Dear John & Greg,
This is it!
OpenBabel11041515532D
16 18 0 0 1 0 0 0 0 0999 V2000
0.0000 1.1700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3600 0.6300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0800 0.4500 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
1.6200 0.6300 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
1.2600 1.1700 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
0.7200 0.9900 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
0.9000 -0.0900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8000 1.6200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3500 1.7100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8000 1.1700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1600 0.3600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2500 0.9900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.0800 2.1600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7000 0.5400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2400 0.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7000 1.0800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
3 7 1 0 0 0 0
4 5 1 0 0 0 0
4 10 1 0 0 0 0
4 11 1 0 0 0 0
5 6 1 0 0 0 0
5 9 1 0 0 0 0
6 7 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
9 13 2 0 0 0 0
10 12 2 0 0 0 0
11 14 1 0 0 0 0
14 15 1 0 0 0 0
14 16 2 0 0 0 0
M END
CC(=O)OC12C(=O)OC(=O)C1C1CCC2C1
[14,13,15,10,3,9,11,7,8,12,4,5,0,1,2,6,]
it return the original mol indexes.
thanks for your help.
Guillaume
using javascript version it can be done like this...
var RDKit = require('rdkit');
var fs = require('fs');?
var molfile = fs.readFileSync( 'bu01chemicals_1.mol', "utf8");
console.log(molfile);
var mol = RDKit.Molecule.MolBlockToMol(molfile);
var smi = mol.toSmiles();
console.log(smi);
var c = mol.getProp('_smilesAtomOutputOrder');
console.log(c);
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