Dear Greg,
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.
--
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?
Best regards,
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 6229
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/JmnSoft
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