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.
- stop_on_warning
Logical. If set to TRUE, the function will stop and throw an error if any substances are not found in PubChem. Defaults to FALSE, in which case a warning is issued.
Value
A data frame with information on the queried compounds, including:
- 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 712 and 186907.
#> cid iupac_name cas_rn cid_all cas_rn_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 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
#> in_ch_i
#> 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
#> in_ch_i_key
#> 1 OQIQSTLJSLGHID-WNWIJWBNSA-N
#> 2 WSFSSNUMVMOOMR-UHFFFAOYSA-N
#> iupac_name_y
#> 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 71.1 650 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
# }