You should add some coordinates to the OpenBabel file. Try calling make3D().
- Noel On 12 April 2010 20:13, Craig Swank <[email protected]> wrote: > Hello, > I am working on displaying molecules on a web-app. The web-app uses pybel > to generate mol files that are then displayed by Cheme's JSDraw > (http://www.chemene.com:8080/CCD/jsdraw). It seems that the output from > pybel can't be read by JSDraw. > The two examples below are different molecules, but I hope it is good enough > to illustrate what I'm talking about. Does anyone know if this is a known > problem with open babel's mol file output, or is the problem with JDDraw? > Here is an example from pybel that can't be drawn > OpenBabel04121013092D > 6 6 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 1 2 2 0 0 0 > 1 4 1 0 0 0 > 2 3 1 0 0 0 > 3 6 2 0 0 0 > 4 5 2 0 0 0 > 5 6 1 0 0 0 > M END > > and one from JSDraw's demo page that does work: > > ChemJSDraw11070913082D > > 19 21 0 0 0 0 0 0 0 0 1 V2000 > 4.8940 7.4100 0.0000 C 0 0 > 6.2450 8.1900 0.0000 C 0 0 > 7.5960 7.4100 0.0000 C 0 0 > 8.9470 8.1900 0.0000 C 0 0 > 10.2980 7.4100 0.0000 O 0 0 > 11.6490 8.1900 0.0000 C 0 0 > 11.6490 9.7500 0.0000 C 0 0 > 13.0000 10.5300 0.0000 C 0 0 > 14.3510 9.7500 0.0000 N 0 0 > 14.3510 8.1900 0.0000 C 0 0 > 13.0000 7.4100 0.0000 C 0 0 > 13.0000 5.8500 0.0000 C 0 0 > 14.3510 5.0700 0.0000 C 0 0 > 15.7020 5.8500 0.0000 C 0 0 > 15.7020 7.4100 0.0000 C 0 0 > 17.0530 5.0700 0.0000 C 0 0 > 18.4040 5.8500 0.0000 C 0 0 > 18.4040 7.4100 0.0000 C 0 0 > 17.0530 8.1900 0.0000 N 0 0 > 1 2 1 0 > 2 3 1 0 > 3 4 1 0 > 4 5 1 0 > 5 6 1 0 > 6 7 2 0 > 7 8 1 0 > 8 9 2 0 > 9 10 1 0 > 10 11 2 0 > 11 6 1 0 > 11 12 1 0 > 12 13 2 0 > 13 14 1 0 > 14 15 2 0 > 15 10 1 0 > 16 14 1 0 > 16 17 2 0 > 17 18 1 0 > 18 19 2 0 > 19 15 1 0 > M END > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-Devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
