- B-factor (temperature factor) describes the displacement of the atomic positions from an average value. The more flexible an atom is the larger the displacement from the mean position will be (mean-squares displacement). The values of the B-factors are normally between 15 to 30 (sq. Ångströms), but can be much higher for more flexible regions. B-factors can indicate the mobility of atoms and they can also indicate where there are errors in model building.
- canonical isomeric SMILES
In OEChem TK, 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 OEMolToSmiles function.
OEChem TK’s canonical isomeric SMILES terminology corresponds to Daylight’s ‘absolute’ SMILES definition.
- chiral atom
In OEChem TK, an atom is considered chiral, if it is connected to four different substituent groups i.e. its mirror image is non-superimposable.
In OEChem TK, 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.
Comma-separated-values file format.
- Popcount stands for population count and it is the procedure of counting number of ones in a bit string. It is available on most modern processors (both Intel and AMD) so it is hardware and not platform dependent.
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.
- SMARTS Pattern Matching section of the OEChem TK manual that provides an introduction to SMARTS syntax
- SMARTS - A Language for Describing Molecular Patterns
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.
SMIRKS is a reaction transform language.