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.
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).
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 AFLATOXIN B1 186907 AFLATOXIN B1 C17H12O6
#> 2 712 Formaldehyde formaldehyde 712 formaldehyde CH2O
#> molecular_weight canonical_smiles
#> 1 312.27 COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4C5C=COC5OC4=C1
#> 2 30.026 C=O
#> isomeric_smiles
#> 1 COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4[C@@H]5C=CO[C@@H]5OC4=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
#> 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==
#> query
#> 1 Aflatoxin B1
#> 2 Formaldehyde
# }