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New MMFFBasedParameterSetReaderTest
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@danielszisz @egonw
danielszisz authored and egonw committed Jul 29, 2012
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225 changes: 225 additions & 0 deletions src/test/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReaderTest.java
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package org.openscience.cdk.modeling.builder3d;


import static org.junit.Assert.*;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Map;
import java.util.Hashtable;
import java.util.List;
import java.util.Map.Entry;

import org.junit.Test;
import org.openscience.cdk.interfaces.IAtomType;




/**
* This class is for testing the MMFF94 based parameter
* reading in CDK.
*
* @author danielszisz
* @see org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
*/
public class MMFF94BasedParameterSetReaderTest {

private String line, atomline, bondline, angleline, strbndline, torsionline,
opbendline, dataline;
private boolean firstatomline = true;
private boolean firstbondline = true;
private boolean firstangleline = true;
private boolean firststrbndline = true;
private boolean firsttorsionline = true;
private boolean firstopbendline = true;
private boolean firstdataline = true;

@Deprecated
public void initializeMMFF94ParameterFileLines() {
String fname = "org/openscience/cdk/modeling/forcefield/data/mmff94.prm";
ClassLoader loader = MMFF94BasedParameterSetReader.class.getClassLoader();
InputStream inps = loader.getResourceAsStream(fname);
BufferedReader r = new BufferedReader(new InputStreamReader(inps), 1024);
try {
while(true) {
line = r.readLine();
if(line == null) {
break;
}
else if(line.startsWith("atom")) {
if(firstatomline) {
atomline = line;
firstatomline = false;
}
else continue;
}
else if(line.startsWith("bond")) {
if(firstbondline) {
bondline = line;
firstbondline = false;
}
else continue;
}
else if(line.startsWith("angle")) {
if(firstangleline) {
angleline = line;
firstangleline = false;
}
else continue;
}
else if(line.startsWith("strbnd")) {
if(firststrbndline) {
strbndline = line;
firststrbndline = false;
}
}
else if(line.startsWith("torsion")) {
if(firsttorsionline) {
torsionline = line;
firsttorsionline = false;
}
}
else if(line.startsWith("opbend")) {
if(firstopbendline) {
opbendline = line;
firstopbendline = false;
}
}
else if(line.startsWith("data")) {
if(firstdataline) {
dataline = line;
firstdataline = false;
}
}
}
} catch (IOException ioe) {
ioe.printStackTrace();
}
}

@Test
public void testreadParameterSets() {
MMFF94BasedParameterSetReader mmff94bpsr = new MMFF94BasedParameterSetReader();
try {
mmff94bpsr.readParameterSets();
} catch(Exception e) {
e.printStackTrace();
}
Map<String, Object> parameterSet = new Hashtable<String, Object>();
parameterSet = mmff94bpsr.getParamterSet();

//test atom type
List<IAtomType> atomtypes = mmff94bpsr.getAtomTypes();
IAtomType atomtype = atomtypes.get(0);
String sid = "C";
assertEquals(sid, atomtype.getAtomTypeName());
String rootType = "C";
assertEquals(rootType, atomtype.getSymbol());
String smaxbond = "4";
assertEquals(Integer.parseInt(smaxbond), (int) atomtype.getFormalNeighbourCount());
String satomNr = "6";
assertEquals(Integer.parseInt(satomNr), (int) atomtype.getAtomicNumber());

//atom
//TODO testing


//bond
// String scode = "0";
String sid1 = "C";
String sid2 = "C";
String slen = "1.508";
String sk2 = "306.432";
String sk3 = "-612.865";
String sk4 = "715.009";
String sbci = "0.0000";
String bondkey = "bond" + sid1 + ";" + sid2;
List<Double> bonddata = new ArrayList<Double>();
bonddata.add((Double) (new Double(slen).doubleValue()) );
bonddata.add((Double) (new Double(sk2).doubleValue()) );
bonddata.add((Double) (new Double(sk3).doubleValue()) );
bonddata.add((Double) (new Double(sk4).doubleValue()) );
bonddata.add((Double) (new Double(sbci).doubleValue()) );

//strbnd
// scode = "0";
sid1 = "C";
sid2 = "C";
String sid3 = "C";
String value1 = "14.82507";
String value2 = "14.82507";
String strbndkey = "strbnd" + sid1 + ";" + sid2 + ";" + sid3;
List<Double> strbnddata = new ArrayList<Double>();
strbnddata.add((Double) (new Double(value1).doubleValue()));
strbnddata.add((Double) (new Double(value2).doubleValue()));

//angle
// scode = "0";
sid1 = "C=";
sid2 = "C";
sid3 = "N";
value1 = "105.837";
value2 = "86.1429";
String value3 = "-34.5494";
String value4 = "0";
String anglekey = "angle" + sid1 + ";" + sid2 + ";" + sid3;
List<Double> angledata = new ArrayList<Double>();
angledata.add((Double) (new Double(value1).doubleValue()));
angledata.add((Double) (new Double(value2).doubleValue()));
angledata.add((Double) (new Double(value3).doubleValue()));
angledata.add((Double) (new Double(value4).doubleValue()));

//torsion
// scode = "0";
sid1 = "HC";
sid2 = "C";
sid3 = "C";
String sid4 = "HC";
value1 = "0.142";
value2 = "0.693";
value3 = "0.157";
value4 = "0.000";
String value5 = "0.000";
String torsionkey = "torsion" + ";" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
List<Double> torsiondata = new ArrayList<Double>();
torsiondata.add((Double) (new Double(value1).doubleValue()));
torsiondata.add((Double) (new Double(value2).doubleValue()));
torsiondata.add((Double) (new Double(value3).doubleValue()));
torsiondata.add((Double) (new Double(value4).doubleValue()));
torsiondata.add((Double) (new Double(value5).doubleValue()));

//opbend
// scode = "0";
sid1 = "O=";
sid2 = "C=";
sid3 = "CR4R";
sid4 = "CR4R";
value1 = "10.86681780";
String opbendkey = "opbend" + ";" + sid1+ ";" + sid2 + ";" + sid3 + ";" +sid4 ;
List<Double> opbenddata = new ArrayList<Double>();
opbenddata.add((Double) (new Double(value1).doubleValue()));

//TODO data lines testing

for(Entry<String, Object> e : parameterSet.entrySet()) {
if(e.getKey().equals(bondkey)) assertEquals(bonddata, e.getValue());
else if(e.getKey().equals(strbndkey)) assertEquals(strbnddata, e.getValue());
else if(e.getKey().equals(anglekey)) assertEquals(angledata, e.getValue());
else if(e.getKey().equals(torsionkey)) assertEquals(torsiondata, e.getValue());
else if(e.getKey().equals(opbendkey)) assertEquals(opbenddata, e.getValue());
}





}




}

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