> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# Operator Site Occlusion
> Score presence of an inverted-repeat operator occluding the -35/-10 box or TSS
This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.
Score whether a promoter carries an occluding inverted-repeat operator.
Each sequence is anchored to its best consensus -35/-10 promoter, the -35 box,
-10 box, and a downstream TSS window are taken as occlusion targets, and the
sequence is scanned for inverted-repeat operators (two half-sites of length
> \= `min_half_site` separated by a gap \<= `max_gap` whose first half-site
> matches the reverse complement of the second within `max_mismatch`
> mismatches). The best operator that overlaps a target by >= `min_overlap` bp
> determines the score.
## API Reference
Configuration for the repressor-operator presence constraint.
Locates the -35 / -10 boxes by best consensus match, defines a TSS window
just downstream of the -10 box, then scans for inverted-repeat operators
(two half-sites separated by a short gap whose first half-site matches the
reverse complement of the second) and checks whether any occludes a promoter
element. Lower score = an occluding operator is present.
Minimum half-site length (bp) for an inverted-repeat operator candidate.
Maximum gap (bp) between the two operator half-sites.
Max Hamming mismatches between half-site 1 and reverse complement of half-site 2.
Minimum overlap (bp) between an operator and a -35/-10/TSS element to occlude it.
Consensus -35 box (6 bp) used to anchor the promoter.
Consensus -10 box (6 bp) used to anchor the promoter.
Minimum -35/-10 spacer (bp) considered when anchoring the promoter.
Maximum -35/-10 spacer (bp) considered when anchoring the promoter.
Width (bp) of the TSS window placed just downstream of the -10 box.
ReturnsConstraintOutput
One result per sequence. `score` is 0.0 when an
occluding operator (mismatch \<= `max_mismatch`) is present and rises
toward 1.0 as the best occluding candidate drifts away from a valid
operator (always >= 0.5 when no valid operator occludes a target, so
`threshold=0.5` acts as a presence filter). `metadata` carries an
`operator` dict with the located boxes and best-operator details
(`None` when no candidate can occlude a target).
evo-design/proto-language/proto\_language/constraint/sequence\_annotation/operator\_site\_constraint.py
