The smile format from MARVIN is not consistent with MetaCyc.

Hi everyone,

I was wondering that what i used the wrong option to export output as the SMILEs format.

At first, I downloaded C00024.mol (Pyruvate) from KEGG database, and i want to use MARVIN to calculate net charge by using Jython interface. After that i want to export the result of net charge including SMILEs format.

The table below is the results that i used different options.

mol.toFormat("smiles:u")	CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12
MetaCyc	S(CCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(OP(=O)(OCC1(C(OP([O-])(=O)[O-])C(O)C(O1)N3(C2(=C(C(N)=NC=N2)N=C3))))[O-])[O-])C(=O)C
mol.toFormat("smiles:-H")	CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N

Actually, I tried to find what version of SMILEs that MetaCyc used, but i cannot find it.

So if you could answer me, I really appreciate.

Thank you in advance.

sunisa

Hi,

I don't really understand the situation.

The molecule you would like to export to smiles is not the same as the one in MetaCyc's. The difference is not that big, but in the MetaCyc's molecule the acidic Hydrogen atoms are missing so the molecule has 4 negative charge. Do you want to transform your molecule such a way to remove acidic hydrogen atoms?

Standardizer's transform action (see 7. <Transformation> section here) can do this, but you have to give the specific transform action.

Andras

Thank you for your reply.

Actually, i need to compare compound structure between database. The structure information is different since charge as you said. i will see the detail of standardizer as your advise.

 

kuk_sc wrote:

The structure information is different since charge as you said.

In this case you should definitely standardize the two different form of the same structure to the same form. So standardizer is the solution.