def _annotate_kr_domain(self, domain: NRPSPKSQualifier.Domain) -> None:
assert domain.name == "PKS_KR"
predictions = self.domain_predictions[domain.feature_name]
activity = predictions["kr_activity"].get_classification()[0]
domain.predictions["KR activity"] = activity
stereo_chem = UNKNOWN
stereo_pred = predictions.get("kr_stereochem")
if stereo_pred:
stereo_chem = stereo_pred.get_classification()[0]
domain.predictions["KR stereochemistry"] = stereo_chem
def _annotate_at_domain(self, domain: NRPSPKSQualifier.Domain, transat_cluster: bool) -> None:
assert domain.name == "PKS_AT"
predictions = self.domain_predictions[domain.feature_name]
if transat_cluster:
consensus = self.consensus_transat[domain.feature_name]
else:
consensus = self.consensus[domain.feature_name]
domain.predictions["consensus"] = consensus
sig = UNKNOWN
pks_sig = predictions["signature"]
if pks_sig and pks_sig.get_classification():
sig = pks_sig.get_classification()[0]
domain.predictions["PKS signature"] = sig
minowa = predictions["minowa_at"].get_classification()[0]
domain.predictions["Minowa"] = get_short_form(minowa)
def _annotate_cal_domain(self, domain: NRPSPKSQualifier.Domain) -> None:
assert domain.name == "CAL_domain"
minowa = self.domain_predictions[
domain.feature_name]["minowa_cal"].get_classification()[0]
domain.predictions["Minowa"] = get_short_form(minowa)
def _annotate_a_domain(self, domain: NRPSPKSQualifier.Domain) -> None:
assert domain.name in ["AMP-binding", "A-OX"]
predictions = self.domain_predictions[domain.feature_name]
domain.predictions["consensus"] = generate_nrps_consensus(predictions)