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match_backbones
Find the largest ordered residue match under a contact-error limit.
from proteinmotion import match_backbonesSignature
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_chainkeyword only | None | Source chain ID; select one chain with protein Cα or nucleotide C1′ anchors. |
target_chainkeyword only | None | Target chain ID; select one chain with protein Cα or nucleotide C1′ anchors. |
cutoffkeyword only | 8.0 | Distance cutoff in ångströms. |
softnesskeyword only | 1.5 | Fraction of the window used for its fading edge, in (0, 1]. |
max_contact_errorkeyword only | 0.3 | Maximum discrepancy between matched soft contacts, in [0, 1]. |
search_secondskeyword only | 8.0 | Branch-and-bound time budget in seconds; preparation is additional. |
max_candidateskeyword only | 6000 | Candidate correspondence limit; None searches all candidates up to the safety limit. |
Returns: ContactMatch
Notes
Uses Cα for proteins and C1′ for DNA/RNA. Each input selects one chain with at least three anchors of the same type. Missing anchors are skipped. For equal-sized matches, the search minimizes contact-map discrepancy. Check the report for full-space, candidate-restricted, or time-limited optimality. The shorter chain supports at most 800 anchored residues; full candidate search supports at most 30,000 pairings. Reports include the anchor atom names, counts, and aligned_anchor_rmsd_angstrom.
Example and output
Run this command from a repository checkout.
Code Render command
proteinmotion render examples/backbone_morph.py BackboneDemo \
-o morph.mp4 --fps 60Output Preview · 11.5 s · 30 fps
A contact-map match selects 114 Cα pairs. Matched residues move in sequence from N to C; unmatched residues fade out or in.