MolConvert

Hello...





I have (again) a short and simple question.


I would like to generate a PDB from a SMILES. I know there exists the molconvert command-line tool and I used this to generate the PDB:

Code:

molconvert -3:S{fast} pdb test.smi -o test.pdb

Now I would like to generate the PDB using the MolConverter class in your API. Therefore I have to specify the format. What is the syntax for that?





Thanks a lot for your help,





tobias

The simplest way is the following:

Code:

String[] args = {"-3:S{fast}", "pdb", "test.smi", "-o", "test.pdb" }; ... int n = 0; OutputStream[] theOut = new OutputStream[1]; int[] theVerboseargs = new int[1]; MolConverter conv = MolConverter.createMolConverter(null, null, args,                                              theOut, theVerboseargs); try {     while(conv.convert()) {          ++n;     }     if(theOut[0] != System.out) {          theOut[0].close();     }     if(n == 0) {          System.err.println("no structure found");     } } catch(Exception ex) {     ex.printStackTrace(); }