Dear Jean-Marc, On Tue, Feb 9, 2010 at 9:44 AM, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> wrote: > > A 21:23 08/02/2010 +0100, Greg Landrum a écrit : >> > The MinimizeCLI.cpp file in Minimize has a few "mol" instead of "*mol" as >> > function parameter that prevent it to be compiled right out of the box. >> >>Yes, the MinimizeCLI stuff has not been maintained for rather a long >>time; I'm not surprised that it doesn't work. > > It works fine, once the * have been added at the right places.
hmm, good to know. I will take a look at some point to see if it's worth updating that demo. > > I experimented with RDDepict::compute2DCoords on a set 2870 automatically > generated isomers > of santonin. > Surprisingly, the generation of 2D coordinates failed for four of them. > Here is one faulty structure: > > 1537 > RDKit 3D > > 18 20 0 0 0 0 0 0 0 0999 V2000 > 2.4100 2.5288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.0424 0.7717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5681 -1.2020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8708 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.1724 2.3187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.1727 -0.9352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.1727 2.4352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.3064 -0.8435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.6351 2.1015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.2418 -2.0161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.6771 -0.8937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4996 1.5329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3582 3.5984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.6771 2.3937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.7382 -1.3058 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.6672 -2.6987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 6 1 0 > 1 5 2 0 > 1 15 1 0 > 2 10 1 0 > 2 7 1 0 > 2 17 2 0 > 3 6 2 0 > 3 9 1 0 > 4 9 1 0 > 4 7 1 0 > 4 18 2 0 > 5 16 1 0 > 5 13 1 0 > 7 16 1 0 > 8 11 1 0 > 8 10 1 0 > 8 13 1 0 > 9 12 1 0 > 9 11 1 0 > 10 14 1 0 > M END > > The existing 2D coordinates were generated by the CDK from atom connectivities > and I wanted to replace them by possibly better ones. > The problem is that I do not see the reason for which this structure is > particular > while so many other ones are not. Any idea? It's a bug. Thanks for letting me know about it. I've entered into the bug tracking system: https://sourceforge.net/tracker/?func=detail&aid=2948402&group_id=160139&atid=814650 and I will try to get it fixed in the next few days. -greg ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
