Automated Evaluation of Homoloy Models

Source code for Eval.java

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;

public class Eval
{
public static String USAGE = "java -jar Eval.jar <modelContainer> <modelDir> <refContainer> <refDir>" +
"\n\t <modelContainer> contains in each line one id of the used models (the filename before the .pdb)" +
"\n\t <modelDir> the directory where the model-files lie" +
"\n\t <refContainer> contains in each line one id of the used reference structures (the filename before the .pdb)" +
"\n\t <refDir> the directory where the model-files lie";

public static void main(String[] args)
{
if(args.length != 4)
{
System.out.println(Eval.USAGE);
System.exit(1);
}

File modelContainer = new File(args[0]);
File modelDir = new File(args[1]);
File refContainer = new File(args[2]);
File refDir = new File(args[3]);

ArrayList <String> modelIds = Eval.readContainer(modelContainer);
ArrayList <String> refIds = Eval.readContainer(refContainer);

for(String modelId : modelIds)
{
File model = Eval.getPDB(modelDir, modelId);
for(String refId : refIds)
{
System.out.println(modelId+" vs. " +refId);
File reference = Eval.getPDB(refDir, refId);
System.out.println("RMSD: "+Eval.calcRMSD(reference, model));
System.out.println("TM: "+Eval.calcTM(reference, model));
System.out.println("ALL RMSD: "+Eval.calcFeRMSD(reference, model));
}
}
}

public static String calcRMSD(File reference, File model)
{
String res = "";

try
{
Process p = Runtime.getRuntime().exec("sap "+reference.getAbsolutePath()+" "+model.getAbsolutePath());
BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line;
while((line = in.readLine()) != null)
{
if(line.startsWith("Un-weighted RMSd ="))
{
int off = line.indexOf("over all matched atoms");
if(off != -1)
{
res = line.substring(18, off);
res.replaceAll(" ", "");
}
}
}
}
catch (IOException e)
{
e.printStackTrace();
}

return res;
}

public static String calcAllRMSD(File reference, File model)
{
String res = "";

try
{
Process p = Runtime.getRuntime().exec("rms.pl -out all "+reference.getAbsolutePath()+" "+model.getAbsolutePath());
p.waitFor();

BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));

String line;
while((line = in.readLine()) != null)
{
res = line.replaceAll(" all", "");
res = res.replaceAll(" ", "");
}

in.close();
}
catch (IOException e)
{
e.printStackTrace();
}
catch (InterruptedException e)
{
e.printStackTrace();
}

return res;
}

public static String calcTM(File reference, File model)
{
String res = "";

try
{
Process p = Runtime.getRuntime().exec("TMS "+reference.getAbsolutePath()+" "+model.getAbsolutePath());

BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line;
while((line = in.readLine()) != null)
{
res = line.substring(5);
}
}
catch (IOException e)
{
e.printStackTrace();
}

return res;
}

public static String calcFeRMSD(File reference, File model)
{
String res = "";

try
{
File reftemp = File.createTempFile("reftemp", ".pdb");
reftemp.deleteOnExit();
File modtemp = File.createTempFile("modtemp", ".pdb");
modtemp.deleteOnExit();

File script = Eval.writePythonScript(reference, model, reftemp, modtemp);

Process p = Runtime.getRuntime().exec("pymol "+script.getAbsolutePath());
p.waitFor();

res = Eval.calcAllRMSD(reftemp, modtemp);
}
catch (IOException e)
{
e.printStackTrace();
}
catch (InterruptedException e)
{
e.printStackTrace();
}

return res;
}

public static File writePythonScript(File reference, File model, File reftemp, File modtemp)
{
File script = null;
try
{
script = File.createTempFile("fesel", ".pml");
script.deleteOnExit();

BufferedWriter out = new BufferedWriter(new FileWriter(script));

out.write("load "+reference.getAbsolutePath()+", reference\n");
out.write("load "+model.getAbsolutePath()+", mod\n");
out.write("select fe, name fe\n");
out.write("align mod, reference\n");
out.write("select near_7, fe around 7\n");
out.write("select ref_near_7, (fe around 7) and reference\n");
out.write("save "+reftemp.getAbsolutePath()+", ref_near_7\n");
out.write("select mod_near_7, (fe around 7) and mod\n");
out.write("save "+modtemp.getAbsolutePath()+", mod_near_7\n");
out.write("quit\n");

out.close();

}
catch (IOException e)
{
e.printStackTrace();
}

return script;
}

public static File getPDB(File dir, String name)
{
return new File(dir, name+".pdb");
}

public static ArrayList<String> readContainer(File f)
{
ArrayList <String> ids = new ArrayList<String>();

try
{
BufferedReader in = new BufferedReader(new FileReader(f));
String line;

while((line = in.readLine()) != null)
{
ids.add(line);
}

in.close();
}
catch (FileNotFoundException e)
{
e.printStackTrace();
}
catch (IOException e)
{
e.printStackTrace();
}

return ids;
}
}