schrodinger.application.bioluminate.anarci.anarci_adapter module

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType

Bases: Enum

TCR_A = 'A'

TCR_B = 'B'

TCR_G = 'G'

TCR_D = 'D'

ANTIBODY_H = 'H'

ANTIBODY_K = 'K'

ANTIBODY_L = 'L'

class schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo(number: int, ins_code: str, res_name: str)

Bases: object

Class describing the position of a residue in the current numbering scheme, as well as its single-letter code

number: int

ins_code: str

res_name: str

static from_anarci_tuple(numbering_tuple: Tuple[Tuple[int, str], str])

Create a ResInfo instance from the numbering tuple returned from ANARCI :rtype: ResInfo

property number_with_ins_code

__init__(number: int, ins_code: str, res_name: str) → None

class schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering(domain_data: List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]])

Bases: object

Class representing the numbering information for a single domain from an

ANARCI run

__init__(domain_data: List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]])

start_index: int

end_index: int

property numbering: List[ResInfo]

class schrodinger.application.bioluminate.anarci.anarci_adapter.ChainNumbering(seq_data: List[List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]]])

Bases: list, Generic[T]

Class representing the numbering information for any domains in a given single chain from an ANARCI run

__init__(seq_data: List[List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]]])

class schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment(id: str, description: str, evalue: float, bitscore: float, bias: float, query_start: int, query_end: int, species: str, chain_type: AnarciType, scheme: AntibodyCDRScheme, query_name: str)

Bases: object

Class representing the alignment information for a single domain from an

ANARCI run

id: str

description: str

evalue: float

bitscore: float

bias: float

query_start: int

query_end: int

species: str

chain_type: AnarciType

scheme: AntibodyCDRScheme

query_name: str

__init__(id: str, description: str, evalue: float, bitscore: float, bias: float, query_start: int, query_end: int, species: str, chain_type: AnarciType, scheme: AntibodyCDRScheme, query_name: str) → None

class schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment(seq_data: List[Dict[str, Union[str, float, int]]])

Bases: list, Generic[T]

Class representing the alignment information for any domains in a given single chain from an ANARCI run

__init__(seq_data: List[Dict[str, Union[str, float, int]]])

get_antibody_light_domains()

get_antibody_heavy_domains()

property antibody_light_domains

property antibody_heavy_domains

property has_antibody_light

property has_antibody_heavy

class schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit(id: str, description: str, evalue: float, bitscore: float, bias: float, query_start: int, query_end: int)

Bases: object

Class representing the HMMER data for a single HMM hit against a chain

id: str

description: str

evalue: float

bitscore: float

bias: float

query_start: int

query_end: int

__init__(id: str, description: str, evalue: float, bitscore: float, bias: float, query_start: int, query_end: int) → None

class schrodinger.application.bioluminate.anarci.anarci_adapter.ChainHitsTable(table: List[List[Union[str, float, int]]])

Bases: list, Generic[T]

Class representing the HMMER hit table for a single chain from an ANARCI run

__init__(table: List[List[Union[str, float, int]]])

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult(numbering: DomainNumbering, alignment_details: DomainAlignment)

Bases: object

Class representing ANARCI results for a single domain. As the hits table

only exists at the chain level, domains do not have associated HMMER hit table information

numbering: DomainNumbering

alignment_details: DomainAlignment

__init__(numbering: DomainNumbering, alignment_details: DomainAlignment) → None

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult(numbering: ChainNumbering[DomainNumbering], alignment_details: ChainAlignment[DomainAlignment], hits: ChainHitsTable)

Bases: object

Class representing all ANARCI results for a single chain

numbering: ChainNumbering[DomainNumbering]

alignment_details: ChainAlignment[DomainAlignment]

hits: ChainHitsTable

__len__()

property has_antibody_light

property has_antibody_heavy

__init__(numbering: ChainNumbering[DomainNumbering], alignment_details: ChainAlignment[DomainAlignment], hits: ChainHitsTable) → None

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults(anarci_results: Tuple[List[List[List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]]]], List[List[Dict[str, Union[str, float, int]]]], List[List[List[Union[str, float, int]]]]])

Bases: object

Class to handle results of an Anarci run. the return type from anarci is far too complicated to manage directly so this class organizes several layers of nested data into a human-readable API

For reference, the type this class’s constructor expects is:

List[List[List[List[Tuple[Tuple[int,str],str]]]],

List[List[Dict[str,str|int|float]], List[List[List[Union[str,float,int]]]]]

(This is type-hinted as a Tuple below, as List doesn’t allow mixed types)

__init__(anarci_results: Tuple[List[List[List[Tuple[List[Tuple[Tuple[int, str], str]], int, int]]]], List[List[Dict[str, Union[str, float, int]]]], List[List[List[Union[str, float, int]]]]])

numbering: List[ChainNumbering[DomainNumbering]]

alignment_details: List[ChainAlignment[DomainAlignment]]

hit_tables: List[ChainHitsTable[HmmerHit]]

__len__()

property has_antibody_light

property has_antibody_heavy

class schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence(name, sequence)

Bases: tuple

name

Alias for field number 0

sequence

Alias for field number 1

schrodinger.application.bioluminate.anarci.anarci_adapter.get_best_domain_result(query_seq_str, name='Sequence', **kwargs) → Optional[AnarciDomainResult]

Wrapper for anarci which returns the best domain result from the run in a

structured AnarciDomainResult instance

schrodinger.application.bioluminate.anarci.anarci_adapter.get_anarci_chain_result(query_seq_str: str, name='Sequence', **kwargs) → AnarciChainResult

Wrapper for anarci which returns the results from the run in a structured

AnarciChainResult instance

schrodinger.application.bioluminate.anarci.anarci_adapter.get_anarci_results(sequences: List[InputSequence], scheme=AntibodyCDRScheme.IMGT, **kwargs) → AnarciResults

Wrapper for anarci which returns the results from the run in a structured

AnarciResults instance

schrodinger.application.bioluminate.anarci.anarci_adapter.get_hmmerpath()

schrodinger.application.bioluminate.anarci.anarci_adapter.is_antibody_light_type(chain_type: AnarciType) → bool

schrodinger.application.bioluminate.anarci.anarci_adapter.is_antibody_heavy_type(chain_type: AnarciType) → bool

schrodinger.application.bioluminate.anarci.anarci_adapter.is_antibody_type(chain_type: AnarciType) → bool

schrodinger.application.bioluminate.anarci.anarci_adapter.is_tcr_type(chain_type: AnarciType) → bool

schrodinger.application.bioluminate.anarci.anarci_adapter.get_domain_type_shorthand(chain_type: AnarciType) → str

schrodinger.application.bioluminate.anarci.anarci_adapter.get_antibody_type_char(anarci_type: AnarciType) → str

schrodinger.application.bioluminate.anarci.anarci_adapter.validate_chain_type(sequence: str, chain_type: AnarciType) → None

Get the anarci type for the given sequence and check that it matches the expected chain type.

Parameters:

• sequence – The sequence to check

• chain_type – The expected chain type

Raises:

ValueError – If the sequence has no ANARCI result or if the ANARCI result does not match the expected chain type

schrodinger.application.bioluminate.anarci.anarci_adapter.get_requested_seqs_by_chain_type(seqs: list[str], chain_types: set[AnarciType]) → dict[AnarciType, list[str]]

Given a list of sequences and a set of chain types, return a dictionary with the sequences for each chain type.

Parameters:

• seqs – A list of sequences.

• chain_types – A set of chain types to search for.

Returns:

A dictionary with the sequences for each chain type.