rPDBapi (version 2.1.1)

SeqMotifOperator: 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)

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.

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.

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)