoms from asymmetric centering. 3. Both initial noise (_get_initial_structure) and per-step noise (epsilon_L) were applied at full scale to unfixed ligand atoms, placing them ~160A away. Now zeroes noise for unfixed ligand atoms so they stay near their original positions while the model can still softly adjust them through denoising predictions. To support this, is_ligand_atom is now extracted as an atom-level feature in AddIsXFeats and propagated through the diffusion pipeline to the inference sampler. Verified with biotin_2.json partial fix (16/21 atoms fixed): C11-C12 bond improved from 5-11A to ~2.5A. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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