Basic stereo specification
The relative position of ligands on a chiral atom is marked with wedge bonds: up (solid ), down (hatched ), up or down (wiggly ). Having wedge bonds at chiral atoms with the chiral flag on the entire structure implies that a single isomer is present. The absolute configuration (R or S) is known for all chiral centers that are marked with wedge bonds.
Non-stereo bond to atom at stereogenic centers implies that no information is known about the configuration of a stereogenic center. It could be either of two stereoisomers, or a mixture of the two.
The existence of wedge bonds at chiral atoms without chiral flag on the entire structure has two meanings depending on the file format used.
MDL file types (mol, sdf ...): The structure is a racemic mixture of the two enantiomers.
Daylight file types (smiles, smarts): Wedges mean absolute stereo configuration, the structure represents a single enantiomer.
The positions of the double bond ligands already define the stereo configuration of the double bond (cis or trans). Special query double bond types allow us to specify cis or trans, not trans or not cis isomers.
Enhanced stereo specification
Works in MDL molecule formats: mol, rgf, sdf, rxn etc... and in ChemAxon Extended SMILES format: cxsmiles.
Enhanced stereochemical representation introduces three types of identifiers that can be attached to a stereogenic center. A stereochemical group label is composed from an identifier and a group number. Each stereogenic center marked with wedge bonds belongs to one (and only one) stereochemical group. Grouping allows us to specify relative relationships among stereogenic centers.
Stereochemical group types:
Stereogenic center where the absolute configuration is known.
Stereogenic center where the relative configuration is known, but the absolute configuration is not known. The structure represents one stereoisomer that is either the structure as drawn (R,S) OR the epimer in which the stereogenic centers have the opposite configuration (S,R).
Mixture of stereoisomers. It can be a pair of enantiomers or all the diastereomers.