rPDBapi (version 2.1.1)

SequenceOperator: Create a Sequence Operator for Sequence-Based Searches

Description

The `SequenceOperator` function constructs an operator for performing sequence-based searches within the RCSB Protein Data Bank (PDB). This operator allows users to specify a nucleotide or protein sequence, define the type of sequence, and set thresholds for e-value and identity in the search process.

Usage

SequenceOperator(
  sequence,
  sequence_type = NULL,
  evalue_cutoff = 100,
  identity_cutoff = 0.95
)

Value

An object of class `SequenceOperator` that encapsulates the search criteria for sequence-based queries within the RCSB PDB.

Arguments

sequence

A string representing the nucleotide or protein sequence to search for. The sequence should be provided in standard IUPAC format.

sequence_type

Optional: A string indicating the type of sequence. Accepted values are 'DNA', 'RNA', or 'PROTEIN'. If not provided, the sequence type is automatically determined based on the characters present in the sequence using the `autoresolve_sequence_type` function.

evalue_cutoff

A numeric value for the e-value cutoff in the search. This defines the threshold for statistical significance of the search results. Default is 100.

identity_cutoff

A numeric value for the identity cutoff in the search. This sets the minimum percentage of identity required for a match to be considered. Default is 0.95.

Examples

# Example of creating a sequence operator for a protein sequence with specific cutoffs
seq_operator <- SequenceOperator(
  sequence = "MVLSPADKTNVKAAW",
  sequence_type = "PROTEIN",
  evalue_cutoff = 10,
  identity_cutoff = 0.90
)
print(seq_operator)

# Example of creating a sequence operator with automatic sequence type detection
seq_operator_auto <- SequenceOperator(
  sequence = "ATGCGTACGTAGC",
  evalue_cutoff = 50,
  identity_cutoff = 0.85
)
print(seq_operator_auto)