InChI support in BKChem
For InChI generation BKChem uses the official IUPAC InChI program. For Windows platform this program is distributed together with BKChem (from version 0.11.0_pre2) in the instalation package. On Linux and other machines you have to download it manualy and give BKChem the path to the executable (cINChI-1 in the recent version) of the program via the dialog found in menu under Options/INChI program path. Once BKChem has the path to this program it can create InChIs for you - just select some molecules and use the Chemistry/Generate InChI command.
Although InChI was not originaly intended to be read at all, BKChem can read most of the InChIs and convert them to structures. It uses its own library for it and as of now it can correctly read 98.5% of the ~120 000 single-component structures from the NCI database.
The conversion of InChI to chemical structure is accessible via the Chemistry/Read INChI command.
The current implementation of InChI conversion is experimental and has some limitations. Detail are given below.
Features that are supported:
- Reading of the connectivity
- Localization of movable hydrogens
- Generation of atom coordinates
- Charges, both in the q and p form
Features that are not supported:
- multi-component formulas (such as C6H6.H2O)
- fixed hydrogens
After using this tool, you should always try to regenerate the InChI from the generated structure to be sure the results match. This is because InChI has some features causing that there is a possibility for a molecule to completely conform to one InChI, however to have a different one generated by the InChI program. This issue plays role only for a very small fraction of structures and the generated structure should be a tautomeric form of the right structure anyway.