fix motif drift for symmetric fused-motif designs

[TanushGoel]

Issue

When scaffolding a fused/contiguous motif under symmetry (inference_sampler.kind=symmetry), the motif drifts over the trajectory so the output no longer matches the input motif.

Symmetric inference applies a per-step COM recenter, then rebuilds the symmetric copies from the ASU. A fused motif is part of the generated chain, so it isn't marked FIXED_ENTITY_ID and nothing corrects for the shift. The recenter, propagated through the symmetry transforms, moves the motif off its input pose and the error accumulates over the trajectory.

Fix

In SampleDiffusionWithSymmetry.apply_symmetry_to_X_L, we skip the COM recenter when a contiguous motif is present, so it stays put and the symmetric copies rebuild from it correctly.

Scope

Scoped to is_motif_atom_with_fixed_coord & is_sym_asu & ~FIXED_ENTITY_ID and guarded by not self.allow_realignment, so it's a no-op for de novo symmetric, unindexed motifs, and the non-symmetric sampler.

[arhanjain]

facts