bingo.Molfile does not assign atom coordinates on Postgres

[rapo...@metamolecular.com]

Greetings,

Atom coordinates don't appear to be assigned from the bingo.Molfile function.

Using:

bingo.Molfile('c1ccccc1');

resulted in a file with unassigned atom coordinates (see below). I was expecting coordinates to be assigned because the documentation indicates this should happen by default. The indigo-depict command line utility compiled and ran without problems.

Indigo was pulled from GitHub and compiled from the Indigo v1.1.11 tag. The same issue was seen with the build from the current master ffb012e26d.

System details:

Ubuntu 13.04/64

Postgres 9.1.9

Any ideas as to why coordinates don't get assigned on Bingo/Postgres?

Thanks,

Rich

# select bingo.Molfile('c1ccccc1');

                                molfile                                

-----------------------------------------------------------------------

                                                                      +

   -INDIGO-09161318022D                                               +

                                                                      +

   6  6  0  0  0  0  0  0  0  0999 V2000                              +

     0.0000    0.0000    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+

     0.0000    0.0000    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+

     0.0000    0.0000    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+

   1  2  4  0  0  0  0                                                +

   2  3  4  0  0  0  0                                                +

   3  4  4  0  0  0  0                                                +

   4  5  4  0  0  0  0                                                +

   5  6  4  0  0  0  0                                                +

   6  1  4  0  0  0  0                                                +

 M  END                                                               +

 

(1 row)

[greenphar...@gmail.com]

Hello Richard,

See here for the same problem with indigo toolkit :

https://groups.google.com/forum/#!topic/indigo-general/Q2kKCabZ9yY

You can generate coordinates afterwards with molconvet from Chemaxon, follow the link to get an example of how i use molconvert in this case.

Regards

Eric

[ric...@gmail.com]

Re,

You have to the use method mol.layout()