Question: Modeller 9.16 program
gravatar for taylan.cruz
2.6 years ago by
taylan.cruz0 wrote:

I have this script that accesses the folder with the files to be modeled but does not run Modeller. How to make it run?

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package Modeller_modelagem_molecular;
 * @author Lucas
public class Modeller_modelagem_molecular {

     * @param args the command line arguments
    public static void main(String[] args) {
        // TODO code application logic here
        String s = null;

    try {

   //     String[]callAndArgs= {"python\",\"\",\"arg1\",\"arg2"};

   //     String[]callAndArgs= {"python\",\"\",\"arg1\",\"arg2"};3

        Process p;
       p = Runtime.getRuntime().exec("cmd /c start C:\\PipelineGmbio\\Modeller9.16\\bin\\test");

             //C:\Program Files\Modeller9.16\bin\test
           //p = Runtime.getRuntime().exec("cmd /c start C:/Procheck_NT/ pro AB 2.3");
       //p = Runtime.getRuntime().exec("cmd /c start C:/Procheck_NT");

        BufferedReader stdInput = new BufferedReader(new


        BufferedReader stdError = new BufferedReader(new


        // read the output

        while ((s = stdInput.readLine()) != null) {



        // read any errors

        while ((s = stdError.readLine()) != null) {





    catch (IOException e) {

        System.out.println("exception occured");




software error • 821 views
ADD COMMENTlink modified 2.6 years ago by Pierre Lindenbaum123k • written 2.6 years ago by taylan.cruz0
gravatar for Pierre Lindenbaum
2.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

It's not a script. It's a java program. No sorry, it's an ugly java program.

Create a directory Modeller_modelagem_molecular and move the java file in it.



javac Modeller_modelagem_molecular/


 java Modeller_modelagem_molecular.Modeller_modelagem_molecular

pray for something to happen.

t does not run Modeller.

why don't you run 'Modeller' directly ? instead of using this java wrapper ?

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Pierre Lindenbaum123k

I need to build a pipeline to run this and other scripts.

ADD REPLYlink written 2.6 years ago by taylan.cruz0
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