rPDBapi (version 2.1.1)

StructureOperator: Create a Structure Operator for Structure-Based Searches

Description

The `StructureOperator` function constructs an operator object for conducting structure-based searches within the RCSB Protein Data Bank (PDB). This operator allows users to specify a PDB entry ID, an assembly ID, and the mode of search to be used, facilitating precise structural queries.

Usage

StructureOperator(
  pdb_entry_id,
  assembly_id = 1,
  search_mode = "STRICT_SHAPE_MATCH"
)

Value

An object of class `StructureOperator` that encapsulates the criteria for performing structure-based searches in the RCSB PDB.

Arguments

pdb_entry_id

A string representing the PDB entry ID to search for. The PDB entry ID is a unique identifier for each structure in the PDB.

assembly_id

An integer representing the assembly ID within the PDB entry. The assembly ID identifies the specific biological assembly or model within the PDB entry. By default, this is set to 1, which typically corresponds to the first biological assembly or model.

search_mode

A string indicating the search mode to be applied during the structure-based search. Accepted values include 'STRICT_SHAPE_MATCH', 'RELAXED_SHAPE_MATCH', etc. The default is 'STRICT_SHAPE_MATCH', which ensures a precise comparison based on the structural shape of the molecules.

Examples

# Example of creating a structure operator for a specific PDB entry and assembly
struct_operator <- StructureOperator(
  pdb_entry_id = "1XYZ",
  assembly_id = 1,
  search_mode = "STRICT_SHAPE_MATCH"
)
print(struct_operator)

# Example of creating a structure operator with a relaxed search mode
struct_operator_relaxed <- StructureOperator(
  pdb_entry_id = "1ABC",
  assembly_id = 2,
  search_mode = "RELAXED_SHAPE_MATCH"
)
print(struct_operator_relaxed)