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.get_sequence(entry_name, *, conn=None)

Get the sequence for the given entry

Parameters:

  • entry_name (str) – GPCR DB entry name (e.g. 5ht1a_human)

  • conn (sqlite3.Connection) – keyword-only; if not passed, will open default connection

Return type:

str

schrodinger.protein.gpcr.annotate.get_families(entry_name, *, conn=None)

Get the GPCR families for the given entry

Parameters:

  • entry_name (str) – GPCR DB entry name (e.g. 5ht1a_human)

  • conn (sqlite3.Connection) – keyword-only; if not passed, will open default connection

Return type:

list[str]

schrodinger.protein.gpcr.annotate.get_residue_annotations(entry_name, *, conn=None)

Get the residue annotations for the given entry

Parameters:

  • entry_name (str) – GPCR DB entry name (e.g. 5ht1a_human)

  • conn (sqlite3.Connection) – keyword-only; if not passed, will open default connection

Return type:

list[dict]

schrodinger.protein.gpcr.annotate.get_gpcrdb_url(entry_name)

Get the GPCR DB URL for the given entry

Parameters:

entry_name (str) – GPCR DB entry name (e.g. 5ht1a_human)

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.annotate_gpcr_segments(st: Structure) → None

Annotate GPCR segments for qualifying chains in a structure.

Iterates over all chains in the structure, applies a secondary-structure heuristic to identify potential GPCRs, and runs a BLAST-based annotation task for each qualifying chain. The structure is modified in place: 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)