tag:blogger.com,1999:blog-7844526396210378482.post6313632522985299651..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: Measuring information loss in file format conversion Part IINoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-7844526396210378482.post-76521420520553333642012-05-24T08:03:47.708+01:002012-05-24T08:03:47.708+01:00I don't know about InChi but I have seen stere...I don't know about InChi but I have seen stereo centers at het nitrogen atoms. The electron pair of nitrogen when free switches its conformation at 100 Hz so there is no preference, but when bound this is prevented, so, within molecules N effectively becomes a stereo center. Which is widely ignored, of course, until people see a crystal structure and begin to ask questions.<br /><br />The example I encountered was reserpine which somehow wasn't correctly modeled by CORINA compared to the published x-ray structure.<br /><br />I'm glad InChi has support, and that you noted it for openbabel.R Stephanhttps://www.blogger.com/profile/18267577618598521684noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-32993208102754991592010-10-07T17:17:33.940+01:002010-10-07T17:17:33.940+01:00I'm coming around to the same viewpoint, Steve...I'm coming around to the same viewpoint, Steve. It's just that I hadn't seen this problem coming.<br /><br />But to play the devil's advocate, if InChI sees cis/trans isomers where none exist in reality (the C=N bond in the post above being a potential example) then we will see two different InChIs being calculated for the same molecule just by chance depending on whether the apparent geometry in the input file is cis or trans.<br /><br />Perhaps the set of possibly stereogenic centers listed in the InChI technical manual could be tightened up here or there.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-29467071221709774102010-10-07T16:50:30.188+01:002010-10-07T16:50:30.188+01:00If you want interoperability and linking of inform...If you want interoperability and linking of information you need a (arbitrary) standard. While I am biased for InChI, I would argue, not chemistry/stereochemistry, but that InChI has the backing of the publishers and database producers. Thus using the InChI (arbitrary) rules is the correct practical solution.<br /><br />Between chemists and chemistry there never has been and will never be agreement, so we should/must find a workable solution.<br /><br />Steve Hellernyc dadhttps://www.blogger.com/profile/12408630866156325938noreply@blogger.com