スクリプトファイル
# 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
コード
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();
}
}
}
出力
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
エラー
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;
このコードは、出力部分で確認できるようにモデラープログラムにアクセスしています。実行を開始すると、エラー部分で確認できるように、エラーalign.aliが見つかりません。スタンドアロンscript.pyファイルとして実行されます。