This function takes a vector of IUPAC names and queries the PubChem database
(using the webchem package) to obtain the corresponding CASRN and CID for
each compound. It reshapes the resulting data, ensuring that each compound
has a unique row with the CID, CASRN, and additional chemical properties.
Arguments
- iupac_names
A character vector of IUPAC names. These are standardized names of chemical compounds that will be used to search in the PubChem database.
- verbose
A logical value indicating whether to print detailed messages. Default is TRUE.
- domain
A character string specifying the PubChem domain to query. One of
"compound"orsubstance. Default iscompound.- delay
A numeric value indicating the delay (in seconds) between API requests. This controls the time between successive PubChem queries. Default is 0. See Details for more info.
Value
A data frame with phisio-chemical information on the queried compounds, including but not limited to:
- iupac_name
The IUPAC name of the compound.
- cid
The PubChem Compound Identifier (CID).
- isomeric_smiles
The SMILES string (Simplified Molecular Input Line Entry System).
Details
The function performs two queries to PubChem:
The first query retrieves the PubChem Compound Identifier (CID) for each IUPAC name.
The second query retrieves additional information using the obtained CIDs. In cases of multiple rapid successive requests, the PubChem server may deny access. Introducing a delay between requests (using the
delayparameter) can help prevent this issue.
Examples
# \donttest{
# Example with formaldehyde and aflatoxin
extr_chem_info(iupac_names = c("Formaldehyde", "Aflatoxin B1"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Querying Formaldehyde.
#> OK (HTTP 200).
#>
#> Querying Aflatoxin B1.
#> OK (HTTP 200).
#>
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> ℹ Querying pubchem_ids.
#> cid iupac_name casrn cid_all casrn_all molecular_formula
#> 1 186907 Aflatoxin B1 1162-65-8 186907 1162-65-8 C17H12O6
#> 2 712 Formaldehyde 50-00-0 712 50-00-0 CH2O
#> molecular_weight smiles
#> 1 312.27 COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4[C@@H]5C=CO[C@@H]5OC4=C1
#> 2 30.026 C=O
#> connectivity_smiles
#> 1 COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4C5C=COC5OC4=C1
#> 2 C=O
#> inchi
#> 1 InChI=1S/C17H12O6/c1-20-10-6-11-14(8-4-5-21-17(8)22-11)15-13(10)7-2-3-9(18)12(7)16(19)23-15/h4-6,8,17H,2-3H2,1H3/t8-,17+/m0/s1
#> 2 InChI=1S/CH2O/c1-2/h1H2
#> inchi_key
#> 1 OQIQSTLJSLGHID-WNWIJWBNSA-N
#> 2 WSFSSNUMVMOOMR-UHFFFAOYSA-N
#> iupac_name_2
#> 1 (3S,7R)-11-methoxy-6,8,19-trioxapentacyclo[10.7.0.02,9.03,7.013,17]nonadeca-1,4,9,11,13(17)-pentaene-16,18-dione
#> 2 formaldehyde
#> x_log_p exact_mass monoisotopic_mass tpsa complexity charge
#> 1 1.6 312.06338810 312.06338810 71.1 649 0
#> 2 1.2 30.010564683 30.010564683 17.1 2 0
#> h_bond_donor_count h_bond_acceptor_count rotatable_bond_count
#> 1 0 6 1
#> 2 0 1 0
#> heavy_atom_count isotope_atom_count atom_stereo_count
#> 1 23 0 2
#> 2 2 0 0
#> defined_atom_stereo_count undefined_atom_stereo_count bond_stereo_count
#> 1 2 0 0
#> 2 0 0 0
#> defined_bond_stereo_count undefined_bond_stereo_count covalent_unit_count
#> 1 0 0 1
#> 2 0 0 1
#> volume3d x_steric_quadrupole3d y_steric_quadrupole3d z_steric_quadrupole3d
#> 1 226.6 8.20 3.35 0.83
#> 2 26.8 0.93 0.56 0.56
#> feature_count3d feature_acceptor_count3d feature_donor_count3d
#> 1 10 5 0
#> 2 1 1 0
#> feature_anion_count3d feature_cation_count3d feature_ring_count3d
#> 1 0 0 5
#> 2 0 0 0
#> feature_hydrophobe_count3d conformer_model_rmsd3d effective_rotor_count3d
#> 1 0 0.6 1.8
#> 2 0 0.4 0.0
#> conformer_count3d
#> 1 1
#> 2 1
#> fingerprint2d
#> 1 AAADccB4OAAAAAAAAAAAAAAAAAAAASIEAAAwQAAAAAAQAEiBAAAAGgAAAAAADQSwmAMyDoAABACIAqDSCAACCAAgIAAIiAEGCMgcJzaMMRqiOiCl4BUMqQfI6PyOoAACCAAIAABAAAQQABAAAAAAAAAAAA==
#> 2 AAADcQAAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEgAAAAAAAAAAAAIAAAAAAAAIAAAAgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==
#> title patent_count patent_family_count literature_count
#> 1 Aflatoxin B1 11735 6552 19410
#> 2 Formaldehyde 765506 397648 148568
#> annotation_types
#> 1 Biological Test Results: Active|Associated Disorders and Diseases|Biological Test Results|Chemical and Physical Properties|Classification|Drug and Medication Information|Identification|Interactions and Pathways|Literature|Patents|Pharmacology and Biochemistry|Safety and Hazards|Spectral Information|Taxonomy|Toxicity
#> 2 Agrochemical Information|Biological Test Results: Active|Associated Disorders and Diseases|Biological Test Results|Chemical and Physical Properties|Classification|Drug and Medication Information|Food Additives and Ingredients|Identification|Interactions and Pathways|Literature|Patents|Pharmacology and Biochemistry|Safety and Hazards|Spectral Information|Taxonomy|Toxicity
#> annotation_type_count
#> 1 15
#> 2 17
#> source_categories
#> 1 Chemical Vendors|Curation Efforts|Governmental Organizations|Journal Publishers|Legacy Depositors|NIH Initiatives|Research and Development|Subscription Services
#> 2 Chemical Vendors|Curation Efforts|Governmental Organizations|Journal Publishers|Legacy Depositors|NIH Initiatives|Research and Development|Subscription Services
#> query
#> 1 Aflatoxin B1
#> 2 Formaldehyde
# }