Indigo
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substructure search
My database is not a bingo supported database, so I want to use the substructureMatcher method that comes with indigo. Gives a substructure to compare to another, if it is a substructure. Returns true, otherwise, returns false. But I don't know how to use this method, can there be an example for me to refer to, thank you very much.
Hi @edgeTurbo,
This is the link to the documentation for indigo.substructureMatcher method: https://lifescience.opensource.epam.com/indigo/api/index.html?highlight=indigo#molecule-substructure-matching
The full description of the substructure search with lots of queries and examples of the molecules retrieved you can find here: https://lifescience.opensource.epam.com/bingo/user-manual-oracle.html#substructure-search
Hi @AATDev21 , thanks but i used indigo.substructureMatcher method, An error occurred: this is my code:
public static void main(String[] args) {
String queryMol = "\n" +
" Ketcher 7122215582D 1 1.00000 0.00000 0\n" +
"\n" +
" 6 6 0 0 0 0 999 V2000\n" +
" 9.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 8.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 8.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 2 0 0 0\n" +
" 2 3 1 0 0 0\n" +
" 3 4 2 0 0 0\n" +
" 4 5 1 0 0 0\n" +
" 5 6 2 0 0 0\n" +
" 6 1 1 0 0 0\n" +
"M END\n";
String mol = "\n" +
" Ketcher 7122215572D 1 1.00000 0.00000 0\n" +
"\n" +
" 9 9 0 0 0 0 999 V2000\n" +
" 10.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 10.4750 -6.5580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 9.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 8.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 7.4750 -4.8260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 8.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 1 0 0 0\n" +
" 2 3 1 0 0 0\n" +
" 3 4 2 0 0 0\n" +
" 4 5 1 0 0 0\n" +
" 5 6 2 0 0 0\n" +
" 6 7 1 0 0 0\n" +
" 7 8 1 0 0 0\n" +
" 7 9 2 0 0 0\n" +
" 9 3 1 0 0 0\n" +
"M END\n";
Indigo indigo = new Indigo();
IndigoObject matcher = indigo.substructureMatcher(indigo.loadMolecule(mol));
IndigoObject queryMolecule = indigo.loadQueryMolecule(queryMol);
IndigoObject match = matcher.match(queryMolecule);
System.out.println(match == null);
}
Normally, match should not be null, because it is a substructure of the target molecule. Can you help me figure out what the problem is? Or is there something wrong in my usage?
Hi @edgeTurbo, Sorry for the late response. I didn't get any notifications about your question. Have a look at the Ketcher snap: both your molecule and query molecule have benzene rings in the structure. So you should aromatize them first and then use in subtsructure search. A code example for python is below:
>>> from indigo import Indigo
>>> i = Indigo()
>>> str_mol = "\n" + " Ketcher 7122215572D 1 1.00000 0.00000 0\n" + "\n" + " 9 9 0 0 0 0 999 V2000\n" + " 10.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 10.4750 -6.5580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 9.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 8.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.4750 -4.8260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 8.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 1 2 1 0 0 0\n" + " 2 3 1 0 0 0\n" + " 3 4 2 0 0 0\n" + " 4 5 1 0 0 0\n" + " 5 6 2 0 0 0\n" + " 6 7 1 0 0 0\n" + " 7 8 1 0 0 0\n" + " 7 9 2 0 0 0\n" + " 9 3 1 0 0 0\n" + "M END\n"
>>> str_query = "\n" + " Ketcher 7122215582D 1 1.00000 0.00000 0\n" + "\n" + " 6 6 0 0 0 0 999 V2000\n" + " 9.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 8.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.9750 -7.4240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.4750 -6.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 8.9750 -5.6920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 1 2 2 0 0 0\n" + " 2 3 1 0 0 0\n" + " 3 4 2 0 0 0\n" + " 4 5 1 0 0 0\n" + " 5 6 2 0 0 0\n" + " 6 1 1 0 0 0\n" + "M END\n"
>>> mol = i.loadMolecule(str_mol)
>>> query = i.loadQueryMolecule(str_query)
>>> matcher = i.substructureMatcher(mol)
>>> matcher.match(query)
None <---------------------------------------- NO MATCH!
>>> mol.aromatize()
1
>>> query.aromatize()
1
>>> matcher.match(query)
<indigo.IndigoObject object at 0x111367340> <------ MATCH!