Module transform 

Coordinate transformation utilities.

Provides functions for extracting, filtering, and aligning coordinates:

• Backbone/CA extraction
• Atom filtering
• Kabsch alignment

Structs

NamedResidueAtomSearch

Spatial data for per-residue atom proximity lookups that also carry atom names.

ResidueAtomSearch

Spatial data needed for per-residue atom proximity lookups.

Constants

PROTEIN_RESIDUES

Standard amino acid residue names

Functions

align_coords_bytes

Align coordinate bytes to match reference CA positions.

align_to_reference

Align COORDS to match reference CA positions using Kabsch algorithm.

backbone_only

Filter COORDS to only backbone atoms (N, CA, C, O).

build_ca_position_map

Build a map of (chain_id, res_num) -> CA position for efficient lookup.

centroid

Compute centroid of a point set.

extract_backbone_chains

Extract backbone chains from COORDS data.

extract_ca_from_chains

Extract CA positions from backbone chains (every 2nd element in N-CA-C pattern).

extract_ca_positions

Extract CA positions from COORDS data.

filter_atoms

Filter atoms by predicate on atom name.

filter_residues

Filter atoms by predicate on residue name.

get_atom_by_name

Get position of a specific atom by residue number, chain ID, and atom name.

get_atom_position

Get atom position by index.

get_backbone_atoms_from_chains

Get all backbone atom positions (N, CA, C) for a residue by index. Returns None if residue_idx is out of bounds.

get_ca_for_residue

Get CA position for a specific residue by residue number and chain ID.

get_ca_position_from_chains

Get a single CA position by residue index from backbone chains. Returns None if residue_idx is out of bounds.

get_closest_atom_for_residue

Get the closest atom (backbone or sidechain) to a reference point for a residue.

get_closest_atom_with_name

Find the closest atom to a reference point within a residue, returning both position and atom name.

get_closest_backbone_atom

Get the closest backbone atom position to a reference point for a residue.

heavy_atoms_only

Filter COORDS to only heavy atoms (exclude hydrogens).

interpolate_coords

Linear interpolation between two Coords instances.

interpolate_coords_collapse

Interpolate Coords with a collapse/expand effect through a collapse point.

kabsch_alignment

Kabsch algorithm: find optimal rotation and translation to align target to reference.

kabsch_alignment_with_scale

Kabsch-Umeyama algorithm: find optimal rotation, translation, AND scale.

protein_only

Filter COORDS to only protein residues (remove water, ligands, etc.).

set_atom_position

Set atom position by index.

transform_coords

Apply transformation to all atoms in COORDS.

transform_coords_with_scale

Apply transformation with scale to all atoms in COORDS.