Question

脚本文件

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request ver`enter code here`bose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

a = automodel(env,
alnfile  = 'align.ali',     # alignment filename
knowns   = '1GJZ',              # codes of the templates
sequence = 'target')              # code of the target

a.starting_model= 1       
a.ending_model= 10           # index of the first model
# (determines how many models to calculate)
a.make()                            # do the actual homology modeling

代码

import java.io.*;


public class Demo 
{


        public static void main(String args[])
        {

        try 
        {
Runtime r = Runtime.getRuntime();
Process p = r.exec("cmd /c \"C:/model2/script.py\"");
BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = "";
while ((line = br.readLine()) != null) {
    System.out.println(line);
}
} 
catch (Exception e) 
{
e.printStackTrace();
}
        }
    }

输出

                     MODELLER 9.10, 2011/09/28, r8346

 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                 Copyright(c) 1989-2011 Andrej Sali
                        All Rights Reserved

                         Written by A. Sali
                           with help from
       B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
            N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                R. Sanchez, B. Yerkovich, A. Badretdinov,
                  F. Melo, J.P. Overington, E. Feyfant
             University of California, San Francisco, USA
                Rockefeller University, New York, USA
                  Harvard University, Cambridge, USA
               Imperial Cancer Research Fund, London, UK
          Birkbeck College, University of London, London, UK

错误

iodataW> Setting io.atomfilesdirectory to a colon-delimited string is deprecated, as it is not robust on Windows systems. Set it to a list of directories instead. For example: env.io.atomfilesdirectory = ['./', '../atomfiles'] openf__E> Cannot open file align.ali: No such file or directory;

正如我们在输出部分中看到的那样，此代码正在访问建模器程序，一旦开始执行它就会出现错误 align.ali not found ，正如我们在错误部分中看到的那样。它作为独立的script.py文件运行。

Answer 1

它看起来像路径问题。您是否尝试在python脚本中使用align.ali的绝对路径？

通过java代码为Modeller软件执行script.py

1 个答案: