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Has anyone got Dingo to work?

Asked by [ Editor ]

I want to convert SMILES structures to .png and came across another post on this forum about dingo.

I'm unsure what to do with the C-library portion of the program, but I have downloaded and unpacked the command-line utility and tried to run it:

ls dingo-render LICENSE.GPL test.smi

dingo-render test.smi pleaseWork.png dingo-render: command not found

I executed a chmod 757 on the file to see if it needed execute permissions, but it didn't help. Has anyone else tried this program? What am I missing? Thanks.

Imported from: http://blueobelisk.stackexchange.com/questions/172

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3 answers

4

pat walters

If the current working directory isn't in your path (it's a security risk if it is) you need to specify the path to the executable. Do something like

./dingo_render myfile.sdf out.png

note the dot-slash at the beginning

I downloaded dingo-render for OS-X 10.5 and it worked for me (sort of). I can get dingo-render to work with SDF input, but not with SMILES.

This works

./dingo-render test.sdf out.png

This gives an error

./dingo-render test.smi out.png exception: RXN loader: bad header CC1CC2C3CCC4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO

The help message indicates that the program accepts SMILES input. As a disclaimer, I spent about 5 minutes with dingo-render so I may be doing something wrong.

NN comments
jason fuller
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I’m getting the same bad header error now…

Any other suggestions about batch conversion of smiles to 2D Structures?

I have Bioclipse up and running, but it will only convert the structure I’ve highlighted. The convert to MDL2000 script looks like it almost worked as it actually produces a second (blank) row in the table, and checking the properties shows the next smile structure from the original file.

david garcía aristegui
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In a Ubuntu (2.6.24-24-generic) the dingo-render binary works like a charm… for example, with a smi file like CC1CC2C3CCC4=CC(=O)C=CC4©C3(F)C(O)CC2©C1(O)C(=O)CO

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2

jason fuller [ Editor ]

Turns out that Dingo doesn't fully support .smi files. However, a .smi file with a single SMILES string in it (and no description) does work.
The program itself works quite well (better than depict.emolecules.com ), yet I found a few SMILES strings that would cause it to fail. In contrast, if I convert the failed .smi files to .mol files via openbabel, Dingo was flawless.

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