GlossaryΒΆ
- canonical SMILES
In OEChem, the name canonical SMILES is used for a unique SMILES string that encodes the connection table of a molecule, but no chiral or isotopic information. Consequently, two stereoisomers always share the same canonical SMILES, since their stereo information are ignored during the canonicalization process. For generating a canonical SMILES, use the OECreateCanSmiString function.
Note
OChem‘s canonical SMILES terminology corresponds to Daylight‘s ‘unique‘ SMILES definition.
- canonical isomeric SMILES
In OEChem, the name canonical isomeric SMILES is used for a unique SMILES string that also encodes isotopic and stereo information. Due to the unambiguity of canonical isomeric SMILES, they can be used as a universal identifier for a specific chemical structure. For generating an canonical isomeric SMILES, use the OECreateIsoSmiString function.
Note
OChem‘s canonical isomeric SMILES terminology corresponds to Daylight‘s ‘absolute‘ SMILES definition.
- chiral atom
In OEChem, an atom is considered chiral, if it is connected to four different substituent groups i.e. its mirror image is non-superimposable.
Note
In OEChem, an easily invertible nitrogen, i.e. a non-planar nitrogen with one attached hydrogen, is not considered to be chiral. This is due to the fact that trivalent nitrogen compound undergo rapid inversion that interconvert enantiomers.
- SMARTS
- SMARTS is a language that allows specifying substructures by providing a number of primitive symbols describing atomic and bond properties. Atom and bond primitive specifications may be combined to form expressions by using logical operators. An introduction to SMARTS syntax is provided in chapter SMARTS Pattern Matching, for more information go to http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
- SMILES
- A SMILES string represents a molecule by describing only its molecular graph (i.e. atoms and bonds in the connection table, but no chiral or isotopic information). There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol. For generating an arbitrary SMILES string, use the OECreateAbsSmiString function. An introduction to SMILES syntax is provided in chapter SMILES Line Notation, for more information go to http://www.daylight.com/smiles/.
- SMIRKS
SMIRKS is a reaction transform language.
(online tutorial http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html)
