MolecularDiffusion.utils.substituent_builder

Self-contained substituent-fragment placement for outpaint skeleton init.

Uses the bundled idealized fragment geometries in substituent_geometries.py (attachment atom = row 0, bond pointing along local +x) to build clean, connector-anchored placeholder coordinates for the to-be-generated atoms. Only coordinates are used (a geometry prior); node features are randomized and denoised. No external dependency.

Functions

place_fragment(frag_coords, connector_pos, direction)	Align a local fragment so its bond points along direction at the connector.
select_fragment(tags_all, n_extra)	Pick the bundled fragment matching all tags_all closest to n_extra.

Module Contents

MolecularDiffusion.utils.substituent_builder.place_fragment(frag_coords, connector_pos, direction, roll_angle=None)

Align a local fragment so its bond points along direction at the connector.

The fragment’s attachment atom (row 0, local ~(bond, 0, 0)) lands at connector_pos + bond * direction; an optional roll about direction adds orientational diversity. Returns placed coords (M, 3).

MolecularDiffusion.utils.substituent_builder.select_fragment(tags_all, n_extra)

Pick the bundled fragment matching all tags_all closest to n_extra.

Among fragments whose tags include every tag in tags_all (empty tags_all matches any), prefer the one whose atom count is >= n_extra and closest to it (so we subset rather than extend); otherwise the largest available. Returns (name, coords_tensor (M, 3)) or (None, None).