API Documentation

RCSB PDB Sequence Coordinates API.

class rcsbapi.sequence.Alignments(db_from: str, db_to: str, query_id: str, return_data_list: ~typing.List[str], range: ~typing.Optional[~typing.List[int]] = None, suppress_autocomplete_warning: bool = False, data_list_args: ~typing.Optional[~typing.Dict[str, ~typing.Dict[str, ~typing.Union[int, str]]]] = None, _query: mappingproxy = <factory>)

Get sequence alignments.

Parameters

  • db_from (str) – From which query sequence database

  • db_to (str) – To which query sequence database

  • query_id (str) – Sequence identifier specified in db_from

  • return_data_list (List[str]) – Fields to request data for

  • range (Optional, List[]) – Optional integer list to filter annotations that fall in a particular region

  • suppress_autocomplete_warning (bool, optional) – Suppress warning message about field path autocompletion. Defaults to False.

  • data_list_args (Optional[Dict[str, Dict[str, Union[int, str]]]]) – Optional dictionary specifying field-level arguments for entries in return_data_list. The key must match fields in return_data_list. Values currently include “offset” and “first”

Attrs:

_query (MappingProxyType[str, Any]): Attribute for storing GraphQL query

__init__(db_from: str, db_to: str, query_id: str, return_data_list: ~typing.List[str], range: ~typing.Optional[~typing.List[int]] = None, suppress_autocomplete_warning: bool = False, data_list_args: ~typing.Optional[~typing.Dict[str, ~typing.Dict[str, ~typing.Union[int, str]]]] = None, _query: mappingproxy = <factory>) → None
to_dict() → Dict[str, Any]

Get dictionary representation of query and attributes, skips values of None. Skips return_data_list

class rcsbapi.sequence.AnnotationFilterInput(field: str, operation: str, values: List[str], source: Optional[str] = None)

Filter used to select which annotations will be retrieved.

__init__(field: str, operation: str, values: List[str], source: Optional[str] = None)
Parameters

  • field (FieldName) – Defines the field to be compared

  • operation (OperationType) – Defines the comparison method

  • values (List[str]) – List of allowed values

  • source (AnnotationReference, optional) – Only features with the same annotation collections will be filtered

to_string() → str

Generate string to insert in GraphQL query based on GraphQL schema

class rcsbapi.sequence.Annotations(query_id: str, sources: ~typing.List[str], reference: str, return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, range: ~typing.Optional[~typing.List[int]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>)

Get sequence annotations.

Parameters

  • query_id (str) – Database sequence identifier

  • sources (List[str]) – List defining the annotation collections to be requested

  • reference (SequenceReference) – Query sequence database

  • return_data_list (List[str]) – Requested data fields

  • filters (List["AnnotationFilterInput"], optional) – Select what annotations will be retrieved

  • range – (List[int], optional): Optional integer list to filter annotations to a particular region

  • suppress_autocomplete_warning (bool, optional) – Suppress warning message about field path autocompletion. Defaults to False.

Attrs:

_query (MappingProxyType[str, Any]): Attribute for storing GraphQL query

__init__(query_id: str, sources: ~typing.List[str], reference: str, return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, range: ~typing.Optional[~typing.List[int]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>) → None
to_dict() → Dict[str, Any]

Get dictionary representation of query and attributes, skips values of None. Skips return_data_list

class rcsbapi.sequence.GroupAlignments(group: str, group_id: str, return_data_list: ~typing.List[str], filter: ~typing.Optional[~typing.List[str]] = None, suppress_autocomplete_warning: bool = False, data_list_args: ~typing.Optional[~typing.Dict[str, ~typing.Dict[str, ~typing.Union[int, str]]]] = None, _query: mappingproxy = <factory>)

Get alignments for structures in groups

Parameters

  • group_id (str) – Database sequence identifier for group

  • return_data_list (List[str]) – Requested data fields

  • filter (List[str], optional) – Optional string list of allowed identifiers for group members

  • suppress_autocomplete_warning (bool, optional) – Suppress warning message about field path autocompletion. Defaults to False.

