schrodinger.protein.gpcr.annotate module

This module is for annotating GPCR sequences using data from the GPCR DB.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.protein.gpcr.annotate.is_maybe_gpcr(chain) → bool

Determine whether a structure chain might be a GPCR based on its secondary structure content.

A chain is considered a potential GPCR if it is long enough and contains a sufficient number of helical segments, consistent with the 7TM bundle architecture of GPCRs.

Parameters:

chain (_Chain) – a structure chain to evaluate

schrodinger.protein.gpcr.annotate.get_protein_sequence(st: _AtomCollection) → ProteinSequence

Return ProteinSequence of input structure.

Provides a canonical iteration order that is consistent with the annotation code below and avoids issues with offset residue numbering.

schrodinger.protein.gpcr.annotate.annotate_gpcr_segments(st: Structure) → None

Add TM segment and generic residue number annotations to a structure.

Iterates over all chains in the structure, applies a secondary-structure heuristic to identify potential GPCR chains, and runs a BLAST-based annotation task for each qualifying chain. The structure is modified inplace: atoms of annotated residues receive s_bioluminate_gpcr_segment and s_bioluminate_gpcr_generic_number properties.

Parameters:

st – the structure to annotate (modified in place)