JChem for Excel: Use for Reactions

I have a code which generates some reactions in smiles string format. I then use the JChem for Excel tool to convert these strings to structures.

The problem is JChem for excel doesn't recognize any spaces in the smiles string, and also suppose I have 3 molecules of a product forming then the JChem doesn't recognize and converts only the smile string of 1st reactant.

Is there a way to have this functionality in JChem For Excel? I am providing certain reactions in smiles format below. This will help one understand my problem better

Examples:

1. The following reaction will be converted fine using the "From Smiles" option

C1(=CO)C(C(C(CO)O1)O)O>>C1(=CC(C(O1)CO)O)C=O.O 

2. The following will have a problem

C1(=CO)C(C(C(CO)O1)O)O >>C1(=CC(C(O1)CO)O)C=O.O 

C1(C(C(C(CO)O1)O)O)(CO)O>>c1(ccc(C=O)o1)CO.3O  //Here I want to have 3 water molecules as a side product

My product details are

JChem for Excel

Version: 5.5.1.248

I am using it with Microsoft Office Excel 2010

Hi,

I think Marvin cannot import these smiles either. So this is not a JChemExcel specific issue.

Viktor

Zsolt could you please step in. Thanks, Viktor

Yes, but JChemExcel has the functionality to convert structures to smiles and vice-versa. It also works with certain reactions written in smiles. So, I thought  maybe the way it identifies reactions can be modified.

No, not only JChemExcel has this functionality, JChemExcel does not know more than the basic JChem library. E.g. in Marvin you can also import Source as Smiles

Edit Menu in Marvin / Source/ Import as SMILES.

So I think the reactor team or Marvin team can answer, again this is not jChemExcel specific issue.

So, should I redirect this post to somewhere else? Please, if you can direct me to a proper forum or something, that would be great...

I have done it, this is another forum now.

Quickly checked just to prove that what I wrote down re JChem Core lib,

1. smiles can be imported into a reaction

2. The first reactan can be imported, not more

3. I got an exception during the import.

1. The following reaction will be converted fine using the "From Smiles" option


C1(=CO)C(C(C(CO)O1)O)O>>C1(=CC(C(O1)CO)O)C=O.O 


2. The following will have a problem


C1(=CO)C(C(C(CO)O1)O)O >>C1(=CC(C(O1)CO)O)C=O.O 


C1(C(C(C(CO)O1)O)O)(CO)O>>c1(ccc(C=O)o1)CO.3O  //Here I want to have 3 water molecules as a side product

1. It is converted fine as it is a correct SMILES string.

2.This

C1(=CO)C(C(C(CO)O1)O)O >>C1(=CC(C(O1)CO)O)C=O.O 

is not a valid SMILES string. Smiles cannot contain space character.

This

C1(C(C(C(CO)O1)O)O)(CO)O>>c1(ccc(C=O)o1)CO.3O

is not a valid SMILES due to the '3' before the Oxygen atom.

I would suggest to read the SMILES specification to be able to generate syntactically correct SMILES.

1. The following reaction will be converted fine using the "From Smiles" option


C1(=CO)C(C(C(CO)O1)O)O>>C1(=CC(C(O1)CO)O)C=O.O 


2. The following will have a problem


C1(=CO)C(C(C(CO)O1)O)O >>C1(=CC(C(O1)CO)O)C=O.O 


C1(C(C(C(CO)O1)O)O)(CO)O>>c1(ccc(C=O)o1)CO.3O  //Here I want to have 3 water molecules as a side product

C1(=CO)C(C(C(CO)O1)O)O >>C1(=CC(C(O1)CO)O)C=O.O 

C1(C(C(C(CO)O1)O)O)(CO)O>>c1(ccc(C=O)o1)CO.3O

Thank you for pointing out what was going wrong. After skimming through the specifications part, it seems to me that there is no way to represent more than one molecule in a reaction.

Thank you for pointing out what was going wrong. 

After skimming through the specifications part, it seems to me that 

there is no way to represent more than one molecule in a reaction.

You can represent more molecule eg instead of 3O:

OCC1OC(O)(CO)C(O)C1O>>OCc1ccc(C=O)o1.O.O.O

All the best

Andras