[Open Babel] Issues Maintaining Bond Order Through Conversion
Hello, I’ve been having trouble converting between formats. I have generated some MOL files using RDKit for various substituted subphthalocyanines (attached below) which, when opened with any molecule viewer, show the correct bond order (1 or 2 depending on the atom) between the nitrogen and carbon atoms surrounding the central boron. However, when I convert to any other format (such as PDB or XYZ) with OpenBabel, the bond order between each nitrogen atom and the adjacent carbon atom is reduced to 1. Is there an option that I haven’t included that can solve this problem, or is this a bug that hasn’t been addressed? Any help would be appreciated. Thanks, Biruk ULIWKVYKBWIIEK-UHFFFAOYSA-N_0.mol Description: MOL mdl chemical test HHZNZQDCTKUBQG-UHFFFAOYSA-N_0.mol Description: MOL mdl chemical test -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Issues Maintaining Bond Order Through Conversion
Neither PDB nor XYZ files store the bond order. XYZ files do not even store which atoms are connected to which atoms. If you want to learn more about this, you should open chemical structure files in a text editor and familiarise yourself with the information contained within. I gave a talk which touches upon some of this (see slide 3 of https://www.slideshare.net/baoilleach/so-i-have-an-sd-file-what-do-i-do-next-51825001 ). - Noel On 27 June 2018 at 20:31, Biruk Abreha wrote: > Hello, > > I’ve been having trouble converting between formats. I have generated some > MOL files using RDKit for various substituted subphthalocyanines (attached > below) which, when opened with any molecule viewer, show the correct bond > order (1 or 2 depending on the atom) between the nitrogen and carbon atoms > surrounding the central boron. However, when I convert to any other format > (such as PDB or XYZ) with OpenBabel, the bond order between each nitrogen > atom and the adjacent carbon atom is reduced to 1. > > Is there an option that I haven’t included that can solve this problem, or > is this a bug that hasn’t been addressed? Any help would be appreciated. > > Thanks, > Biruk > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Issues Maintaining Bond Order Through Conversion
> Is there an option that I haven’t included that can solve this problem, or is > this a bug that hasn’t been addressed? Any help would be appreciated. The two formats you mention don't store bond orders. (In particular XYZ only stores atoms - not even bond connections.) OB includes an algorithm to perceive bond orders, but it's hardly foolproof. So if you want to ensure bond orders are preserved, don't use those formats. Best regards, -Geoff -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
