A list of commonly encountered functional groups is now used when identifying atom groups of the ligand for purposes of "best binding" docking. Ligand moieties are now more cleanly demarcated, so that the pre-dock algorithm can more effectively identify targets for ligand-protein alignment. The difference can be seen in the TAAR8 test which now produces significantly improved contact energies.
A new data file called moieties.dat lists these functional groups. It can be edited to adjust the behavior of the dock, however doing so is likely to affect the unit tests, changing their output which is treated as a fail condition. Additionally, not all possible moiety definitions are working properly; while the pattern HC(C)=O correctly matches aldehyde groups in molecules such as vanillin or cinnamaldehyde, CC(H)=O does not.
A list of commonly encountered functional groups is now used when identifying atom groups of the ligand for purposes of "best binding" docking. Ligand moieties are now more cleanly demarcated, so that the pre-dock algorithm can more effectively identify targets for ligand-protein alignment. The difference can be seen in the TAAR8 test which now produces significantly improved contact energies.
A new data file called
moieties.datlists these functional groups. It can be edited to adjust the behavior of the dock, however doing so is likely to affect the unit tests, changing their output which is treated as a fail condition. Additionally, not all possible moiety definitions are working properly; while the patternHC(C)=Ocorrectly matches aldehyde groups in molecules such as vanillin or cinnamaldehyde,CC(H)=Odoes not.