pdbsearch.models

class pdbsearch.models.QueryNode[source]

A base class for all query nodes.

query(return_type, **request_options)[source]

Queries the RCSB search API with this node.

Parameters:

return_type (str) – the type of data to return.
return_all (bool) – whether to return all results, unpaginated.
start (int) – the start index of the results.
rows (int) – the number of results to return.
sort (str or list[str]) – the attribute or attributes to sort by.
counts_only (bool) – whether to return only the count of results.
content_types (list[str]) – the PDB types (experimental/computational).
facets (list[str]) – RCSB aggregation terms.

Return type:

dict

class pdbsearch.models.TerminalNode(service: str, parameters: dict)[source]

A terminal node in a query graph, which represents a single search term.

Parameters:

service (str) – the service to use for the terminal node.
parameters (dict) – the parameters to use for the terminal node.

serialize()[source]

Creates the JSON-serializable representation of the node.

Parameters:: node (QueryNode) – the node to combine with.
Return type:: dict

and_(node)[source]

Combines this terminal node with another node using the AND logical operator, to create a new group node.

Parameters:: node (QueryNode) – the node to combine with.
Return type:: GroupNode

or_(node)[source]

Combines this terminal node with another node using the OR logical operator, to create a new group node.

Parameters:: node (QueryNode) – the node to combine with.
Return type:: GroupNode

query(return_type, **request_options)

Queries the RCSB search API with this node.

Parameters:

return_type (str) – the type of data to return.
return_all (bool) – whether to return all results, unpaginated.
start (int) – the start index of the results.
rows (int) – the number of results to return.
sort (str or list[str]) – the attribute or attributes to sort by.
counts_only (bool) – whether to return only the count of results.
content_types (list[str]) – the PDB types (experimental/computational).
facets (list[str]) – RCSB aggregation terms.

Return type:

dict

class pdbsearch.models.GroupNode(logical_operator: str, nodes: list[TerminalNode])[source]

A group node in a query graph, which combines other nodes with boolean logic.

Parameters:

logical_operator (str) – the logical operator to use for the group node.
nodes (list[TerminalNode]) – the nodes to combine.

serialize()[source]

Returns a JSON-serializable representation of the node.

Return type:: dict

and_(node)[source]

Combines this group node with another node using the AND logical operator, to create a new group node.

Parameters:: node (QueryNode) – the node to combine with.
Return type:: GroupNode

or_(node)[source]

Combines this group node with another node using the OR logical operator, to create a new group node.

Parameters:: node (QueryNode) – the node to combine with.
Return type:: GroupNode

query(return_type, **request_options)

Queries the RCSB search API with this node.

Parameters:

return_type (str) – the type of data to return.
return_all (bool) – whether to return all results, unpaginated.
start (int) – the start index of the results.
rows (int) – the number of results to return.
sort (str or list[str]) – the attribute or attributes to sort by.
counts_only (bool) – whether to return only the count of results.
content_types (list[str]) – the PDB types (experimental/computational).
facets (list[str]) – RCSB aggregation terms.

Return type:

dict