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.
OEChem‘s canonical SMILES terminology corresponds to Daylight‘s ‘unique‘ SMILES definition.
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.
OEChem‘s canonical isomeric SMILES terminology corresponds to Daylight‘s ‘absolute‘ SMILES definition.
In OEChem, an atom is considered chiral, if it is connected to four different substituent groups i.e. its mirror image is non-superimposable.
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.
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.
LINGO is a very fast text-based molecular similarity search method. It is based on fragmentation of canonical isomeric SMILES strings into overlapping substrings.
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:
SMIRKS is a reaction transform language. A reaction considered valid according to the strict SMIRKS semantics if:
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.
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.
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.
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.
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.
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.
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.