returns the geometry or the 2D chemical structure of a molecule
MolecularData(molecule, output, options)
string, integer; name of the molecule as a string, CID number as an integer, or SMILES formula (see below for format)
string; either "geometry3d", "image2d", or "dictionary"
(optional) equation(s) of the form option = value where option is one of returnbonds
MolecularData(molecule,output) returns the geometry or the 2D chemical structure of a molecule.
The molecule can be a name, CID number, or SMILES formula in the format "smiles=formula".
If the output is "geometry3d", then MolecularData returns the molecular geometry as a Maple list of lists in the standard molecular geometry format of the QuantumChemistry package.
If the output is "image2d", then MolecularData returns an image of the 2D chemical structure.
If the output is "dictionary", then MolecularData returns a dictionary entry for the molecule.
Geometries and structures are retrieved from a web database. A connection to the internet is required. Currently, the procedure has access to over 96 million molecules contained in the PubChem database.
The standard geometry format of the QuantumChemistry package is a Maple list of lists in which each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates.
The optional keyword returnbonds can be set to true or false (default). If set to true with "geometry3d", MolecularData returns two variables as a sequence : (1) the molecule's geometry as a list of lists and (2) the bonds of the molecule as a set of sets where each set contains two integers denoting the atoms to be connected by a chemical bond. The integers correspond to the positions of the atoms in the output list of the molecule's geometry.
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2023 update. Nucleic Acids Res. 2023 Jan 6;51(D1):D1373-D1380. doi:10.1093/nar/gkac956. PMID: 36305812.
molecule ≔ MolecularDatatylenol,geometry3d;
Acetaminophen: Paracetamol is a member of the class of phenols that is 4-aminophenol in which one of the hydrogens attached to the amino group has been replaced by an acetyl group. It has a role as a cyclooxygenase 2 inhibitor, a cyclooxygenase 1 inhibitor, a non-narcotic analgesic, an antipyretic, a non-steroidal anti-inflammatory drug, a cyclooxygenase 3 inhibitor, a xenobiotic, an environmental contaminant, a human blood serum metabolite and a hepatotoxic agent. It is a member of phenols and a member of acetamides. It derives from a 4-aminophenol. -ChEBI
Acetaminophen: Acetaminophen is a p-aminophenol derivative with analgesic and antipyretic activities. Although the exact mechanism through which acetaminophen exert its effects has yet to be fully determined, acetaminophen may inhibit the nitric oxide (NO) pathway mediated by a variety of neurotransmitter receptors including N-methyl-D-aspartate (NMDA) and substance P, resulting in elevation of the pain threshold. The antipyretic activity may result from inhibition of prostaglandin synthesis and release in the central nervous system (CNS) and prostaglandin-mediated effects on the heat-regulating center in the anterior hypothalamus. -NCI Thesaurus (NCIt)
molecule,bonds ≔ MolecularDatatylenol,geometry3d,returnbonds=true;
nicotine ≔ MolecularDatasmiles=CN1CCC[C@H]1c2cccnc2,geometry3d;
Nicotine: (S)-nicotine is a 3-(1-methylpyrrolidin-2-yl)pyridine in which the chiral centre has S-configuration. The naturally occurring and most active enantiomer of nicotine, isolated from Nicotiana tabacum. It has a role as a phytogenic insecticide, a teratogenic agent, a neurotoxin, an anxiolytic drug, a nicotinic acetylcholine receptor agonist, a biomarker, an immunomodulator, a mitogen, a peripheral nervous system drug, a psychotropic drug, a plant metabolite and a xenobiotic. It is a conjugate base of a (S)-nicotinium(1+). It is an enantiomer of a (R)-nicotine. -ChEBI
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