SeqMotifOperator: Create a Sequence Motif Operator for RCSB PDB Searches

In rPDBapi: A Comprehensive Interface for Accessing the Protein Data Bank

Create a Sequence Motif Operator for RCSB PDB Searches

Description

The 'SeqMotifOperator' function constructs an operator for searching sequence motifs within the RCSB Protein Data Bank (PDB). This operator is used to specify a search pattern, the type of biological sequence, and the pattern-matching method to be applied in the search.

Usage

SeqMotifOperator(pattern, sequence_type, pattern_type)

Arguments

pattern	A string representing the motif pattern to search for. This can be a simple string or a more complex pattern, depending on the 'pattern_type'.
sequence_type	A string indicating the type of sequence being searched. Accepted values are 'DNA', 'RNA', or 'PROTEIN'.
pattern_type	A string indicating the pattern matching method to use. Options include 'SIMPLE' for basic patterns, 'PROSITE' for PROSITE-style patterns, and 'REGEX' for regular expressions.

Value

An object of class 'SeqMotifOperator' that encapsulates the specified search criteria. This object can be used as part of a search query within the RCSB PDB system.

Examples

# Example of creating a sequence motif operator to search for a DNA motif using a regular expression
seq_motif_operator <- SeqMotifOperator(
  pattern = "A[TU]G",
  sequence_type = "DNA",
  pattern_type = "REGEX"
)
print(seq_motif_operator)

rPDBapi documentation built on Sept. 11, 2024, 6:37 p.m.