Modeller 9.16 program

Question

[taylan.cruz]

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

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package Modeller_modelagem_molecular;
import java.io.*;
/**
 *
 * @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\",\"my_python.py\",\"arg1\",\"arg2"};

   //     String[]callAndArgs= {"python\",\"my_python.py\",\"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

             InputStreamReader(p.getInputStream()));

        BufferedReader stdError = new BufferedReader(new

             InputStreamReader(p.getErrorStream()));

        // read the output

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

            System.out.println(s);

        }

        // read any errors

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

            System.out.println(s);

        }

        System.exit(0);

    }

    catch (IOException e) {

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


        System.exit(-1);

    }


    }

}

Answer 1

[Pierre Lindenbaum]

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.

Modeller_modelagem_molecular/Modeller_modelagem_molecular.java

compile:

javac Modeller_modelagem_molecular/Modeller_modelagem_molecular.java

execute

 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 ?

[taylan.cruz]

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