match_backbones

Find the largest ordered residue match under a contact-error limit.

from proteinmotion import match_backbones

Signature

match_backbones(
    source,
    target,
    *,
    source_chain=None,
    target_chain=None,
    cutoff=8.0,
    softness=1.5,
    max_contact_error=0.3,
    search_seconds=8.0,
    max_candidates=6000,
)

Parameters

Parameter	Default	Description
`source`	Required	Source Protein.
`target`	Required	Destination Protein.
`source_chain`keyword only	`None`	Source chain ID; required if several chains contain Cα atoms.
`target_chain`keyword only	`None`	Target chain ID; required if several chains contain Cα atoms.
`cutoff`keyword only	`8.0`	Distance cutoff in ångströms.
`softness`keyword only	`1.5`	Width of the soft contact transition in ångströms.
`max_contact_error`keyword only	`0.3`	Maximum discrepancy between matched soft contacts, in [0, 1].
`search_seconds`keyword only	`8.0`	Branch-and-bound time budget in seconds; preparation is additional.
`max_candidates`keyword only	`6000`	Candidate correspondence limit; None searches all candidates up to the safety limit.

Returns: ContactMatch

Notes

For equally sized matches, the search minimizes contact-map discrepancy. Check the report for full-space, candidate-restricted, or time-limited optimality. Each input must resolve to one chain with at least three Cα atoms. The shorter chain supports at most 800 Cα residues; full candidate search supports at most 30,000 pairings.

Example and output

Run this command from a repository checkout.

Code Render command

proteinmotion render examples/backbone_morph.py BackboneDemo \
  -o morph.mp4 --fps 60

Output Preview · 11.5 s · 30 fps

Calmodulin to troponin C morph

A contact-map match selects 114 Cα pairs. Matched residues move in sequence from N to C; unmatched residues fade out or in.

Full source: BackboneDemo Download MP4