schrodinger.application.bioluminate.anarci.anarci_pyhmmer module¶

PyHMMER-based acceleration for ANARCI antibody/TCR numbering.

Replaces subprocess-based HMMER calls with in-process pyhmmer library, providing significant performance improvements. Falls back to subprocess implementation on errors or when disabled via environment variable.

schrodinger.application.bioluminate.anarci.anarci_pyhmmer.read_hmm_file(hmm_file)¶

class schrodinger.application.bioluminate.anarci.anarci_pyhmmer.PyHmmerHSP(domain, hit_name, hit_description, query_name, query_length)¶

Bases: object

Biopython HSP-compatible wrapper for pyhmmer domain hits.

__init__(domain, hit_name, hit_description, query_name, query_length)¶

class schrodinger.application.bioluminate.anarci.anarci_pyhmmer.PyHmmerQuery(query_name, query_sequence)¶

Bases: object

Biopython Query-compatible wrapper for pyhmmer results.

__init__(query_name, query_sequence)¶

add_hsp(hsp)¶

schrodinger.application.bioluminate.anarci.anarci_pyhmmer.get_hmm_length(species, ctype)¶: Get HMM length for species and chain type (default 128 for IMGT).

schrodinger.application.bioluminate.anarci.anarci_pyhmmer.use_pyhmmer()¶

Temporarily replace anarci’s run_hmmer with pyhmmer implementation.

Disabled by setting SCHRODINGER_DISABLE_PYHMMER_FOR_ANARCI=1.