schrodinger.application.bioluminate.anarci.anarci_adapter module¶

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: enum.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[schrodinger.application.bioluminate.anarci.anarci_adapter.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[schrodinger.application.bioluminate.anarci.anarci_adapter.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: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, scheme: schrodinger.infra.util.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: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType¶

scheme: schrodinger.infra.util.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: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, scheme: schrodinger.infra.util.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[schrodinger.application.bioluminate.anarci.anarci_adapter.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[schrodinger.application.bioluminate.anarci.anarci_adapter.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: schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering, alignment_details: schrodinger.application.bioluminate.anarci.anarci_adapter.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: schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering¶

alignment_details: schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment¶

__init__(numbering: schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering, alignment_details: schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment) → None¶

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

Bases: object

Class representing all ANARCI results for a single chain

numbering: schrodinger.application.bioluminate.anarci.anarci_adapter.ChainNumbering[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering]¶

alignment_details: schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment]¶

hits: schrodinger.application.bioluminate.anarci.anarci_adapter.ChainHitsTable¶

__len__()¶

property has_antibody_light¶

property has_antibody_heavy¶

__init__(numbering: schrodinger.application.bioluminate.anarci.anarci_adapter.ChainNumbering[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering], alignment_details: schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment], hits: schrodinger.application.bioluminate.anarci.anarci_adapter.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[schrodinger.application.bioluminate.anarci.anarci_adapter.ChainNumbering[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering]]¶

alignment_details: List[schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment[schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment]]¶

hit_tables: List[schrodinger.application.bioluminate.anarci.anarci_adapter.ChainHitsTable[schrodinger.application.bioluminate.anarci.anarci_adapter.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[schrodinger.application.bioluminate.anarci.anarci_adapter.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) → schrodinger.application.bioluminate.anarci.anarci_adapter.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[schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence], scheme=AntibodyCDRScheme.IMGT, **kwargs) → schrodinger.application.bioluminate.anarci.anarci_adapter.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: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType) → bool¶

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

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

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

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