schrodinger.application.bioluminate.anarci.anarci_adapter module

class schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType(value)

Bases: enum.Enum

An enumeration.

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

__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]]])

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

append(object, /)

Append object to the end of the list.

clear()

Remove all items from list.

copy()

Return a shallow copy of the list.

count(value, /)

Return number of occurrences of value.

extend(iterable, /)

Extend list by appending elements from the iterable.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

insert(index, object, /)

Insert object before index.

pop(index=- 1, /)

Remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value, /)

Remove first occurrence of value.

Raises ValueError if the value is not present.

reverse()

Reverse IN PLACE.

sort(*, key=None, reverse=False)

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.

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: str, 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: str

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: str, 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]]])

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

append(object, /)

Append object to the end of the list.

clear()

Remove all items from list.

copy()

Return a shallow copy of the list.

count(value, /)

Return number of occurrences of value.

extend(iterable, /)

Extend list by appending elements from the iterable.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

insert(index, object, /)

Insert object before index.

pop(index=- 1, /)

Remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value, /)

Remove first occurrence of value.

Raises ValueError if the value is not present.

reverse()

Reverse IN PLACE.

sort(*, key=None, reverse=False)

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.

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]]])

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

append(object, /)

Append object to the end of the list.

clear()

Remove all items from list.

copy()

Return a shallow copy of the list.

count(value, /)

Return number of occurrences of value.

extend(iterable, /)

Extend list by appending elements from the iterable.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

insert(index, object, /)

Insert object before index.

pop(index=- 1, /)

Remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value, /)

Remove first occurrence of value.

Raises ValueError if the value is not present.

reverse()

Reverse IN PLACE.

sort(*, key=None, reverse=False)

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.

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__()

__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__()

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

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

name

Alias for field number 0

sequence

Alias for field number 1

schrodinger.application.bioluminate.anarci.anarci_adapter.get_anarci_results(sequences: List[schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence], **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()