Convert RDF to SDF

Dear All,





I have an RDF which is needed to convert into SDF. I dont have any problem in converting the root fields in RDF but when it comes to fields in table part i am facing with the problem of how to loop the program so that all fields in table are read.





I am describing the problem below





1) This i don't have any problem with the following one





$DTYPE ROOT:ID


$DATUM 1





2) I want solution for the following one





$DTYPE ROOT:INVENTORY(1):NAME


$DATUM XYZ


$DTYPE ROOT:INVENTORY(1):QUANTITY


$DATUM 10gm


$DTYPE ROOT:INVENTORY(2):NAME


$DATUM ABC


$DTYPE ROOT:INVENTORY(2):QUANTITY


$DATUM 50gm





I want to know how many times each field in a table is present in RDF and loop it so many times to get data to write in the following format





> <NAME_1>


XYZ


> <QUANTITY_1>


10gm


> <NAME_2>


ABC


> <QUNATITY_2>


50gm





Thanking you in Advance





Anil

Dear All,





Can anyone help on this as i have to use the molecules with different activities in the docking and QSAR studies. I am able to convert the root fields but i am not getting how to convert the table fields with multiple rows into flat file format of SDF.





Please help





Anil

Indeed, Marvin does not support converting these fields into SD file.


We are checking the issue.

Dear All,





I thank Tamas for the response but i have a small idea how to do it. may be this can help you.





Please find the attached Program which finds how many properties are present in a given RDF and prints out the unique property keys.





I want to use this to get the values of properties to print out in flat file SDF format. I can get the root fields like ID (in sample RDF) to print in SDF but when it comes to STOCK table, i want to know for each molecule how many properties (each single one) are present for the given molecule and how to loop it around the molecule to get the same.





I attach sample program and also the sample RDF.





Thanks in Advance





Anil

If you write a custom code, you can change the name of fields:

Code:

// save RDfile properties into a temporary object int pcount = molecule.getPropertyCount(); Enumeration keys = molecule.getPropertyKeys(); Object[][] table = new Object[pcount][2]; for(int i=0;i<table.length;i++) {     String key = (String)keys.nextElement();     table[i] = new Object[]{ key, molecule.getProperty(key) }; } // delete all RDfile properties of the molecule molecule.clearProperties(); // add old properties with new names for(int i=0;i<table.length;i++) {       String key = (String)table[i][0];       Object value = table[i][1];       String newkey;       // generate new name from old one       ...       molecule.setPropertyObject(newkey,value); } // convert to SDfile format System.out.println(molecule.toFormat("sdf"));