various IDockYa improvements

src/main/java/com/actelion/research/chem/docking/DockingEngine.java

@@ -157,7 +157,7 @@ private double getStartingPositions(StereoMolecule mol, List<Conformer> initialP
 				catch(Exception e) {
 					throw new DockingFailedException("could not assess atom types");
 				}
-				MMFFPositionConstraint constraint = new MMFFPositionConstraint(conf,50,0.2);
+				MMFFPositionConstraint constraint = new MMFFPositionConstraint(conf,50,0.5);
 				mmff.addEnergyTerm(constraint);
 				mmff.minimise();
 				Conformer ligConf = new Conformer(conf);
@@ -336,8 +336,9 @@ public DockingResult dockMolecule(StereoMolecule mol) throws DockingFailedExcept
 
 			}
 			double energy = mcSearch(pose,steps);
+
 			if(energy<bestEnergy) {
-				bestEnergy = energy;
+				bestEnergy = pose.getScore();
 				bestPose = pose.getLigConf();
 				contributions = pose.getContributions();
 			}
@@ -419,7 +420,7 @@ private double mcSearch(LigandPose pose, int steps) {
 
 		pose.setState(bestState);
 		pose.removeConstraints();
-		bestEnergy = pose.getFGValue(new double[bestState.length]);
+		bestEnergy = pose.getScore();
 		return bestEnergy;
 
 	}
@@ -510,7 +511,7 @@ public double refineNativePose(double d, double[] coords) {
 				StereoMolecule conf = conformer.toMolecule();
 				conf.ensureHelperArrays(Molecule.cHelperParities);
 				mmff = new ForceFieldMMFF94(conf, ForceFieldMMFF94.MMFF94SPLUS, ffOptions);
-				constraint = new MMFFPositionConstraint(conf,50,0.2);
+				constraint = new MMFFPositionConstraint(conf,50,0.5);
 				mmff.addEnergyTerm(constraint);
 				mmff.minimise();
 				Conformer ligConf = new Conformer(conf);

src/main/java/com/actelion/research/chem/docking/DockingTest.java

@@ -0,0 +1,76 @@
+package com.actelion.research.chem.docking;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import com.actelion.research.chem.Canonizer;
+import com.actelion.research.chem.IDCodeParser;
+import com.actelion.research.chem.Molecule;
+import com.actelion.research.chem.Molecule3D;
+import com.actelion.research.chem.MolfileCreator;
+import com.actelion.research.chem.StereoMolecule;
+import com.actelion.research.chem.docking.DockingEngine.DockingResult;
+import com.actelion.research.chem.docking.DockingEngine.ScoringFunction;
+import com.actelion.research.chem.io.Mol2FileParser;
+
+public class DockingTest {
+
+	public static final String DUDE_PLUS_DIR = "C:\\Users\\wahljo1\\benchmark_phesa\\DUD_E-PLUS\\DUDE-plus-rev1\\ace";
+
+
+
+	public static void main(String[] args) throws Exception {
+		String receptor = DUDE_PLUS_DIR +"/" + "protein.mol2";
+		String ligand = DUDE_PLUS_DIR +"/"+ "ligand.mol2";
+		Mol2FileParser m2fp = new Mol2FileParser();
+
+		Molecule3D lig = new Molecule3D(m2fp.load(new File(ligand)));
+		Canonizer can = new Canonizer(lig);
+		DockingUtils.repairMolecule3D(lig);
+		StereoMolecule canMol = can.getCanMolecule(true);
+		lig = new Molecule3D(canMol);
+		lig.ensureHelperArrays(Molecule.cHelperCIP);
+
+		int[] ligAtomTypes = new int[lig.getAtoms()];
+
+
+		//mols.values().forEach(e -> e.forEach(i -> rec.addMolecule(i)));
+		Molecule3D rec = m2fp.load(receptor);
+		rec.normalizeAmbiguousBonds();
+		can = new Canonizer(rec);
+		rec = new Molecule3D(rec);
+		rec.ensureHelperArrays(StereoMolecule.cHelperCIP);
+		DockingUtils.repairMolecule3D(rec);
+
+		DockingEngine engine = new DockingEngine(rec, lig,50,10,8.0,ScoringFunction.CHEMPLP);
+		StereoMolecule toDock = new StereoMolecule(lig);
+		toDock.ensureHelperArrays(Molecule.cHelperParities);
+		DockingResult result = engine.dockMolecule(toDock);
+
+		System.out.println(result.getScore());
+		System.out.println(result.getContributions());
+
+		String delim = System.getProperty("line.separator");
+		File outfile = new File("docked_random.sdf");
+		   FileWriter fileWriter;
+		try {
+
+		    fileWriter = new FileWriter(outfile);
+		    MolfileCreator mfc = new MolfileCreator(result.getPose());
+		    mfc.writeMolfile(fileWriter);
+		    fileWriter.write(delim);
+		    fileWriter.write("$$$$");
+		    fileWriter.write(delim);
+		    fileWriter.flush();
+			fileWriter.close();
+			System.out.println("written");
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+		e.printStackTrace();
+		}
+
+
+
+	}
+}

src/main/java/com/actelion/research/chem/docking/LigandPose.java

@@ -214,18 +214,7 @@ private void updateDihedralAngles() {
 			torsionHelper.rotateAroundBond(b, deltaTorsion,ligConf,false);
 		}
 	}
-	/*
-	public void updateState() {
-		for(int a=0;a<mol.getAllAtoms();a++) {
-			Coordinates c = ligConf.getCoordinates(a);
-			state[3*a] = c.x;
-			state[3*a+1] = c.y;
-			state[3*a+2] = c.z;
-		}
-		engine.updateState();
 
-	}
-	*/
 
 	@Override
 	public void setState(double[] state){