  • data_list_args (Optional[Dict[str, Dict[str, Union[int, str]]]]) – Optional dictionary specifying field-level arguments for entries in return_data_list. The key must match fields in return_data_list. Values currently include “offset” and “first”

Attrs:

_query (MappingProxyType[str, Any]): Attribute for storing GraphQL query

__init__(group: str, group_id: str, return_data_list: ~typing.List[str], filter: ~typing.Optional[~typing.List[str]] = None, suppress_autocomplete_warning: bool = False, data_list_args: ~typing.Optional[~typing.Dict[str, ~typing.Dict[str, ~typing.Union[int, str]]]] = None, _query: mappingproxy = <factory>) → None
to_dict() → Dict[str, Any]

Get dictionary representation of query and attributes, skips values of None. Skips return_data_list

class rcsbapi.sequence.GroupAnnotations(group: str, group_id: str, sources: ~typing.List[str], return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>)

Get annotations for sequences in groups.

Parameters

  • group (GroupReference) – Query sequence database

  • group_id (str) – Database sequence identifier for group

  • sources (List[AnnotationReference]) – List defining the annotation collections to be requested

  • return_data_list (List[str]) – Requested data fields

  • filters (List[AnnotationFilterInput]) – Optional annotation filter by type or target identifier

  • suppress_autocomplete_warning (bool, optional) – Suppress warning message about field path autocompletion. Defaults to False.

Attrs:

_query (MappingProxyType[str, Any]): Attribute for storing GraphQL query

__init__(group: str, group_id: str, sources: ~typing.List[str], return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>) → None
to_dict() → Dict[str, Any]

Get dictionary representation of query and attributes, skips values of None. Skips return_data_list

class rcsbapi.sequence.GroupAnnotationsSummary(group: str, group_id: str, sources: ~typing.List[str], return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>)

Get a summary of positional annotations for a group of sequences.

Parameters

  • group (GroupReference) – Query sequence database

  • group_id (str) – Database sequence identifier for group

  • sources (List[AnnotationReference]) – List defining the annotation collections to be requested

  • return_data_list (List[str]) – Request data fields

  • filters (List[AnnotationFilterInput], optional) – Optional annotation filter by type or target identifier

  • suppress_autocomplete_warning (bool, optional) – Suppress warning message about field path autocompletion. Defaults to False.

Attrs:

_query (MappingProxyType[str, Any]): Attribute for storing GraphQL query

__init__(group: str, group_id: str, sources: ~typing.List[str], return_data_list: ~typing.List[str], filters: ~typing.Optional[~typing.List[~rcsbapi.sequence.seq_query.AnnotationFilterInput]] = None, suppress_autocomplete_warning: bool = False, _query: mappingproxy = <factory>) → None
to_dict() → Dict[str, Any]

Get dictionary representation of query and attributes, skips values of None. Skips return_data_list

class rcsbapi.sequence.SeqSchema

GraphQL schema defining available fields, types, and how they are connected.

__init__() → None
construct_query(query_type: str, query_args: Dict[str, str] | Dict[str, List[Any]], return_data_list: List[str], suppress_autocomplete_warning: bool = False) → Dict[str, Any]

Construct a GraphQL query - currently only uses rustworkx.

Parameters

  • query_type (str) – type of query to make (ex: Alignments, Annotations, etc)

  • query_args (Dict[str, str] | Dict[str, List[Any]]) – dict of query_type-specific args

  • return_data_list (List[str]) – list of fields to request data for

  • suppress_autocomplete_warning (bool, optional) – Whether to suppress warning when autocompletion of paths is used. Defaults to False.

Raises

ValueError – unknown field in the return_data_list

Returns

GraphQL query in JSON format

Return type

dict

fetch_schema() → Dict[str, Any]

Get the JSON schema defining the Sequence Coordinates API. Fallback to local file if necessary.

Returns

JSON schema for Sequence Coordinates

Return type

Dict[str, Any]

find_field_names(search_string: str) → List[str]

Find field names that fully or partially match the search string.

Parameters

search_string (str) – string to search field names for

Raises

  • ValueError – thrown when a type other than string is passed in for search_string

  • ValueError – thrown when no fields match search_string

Returns

list of matching field names

Return type

List[str]