package name.mjw.jamber.IO.OpenMM;
import name.mjw.jamber.IO.Mol2;
import name.mjw.jamber.IO.AMBER.Lib;
import name.mjw.jamber.IO.AMBER.ParameterStore;
import name.mjw.jamber.IO.OpenMM.OpenMMXML;
import org.apache.log4j.Logger;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.*;
import java.net.URLDecoder;
/**
* Tests based on gaff.dat (version 1.5) AMBER12 with md5sum
* 7392a517db165cc715c63baf9f8c1ace
*
* @author mjw
*
*/
public class OpenMMXMLWithMol2AceticAcidTest {
final Logger LOG = Logger.getLogger(OpenMMXMLWithMol2AceticAcidTest.class);
private static OpenMMXML openMMXML;
private static ParameterStore parameterStore;
private static Mol2 aceticAcidMol2;
private static Lib lib;
@BeforeClass
public static void setUp() {
InputStream gaffIs = OpenMMXMLWithMol2AceticAcidTest.class.getClass()
.getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");
try {
parameterStore = new ParameterStore();
parameterStore.readParm(gaffIs);
} catch (Exception e) {
e.printStackTrace();
}
InputStream aceticAcidMol2Stream = OpenMMXMLWithMol2AceticAcidTest.class
.getClass().getResourceAsStream(
"/name/mjw/jamber/IO/AMBER/aceticAcid/acetic_acid.mol2");
try {
aceticAcidMol2 = new Mol2(aceticAcidMol2Stream);
lib = new Lib(aceticAcidMol2);
} catch (IOException e) {
e.printStackTrace();
}
}
@Test
public void testOpenMMXML() {
// Create the OpenMMXML object
openMMXML = new OpenMMXML(parameterStore, lib);
String coreName = "aceticAcid";
String path;
try {
// Get path relative to the test directory
path = URLDecoder.decode(
this.getClass()
.getResource(
"/name/mjw/jamber/IO/AMBER/" + coreName
+ "/").getFile(), "utf-8");
String filePathFF = path + coreName + "_ff.xml";
String filePathHydrogens = path + coreName + "_hydrogens.xml";
String filePathResidues = path + coreName + "_residues.xml";
String filePathGBSA_OBC = path + coreName + "_obc.xml";
OutputStream outFF = new FileOutputStream(filePathFF);
openMMXML.toFFXMLOutputStream(outFF);
OutputStream outHydrogens = new FileOutputStream(filePathHydrogens);
openMMXML.toHydrogensXMLOutputStream(outHydrogens);
OutputStream outResidues = new FileOutputStream(filePathResidues);
openMMXML.toResiduesXMLOutputStream(outResidues);
OutputStream outGBSA_OBC = new FileOutputStream(filePathGBSA_OBC);
openMMXML.toGBSA_OBC_XMLOutputStream(outGBSA_OBC);
} catch (UnsupportedEncodingException | FileNotFoundException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
}