MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops¶

Functions¶

`center`(→ torch.Tensor)	Center coordinates by mask; supports [N,3], [B,N,3], or [B,S,N,3].
`kabsch_align`(→ torch.Tensor)	Align src to ref using Kabsch; supports [N,3] or [B,N,3].
`random_rotate`(→ torch.Tensor)	Apply random rotation(s) to coords, preserving masked-out positions.
`random_translate`(→ torch.Tensor)	Apply random translation(s) to coords, preserving masked-out positions.

MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops.center(coords: torch.Tensor, mask: torch.Tensor, custom_center: torch.Tensor = None, apply_mask: torch.Tensor = None) → torch.Tensor¶

Center coordinates by mask; supports [N,3], [B,N,3], or [B,S,N,3].

Parameters:

coords – Coordinates tensor [N,3], [B,N,3], or [B,S,N,3]
mask – Mask for computing center
custom_center – Optional pre-computed center to subtract
apply_mask – Optional separate mask for zeroing after centering. If None, NO zeroing is applied (matches old behavior).

MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops.kabsch_align(src: torch.Tensor, ref: torch.Tensor, mask: torch.Tensor, weights: torch.Tensor = None, debug: bool = True) → torch.Tensor¶: Align src to ref using Kabsch; supports [N,3] or [B,N,3].

MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops.random_rotate(coords: torch.Tensor, mask: torch.Tensor) → torch.Tensor¶: Apply random rotation(s) to coords, preserving masked-out positions.

MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops.random_translate(coords: torch.Tensor, mask: torch.Tensor, scale: float = 1.0) → torch.Tensor¶: Apply random translation(s) to coords, preserving masked-out positions.