Generic compound explicit in mol file or not

Hi

 

I wonder how to properly deal with those 2 kinds of MOL file representing the same compound:

- http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMSP02010000

- http://www.genome.jp/dbget-bin/www_bget?compound+C00195

 

Chemaxon produces the right image, with an R group for both.

For KEGG the R group is explicitly written in the atom block and Chemaxon cannot produce an InChI because generics are not allowed in InChI (what is expected). A SMILES is produced properly.

For LipidMaps, the R group is written in the properties block impacting the image but not the formula or the InChI/SMILES produced by ChemAxon.

 

So is there a way to deal with such generic compound hidden in MOL files?

 

I use ChemAxon 6.2.0

Thanks

Hi,

In Kegg  the atom is an undefined R atom which cannot be exported to InChi.

In LIPID it is a Carbon atom with an R label on it, it is an exact structure so it can be converted to InChi.

You need to harmonize the two representation converting them to your preferred representation:

Either convert it to R atom, in this case you will not able to generate InChi or convert it to Carbon atom with R label, in this case the molecule can be converted to InChi but of course it will represent an exact structure.

You can make this conversion using a simple java code or using standardizer tool.

best

Volfi

Yes, it's confusing to have the same graphical representation but different formulae, InChI and SMILES.

And wrong formula, InChI and SMILES looking at the graphical representation for LipidMaps MOL file.

 

No way to standardize with some Chemaxon tools?

Or ChemAxon API?

You can use either java API  or standardizer tool (both provided by ChemAxon) to standardize these structures according to your preference.

Do you know such standardizer tools?

Accidentally yes :D

Here is the documentation of the ChemAxon Standardizer tool.

I don't have it as command line tool in version 6.2.0

but I guess it should be available in the Java API version 6.2.0, right?

 

Do you know which action(s) to use in Standardizer to standardize MOL files (or InChI / SMILES input)?

smoretti wrote:

I don't have it as command line tool in version 6.2.0 but I guess it should be available in the Java API version 6.2.0, right?   Do you know which action(s) to use in Standardizer to standardize MOL files (or InChI / SMILES input)?

What package do you have installed?

What packages do you have license for?

I use the jchem-suite, from jchem-merged-lib with an academic license, version 6.2.0.

Hi,

If you have jchem-suite you should have a jchem directory with a bin folder. In this "jchem/bin" directory you should have a standardizer runnable application. Could you please check it? You need to define a transform action in the standardizer with your defined action to change the atoms. See the earlier linked documentation.

avolford wrote:

Hi, If you have jchem-suite you should have a jchem directory with a bin folder. In this "jchem/bin" directory you should have a standardizer runnable application. Could you please check it? You need to define a transform action in the standardizer with your defined action to change the atoms. See the earlier linked documentation.

Hi

 

I have MarvinBeans 6.2.0 for command line tools but no standardizer tool there.

And jchem-suite for Java API. So this is in the Java API I would like to know actions to perform with Standardizer method.

Ok MarvinBeans does not contain the standardizer command. So you should use the java API or download the standardizer tool from the ChemAxon website. For the java API you should call the Standardizer.class, see more information here.

avolford wrote:

Ok MarvinBeans does not contain the standardizer command. So you should use the java API or download the standardizer tool from the ChemAxon website. For the java API you should call the Standardizer.class, see more information here.

Could you provide a standardizer configuration file for the MOL case I have?

The attached standardizer configuration converts the structure from lipidmaps.org to the expected representation.

For the other structure you can use Structure Checker to detect the carbon atom with "R" alias. Fixing could be done manually.

zmohacsi wrote:

The attached standardizer configuration converts the structure from lipidmaps.org to the expected representation. For the other structure you can use Structure Checker to detect the carbon atom with "R" alias. Fixing could be done manually.

We tried with a user.abbrevgroup dictionary file and it does the job.

Thanks