StructureMatch

Atom correspondence between two structures, with the residue and chain pairs behind it and the rigid core they share.

from proteinmotion import StructureMatch

Constructor

StructureMatch(
    source_atoms: np.ndarray,
    target_atoms: np.ndarray,
    residue_pairs: list=field(default_factory=list),
    chain_pairs: list=field(default_factory=list),
    core: np.ndarray=field(default_factory=lambda: np.empty(0, dtype=int)),
    core_rmsd: float=float('nan'),
)

Parameters

Parameter	Default	Description
`source_atoms`np.ndarray	Required	Matched source atom indices.
`target_atoms`np.ndarray	Required	Target atom indices, one per source atom.
`residue_pairs`list	`field(default_factory=list)`	Matched (source, target) topology residue indices, including ligands.
`chain_pairs`list	`field(default_factory=list)`	(source chain, target chain, sequence identity) for each paired chain.
`core`np.ndarray	`field(default_factory=lambda: np.empty(0, dtype=int))`	Source Cα/C4′ atom indices of the rigid core: matched trace atoms that superpose within 2 Å after pruning the worst pairs and refitting. StructureMorph and domain_motion superpose on it by default.
`core_rmsd`float	`float('nan')`	Root-mean-square deviation of the rigid core after superposition, in Å.

Attributes

Name	Description
`source_atoms`	Matched source atom indices.
`target_atoms`	Target atom indices, one per source atom.
`residue_pairs`	Matched (source, target) topology residue indices, including ligands.
`chain_pairs`	(source chain, target chain, sequence identity) for each paired chain.
`core`	Source Cα/C4′ atom indices of the rigid core: matched trace atoms that superpose within 2 Å after pruning the worst pairs and refitting. StructureMorph and domain_motion superpose on it by default.
`core_rmsd`	Root-mean-square deviation of the rigid core after superposition, in Å.

Example and output

Run this command from a repository checkout.

Code Render command

proteinmotion render examples/structure_morph.py HemoglobinMorph \
  -o hemoglobin-morph.mp4 --fps 60

Output Preview · 17.7 s · 60 fps

Hemoglobin from T to R

Deoxyhemoglobin (2DN2) morphs to oxyhemoglobin (2DN1, expanded to its tetramer), superposed on α1β1. α2β2 turns 14° in the image plane while O₂ appears at each heme. A heatmap shows Cα–Cα distances changing between the αβ dimers but not within them. The path illustrates the difference between the two structures.

Full source: HemoglobinMorph Download MP4

Methods and properties

Name	Description
reportproperty	Chain pairs with sequence identity, counts of matched residues and atoms, and the rigid core.

report

View source

StructureMatch.report

Chain pairs with sequence identity, counts of matched residues and atoms, and the rigid core.