biolm.core.legacy package

Submodules

biolm.core.legacy.api module

References to API endpoints.

class biolm.core.legacy.api.APIEndpoint(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: object

action_classes = ()

api_version = 3

batch_size = 3

encode(**kwargs)

encode_input_classes = ()

encode_input_key = 'sequence'

generate(**kwargs)

generate_input_classes = ()

generate_input_key = 'context'

infer(dat, params=None)

params = None

post_batches(dat, slug, action, payload_maker, resp_key, key='sequence', params=None)

predict(**kwargs)

predict_input_classes = ()

predict_input_key = 'sequence'

transform(**kwargs)

transform_input_classes = ()

unpack_local_validations(dat, response_key)

class biolm.core.legacy.api.EncodeAction

Bases: object

class biolm.core.legacy.api.ExplainAction

Bases: object

class biolm.core.legacy.api.FinetuneAction

Bases: object

class biolm.core.legacy.api.GenerateAction

Bases: object

class biolm.core.legacy.api.PredictAction

Bases: object

class biolm.core.legacy.api.SimilarityAction

Bases: object

class biolm.core.legacy.api.TransformAction

Bases: object

biolm.core.legacy.api.combine_validation(x, y)

biolm.core.legacy.api.convert_input(f)

biolm.core.legacy.api.requests_retry_session(retries=3, backoff_factor=0.3, status_forcelist=None, session=None)

biolm.core.legacy.api.retry_minutes(sess, URL, HEADERS, dat, timeout, mins)

Retry for N minutes.

biolm.core.legacy.api.text_validator(text, c)

Validate some text against a class-based validator, returning a string if invalid, or None otherwise.

biolm.core.legacy.api.validate_action(action)

biolm.core.legacy.api.validate_endpoint_action(allowed_classes, method_name, api_class_name)

biolm.core.legacy.cls module

API inference classes.

class biolm.core.legacy.cls.AbLang(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.PredictAction'>, <class 'biolm.core.legacy.api.EncodeAction'>, <class 'biolm.core.legacy.api.GenerateAction'>)

batch_size = 32

encode_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

generate_input_classes = (<biolm.core.validate.SingleOrMoreOccurrencesOf object>, <biolm.core.validate.AAUnambiguousPlusExtra object>)

generate_input_key = 'sequence'

predict_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

class biolm.core.legacy.cls.AbLangHeavy(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: AbLang

slug = 'ablang-heavy'

class biolm.core.legacy.cls.AbLangLight(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: AbLang

slug = 'ablang-light'

class biolm.core.legacy.cls.BioLMToxV1(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

Example.

python Copy

{
  "instances": [{
    "data": {"text": "MSILVTRPSPAGEELVSRLRTLGQVAWHFPLIEFSPGQQLPQ"}
  }]
}

action_classes = (<class 'biolm.core.legacy.api.TransformAction'>, <class 'biolm.core.legacy.api.PredictAction'>)

api_version = 1

batch_size = 1

predict_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

slug = 'biolmtox_v1'

transform_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

class biolm.core.legacy.cls.DNABERT(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.EncodeAction'>,)

batch_size = 10

encode_input_classes = (<biolm.core.validate.DNAUnambiguous object>,)

slug = 'dnabert'

class biolm.core.legacy.cls.DNABERT2(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.EncodeAction'>,)

batch_size = 10

encode_input_classes = (<biolm.core.validate.DNAUnambiguous object>,)

slug = 'dnabert2'

class biolm.core.legacy.cls.ESM1v(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

Example.

python Copy

{
   "items": [{
     "sequence": "QERLEUTGRSLGYNIVAT"
   }]
}

action_classes = (<class 'biolm.core.legacy.api.PredictAction'>,)

batch_size = 5

predict_input_classes = (<biolm.core.validate.SingleOccurrenceOf object>, <biolm.core.validate.AAExtendedPlusExtra object>)

class biolm.core.legacy.cls.ESM1v1(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-n1'

class biolm.core.legacy.cls.ESM1v2(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-n2'

class biolm.core.legacy.cls.ESM1v3(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-n3'

class biolm.core.legacy.cls.ESM1v4(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-n4'

class biolm.core.legacy.cls.ESM1v5(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-n5'

class biolm.core.legacy.cls.ESM1vAll(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM1v

slug = 'esm1v-all'

class biolm.core.legacy.cls.ESM2(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

Example.

python Copy

{
  "items": [{
    "sequence": "MSILVTRPSPAGEELVSRLRTLGQVAWHFPLIEFSPGQQLPQ"
  }]
}

action_classes = (<class 'biolm.core.legacy.api.EncodeAction'>, <class 'biolm.core.legacy.api.PredictAction'>)

batch_size = 1

encode_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

predict_input_classes = (<biolm.core.validate.SingleOrMoreOccurrencesOf object>, <biolm.core.validate.AAExtendedPlusExtra object>)

class biolm.core.legacy.cls.ESM2_150M(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM2

slug = 'esm2-150m'

class biolm.core.legacy.cls.ESM2_35M(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM2

slug = 'esm2-35m'

class biolm.core.legacy.cls.ESM2_3B(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM2

slug = 'esm2-3b'

class biolm.core.legacy.cls.ESM2_650M(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM2

slug = 'esm2-650m'

class biolm.core.legacy.cls.ESM2_8M(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ESM2

slug = 'esm2-8m'

class biolm.core.legacy.cls.ESMFoldMultiChain(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.PredictAction'>,)

batch_size = 2

predict_input_classes = (<biolm.core.validate.AAExtendedPlusExtra object>,)

slug = 'esmfold-multichain'

class biolm.core.legacy.cls.ESMFoldSingleChain(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.PredictAction'>,)

batch_size = 2

predict_input_classes = (<biolm.core.validate.AAUnambiguous object>,)

slug = 'esmfold-singlechain'

class biolm.core.legacy.cls.ESMIF1(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.GenerateAction'>,)

batch_size = 2

generate_input_classes

alias of PDB

generate_input_key = 'pdb'

slug = 'esm-if1'

class biolm.core.legacy.cls.ProGen2(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.GenerateAction'>,)

batch_size = 1

generate_input_classes = (<biolm.core.validate.AAUnambiguousEmpty object>,)

class biolm.core.legacy.cls.ProGen2BFD90(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProGen2

slug = 'progen2-bfd90'

class biolm.core.legacy.cls.ProGen2Large(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProGen2

slug = 'progen2-large'

class biolm.core.legacy.cls.ProGen2Medium(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProGen2

slug = 'progen2-medium'

class biolm.core.legacy.cls.ProGen2Oas(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProGen2

slug = 'progen2-oas'

class biolm.core.legacy.cls.ProteInfer(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: APIEndpoint

action_classes = (<class 'biolm.core.legacy.api.PredictAction'>,)

batch_size = 64

predict_input_classes = (<biolm.core.validate.AAExtended object>,)

class biolm.core.legacy.cls.ProteInferEC(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProteInfer

slug = 'proteinfer-ec'

class biolm.core.legacy.cls.ProteInferGO(multiprocess_threads=None, compress_requests=True, compress_threshold=256)

Bases: ProteInfer

slug = 'proteinfer-go'

Module contents

Legacy modules - deprecated but kept for backward compatibility.