rPDBapi (version 2.1.1)

describe_chemical: Describe Chemical Compound from RCSB PDB

Description

Retrieves detailed information about a chemical compound from the RCSB Protein Data Bank (PDB) based on its chemical ID.

Usage

describe_chemical(chem_id, url_root = URL_ROOT)

Value

A list containing detailed information about the chemical compound. This list includes various fields such as:

rcsb_chem_comp_descriptor

A sublist containing chemical descriptors like SMILES, InChI strings, molecular weight, and other chemical properties.

rcsb_chem_comp_info

Information regarding the compound’s classification, formula, and additional relevant data.

other

Other fields may also be included, depending on the specific compound and the data available from the RCSB PDB.

Arguments

chem_id

A string representing the 3-character chemical ID. This ID is typically an alphanumeric string used to uniquely identify ligands, cofactors, or other small molecules within macromolecular structures. The string must not exceed 3 characters.

url_root

A string representing the URL for retrieving information about chemical compounds. By default, this is set to the global constant URL_ROOT, but users can specify a different URL if needed.

Examples

if (FALSE) {
# Retrieve chemical information for N-Acetyl-D-Glucosamine (NAG)
chem_desc <- describe_chemical('NAG')
chem_desc

# Access the SMILES string of the compound
smiles_string <- chem_desc$rcsb_chem_comp_descriptor$smiles
smiles_string

}