I'm displaying molfile usign jchempaint applet. the issue is it shows a
pop-up for each molecule being displayed:
"*not all atoms have 2D coordinates. JCP can only display fully specified
2d Structures. Shall we layout the structure?*"
The thing is it is a full 3D mol file and I also tried
StructureDiagrammGenerator to get 2D structure. but that also does not help:
sdg.setMolecule(foundMol);
sdg.generateCoordinates();
foundMol = sdg.getMolecule();
How can I get rid of that message? (if you are loading 1000th of molecules
into a html table...)
Best Regards,
Joos
Example molfile (linearized for loading into JChemPaint Applet):
\n CDK 1117111152\n\n 28 29 0 0 0 0 0 0 0 0999 V2000\n
-0.0169 1.3921 0.0097 C 0 0 0 0 0 0 0 0 0 0 0 0\n
1.1701 2.0948 0.0021 C 0 0 0 0 0 0 0 0 0 0 0 0\n
2.3776 1.4193 -0.0135 C 0 0 0 0 0 0 0 0 0 0 0 0\n
2.4036 0.0359 -0.0216 C 0 0 0 0 0 0 0 0 0 0 0 0\n
1.2241 -0.6793 -0.0137 C 0 0 0 0 0 0 0 0 0 0 0 0\n
0.0021 -0.0041 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.2651 -0.7633 0.0105 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.3267 -0.1731 0.0242 O 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.2433 -2.1103 0.0031 O 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.5059 -2.7796 0.0120 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.2843 -4.2701 0.0018 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.1563 -4.7155 -0.0118 O 0 0 0 0 0 0 0 0 0 0 0 0\n
-3.3397 -5.1084 0.0078 N 0 0 0 0 0 0 0 0 0 0 0 0\n
-3.1243 -6.5574 -0.0021 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.2793 -6.9283 -1.2379 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.6375 -8.2672 -0.9937 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.4671 -9.4319 -1.5672 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-3.9788 -9.2674 -1.3195 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-4.2839 -8.7617 0.0646 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-4.4169 -7.2261 0.0072 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.3826 -6.9368 1.2115 C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.8103 -7.2297 2.1480 N 0 0 0 0 0 0 0 0 0 0 0 0\n
3.8890 2.3249 -0.0236 S 0 0 0 0 0 0 0 0 0 0 0 0\n
4.8286 1.4555 -0.6405 O 0 0 0 0 0 0 0 0 0 0 0 0\n
3.5596 3.5736 -0.6166 O 0 0 0 0 0 0 0 0 0 0 0 0\n
4.3063 2.5551 1.7266 C 0 0 0 0 0 0 0 0 0 0 0 0\n
3.2815 3.2656 2.3608 F 0 0 0 0 0 0 0 0 0 0 0 0\n
4.4556 1.3060 2.3387 F 0 0 0 0 0 0 0 0 0 0 0 0\n 1 6
2 0 0 0 0 \n 1 2 1 0 0 0 0 \n 2 3 2 0 0 0 0 \n 3 4 1
0 0 0 0 \n 3 23 1 0 0 0 0 \n 4 5 2 0 0 0 0 \n 5 6 1 0
0 0 0 \n 6 7 1 0 0 0 0 \n 7 8 2 0 0 0 0 \n 7 9 1 0 0
0 0 \n 9 10 1 0 0 0 0 \n 10 11 1 0 0 0 0 \n 11 12 2 0 0 0
0 \n 11 13 1 0 0 0 0 \n 13 14 1 0 0 0 0 \n 14 20 1 0 0 0 0
\n 14 15 1 0 0 0 0 \n 14 21 1 0 0 0 0 \n 15 16 1 0 0 0 0 \n
16 17 1 0 0 0 0 \n 17 18 1 0 0 0 0 \n 18 19 1 0 0 0 0 \n 19
20 1 0 0 0 0 \n 21 22 3 0 0 0 0 \n 23 24 2 0 0 0 0 \n 23 25
2 0 0 0 0 \n 23 26 1 0 0 0 0 \n 26 27 1 0 0 0 0 \n 26 28 1
0 0 0 0 \nM END
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