RDF to RXN convertion

There is an issue with molconvert. When I convert rdf-file to rxn format all data fields from input file are dropped.

Version of JChem 15.11.2.0 (lastest).

Pavel.

Hi,

Sorry for the late reply. The RXN file contains MOL file blocks, and MOL file cannot store molecule properties (the RDF contains MOL block and some data fileds).

Janos

Thank you. I see, in the official documenation there is no information about additional fields in rxn files. However such a feature looks convenient and cxcalc uses it. If one calls

cxcalc -S charge 1.rdf > 1.rxn

it returns rxn file with converted existed fields and added new ones. These fields will not be displayed with MarvinView but can be parsed manually.

...
  2  3  1  0  0  0  0
  2 11  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  1  0  0  0
  5  6  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 11 12  2  3  0  0  0
 12 13  1  0  0  0  0
M  END
>  <CdId>
1873

>  <CHARGE>
-0,06;-0,03;-0,06;-0,05;0,01;-0,06;-0,05;-0,06;0,01;-0,06;-0,05;-0,06;0,01;-0,05
;-0,07;-0,05;-0,04;-0,06;-0,05;-0,05;-0,07;-0,06;-0,05;-0,04;-0,05;-0,05;-0,06;-
0,05;-0,06;-0,04;-0,03;-0,08;-0,07;-0,03;-0,04;-0,06;-0,06;-0,00;-0,04;-0,05;-0,
05;-0,05;-0,05;-0,03;-0,07;-0,08;-0,03;-0,06;-0,06;-0,05;-0,05;-0,02;-0,03;-0,02
;-0,06;-0,06;-0,06;-0,08;-0,05;-0,06;-0,08;-0,05

$$$$

Hi,

I think in this case the cxcalc makes and rxn file with sdf blocks except mol blocks. It isn't a valid rxn file, this is why the MarvinView dosn't display the additional fields.

Janos

I have a .rdf file with a large set of mapped reactions. Although I'd like to separate each reaction from the .rdf into a individual .rxn file.

What would be the best way of doing this?

Hi,

You can open the file with MarvinView and save the reactions into separate files (File->Save all..., on the right check the Advanced check box, and then select the Into separate files radiobutton).

Janos

Thank you Janos for you answer.

Although my file has almost 3.000.000 lines and open with Marvin View it is a bit problematic, because it crashes MarvinView app on my computer.

There is anyway of doing the same by coding some Java? (I've a chemaxon licence)

 

Thanks a lot,

Nuno

Hi,

here is a code, which does that:

MolImporter mi = new MolImporter("e:\\test.rdf");
        
        Molecule mol = mi.read();
        int counter = 0;
        while(mol != null) {
            counter++;
            String fileName = "test_" + counter + ".rxn"; 
            MolExporter exporter = new MolExporter("e:\\" + fileName, "rxn");
            exporter.write(mol);
            exporter.close();
            
            mol = mi.read();
        }
        
        mi.close();

I hope this will work for you.

Janos

It works prettily Janos. Much faster and this time Marvin doesn't crashes. 

One again, thanks a lot for your reply.

 

Nuno