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

OEChem‘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 a canonical isomeric SMILES, use the OECreateIsoSmiString function.

Note

OEChem‘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.

See also

chiral bond

In OEChem, a double bond is considered chiral, if the cis and trans forms of this bond represent two distinct isomers. A chiral bond can be either a chain bond or a ring bond that does not belong to any ring smaller than 8-membered.

See also

LINGO

LINGO is a very fast text-based molecular similarity search method. It is based on fragmentation of canonical isomeric SMILES strings into overlapping substrings.

non-terminal atom
An atom is considered non-terminal if it is connected to two or more non-hydrogen atoms, i.e. OEAtomBase.GetHvyDegree() >= 2.
rotatable bond

In OEChem, a bond is considered rotatable only if it is a single non-ring bond between two non-terminal, non-triple-bonded atoms. For example the following structures have no rotatable bonds:

  • CCC
  • CCC#CCC
  • C1CCCCC1

Note

Since the ‘rotatable’ property is depends on the ‘in ring’ property. The OEFindRingAtomsAndBonds function must be called before accessing the rotatable bond property via OEBondBase.IsRotor.

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. A reaction considered valid according to the strict SMIRKS semantics if:

  • all mapped product atoms have corresponding mapped reactant atoms
  • all atom maps must be pairwise (i.e. every map class has exactly one reactant and one product atom)

The strict semantics also requires that unmapped reactant atoms are destroyed in the reaction.

The strict semantics means that in full compliance with the SMIRKS defined by its originator, Daylight Inc. For more information about the semantics of SMIRKS language visit http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html.

stereo atom

In OEChem the atom stereo information is stored as a relative positions of neighboring atoms around a tetrahedral center. If an atom has specified stereochemistry, then the OEAtomBase.HasStereoSpecified method returns true.

Warning

In OEChem atom stereochemistry is internally represented by two properties stereo atom and chiral atom. These properties are completely independent and allows OEChem to retain configuration information around atoms that are not chiral atom, or to identify chiral atoms whose configuration is not specified.

Note

In the current version of OEChem, the only class of stereochemistry supported for atoms is OEAtomStereo_Tetrahedral which corresponds to \(sp3\) tetrahedral chirality. Valid return values for the OEAtomStereo_Tetrahedral stereochemistry class are OEAtomStereo_Left and OEAtomStereo_Right.

stereo bond

In OEChem the bond stereo information is stored as a relative positions of neighboring atoms around a bond. If a bond has specified stereochemistry, then the OEBondBase.HasStereoSpecified method returns true.

Warning

In OEChem bond stereochemistry is internally represented by two properties stereo bond and chiral bond. These properties are completely independent and allows OEChem to retain configuration information around bonds that are not chiral bonds, or to identify chiral bonds whose configuration is not specified.

Note

In the current version of OEChem, the only class of stereochemistry supported for bonds is OEBondStereo_CisTrans which corresponds to conjugated E/Z chirality. Valid return values for the OEBondStereo_CisTrans stereochemistry class are OEBondStereo_Cis and OEBondStereo_Trans.