Hi James, On Mon, Aug 15, 2011 at 11:10 AM, James Davidson <j.david...@vernalis.com> wrote: > > It's been a while since I've bothered you - but this good fortune couldn't > last forever! : )
Nonsense! It's always a pleasure to have nice new bugs to fix. :-) > I wasn't quite sure where to post this (RDKit forum, KNIME, not at all!), so > thought I would quickly run something past you to see what you think. I am > very keen to be using the MarvinSketch node in KNIME as a primary way of > allowing users to enter chemical queries - and then convert the resultant > query molecule (via SDF out) into RDKit to use in subsequent substructure > searching. It's an RDKit problem, so I'm CC'ing the RDKit list on the reply. <snip> > > The query mol that I am passing is shown below (exported using the SDF > Writer node): > > Row0 > Mrv0541 08151109232D > > 9 10 3 0 0 0 999 V2000 > -9.2518 -1.7678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -9.9663 -2.1803 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 > -9.9663 -3.0054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -9.2518 -3.4179 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 > -8.5373 -3.0054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -8.5373 -2.1803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -7.7527 -3.2603 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -7.2678 -2.5929 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 > -7.7527 -1.9255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 6 2 0 0 0 0 > 2 3 2 0 0 0 0 > 3 4 1 0 0 0 0 > 4 5 2 0 0 0 0 > 5 7 1 0 0 0 0 > 6 5 1 0 0 0 0 > 6 9 1 0 0 0 0 > 7 8 1 0 0 0 0 > 8 9 2 0 0 0 0 > 2 F 2 6 7 > 4 F 2 6 7 > 8 F 2 6 7 > M ALS 2 2 F C N > M ALS 4 2 F C N > M ALS 8 2 F C N > M END > > > > I have also read the molecule into RDKit (2011_06_1) and printed the > molblock: > > Row0 > RDKit 2D > > 9 10 0 0 0 0 0 0 0 0999 V2000 > -9.2518 -1.7678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -9.9663 -2.1803 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > -9.9663 -3.0054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -9.2518 -3.4179 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > -8.5373 -3.0054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -8.5373 -2.1803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -7.7527 -3.2603 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -7.2678 -2.5929 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > -7.7527 -1.9255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 2 0 > 1 6 1 0 > 2 3 1 0 > 3 4 2 0 > 4 5 1 0 > 5 7 1 0 > 6 5 2 0 > 6 9 1 0 > 7 8 1 0 > 8 9 2 0 > V 2 [#6,#7] > V 4 [#0,#7] > V 8 [#0,#7] > M END > > > I am guessing the #0 atoms are causing the problem(?) - but I couldn't > figure-out at what point I am losing the intended #6 atoms... Any > help/advice greatly appreciated. I can reproduce this in the svn version. I'll file a bug and get it fixed. -greg ------------------------------------------------------------------------------ uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
