conversion of RDF to various formats

I need to split RDF file into individual molecules, retaining the label information for each of them and the ID of the reaction. Ideal output would be SDF. An example of the problem:

RDF :
A (labeled 1a)  + B (labeled 1b)  --> C (labeled cis-12) + D (labeled trans-12) [reaction ID 123]
E (labeled 2a)  + F (labeled 2b)  --> G (labeled alpha-13) + H (labeled beta-13) [reaction ID 124]

Desired output information (SDF format) :
Structure of A
label: 1a
type: reactant
reaction ID : 123
Structure of B
label: 1b
type: reactant
reaction ID : 123
Structure of C
label: cis-12
type: product
reaction ID : 123
Structure of D
label: trans-12
type: product
reaction ID : 123
Structure of E
label: 2a
type: reactant
reaction ID : 124
Structure of F
label: 2b
type: reactant
reaction ID : 124
Structure of G
label: alpha-13
type: product
reaction ID : 124
Structure of H
label: beta-13
type: product
reaction ID : 124

Is molconverter (my version is 5.3.0.1) capable of this or any combined way how to achieve this goal ? Thanks.

Molconverter is not capable of doing this. If you are familiar with Java programming language, then you can use ChemAxon's Java API to implement a simple application which can do the job.

Java API documentation: http://www.chemaxon.com/marvin/help/developer/beans/api/index.html />

Regards,
Zsolt

Zsolt wrote:

Molconverter is not capable of doing this. If you are familiar with Java programming language, then you can use ChemAxon's Java API to implement a simple application which can do the job. Java API documentation: http://www.chemaxon.com/marvin/help/developer/beans/api/index.html /> Regards, Zsolt

Unfortunately I have no experience with Java programming. Any chance to assemble desired application under some skilled guidance ?

Zsolt wrote:

Molconverter is not capable of doing this. If you are familiar with Java programming language, then you can use ChemAxon's Java API to implement a simple application which can do the job. Java API documentation: http://www.chemaxon.com/marvin/help/developer/beans/api/index.html /> Regards, Zsolt

Could InstantJChem be of use for this purpose ? I mean to import the RDF into "flattened" database and export the flat structure as SDF ?

The use of IJC for this purspose is being discussed in this topic on the IJC forum:

https://www.chemaxon.com/forum/ftopic5904.html

Tim

What class should be used to do the process above described by jirikrechl?

Unfortunately, you cannot solve this issue with Marvin or Molconvert. Since there was a mention about similar problem in one of the IJC forum thread, I suggest posting the actual problem there: https://www.chemaxon.com/forum/ftopic5904.html

Best regards,

Efi