minor performance improvements

Author: thsa

src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java

@@ -40,11 +40,13 @@
 /**
  * Typically you should use IDCodeParser instead of this class. You may instantiate this class
  * if you need to avoid a dependency to the CoordinateInventor and if you pass encoded coordinates
- * together with any idcode for parsing.
+ * together with any idcode for parsing, or if you don't need 2D-coordinates, e.g. because you
+ * intend to generate 3D-coordinates afterward.
  * We needed to introduce this class to avoid a cyclic dependency between the IDCodeParser and
- * the CoordinateInventor: If encoded atom coords are not given, then the IDcodeParser needs
- * to invent then in order to assign proper up-/down-bonds. The CoordinateInventor needs the
- * IDCodeParser to unpack its default template list.
+ * the CoordinateInventor: If encoded atom coords are not given and if you later depict the
+ * molecule in 2D, then IDCodeParser needs to invent 2D-coordinates in order to assign
+ * proper up-/down-bonds from stereo parities. CoordinateInventor needs IDCodeParser in turn
+ * to unpack its default template list.
  */
 public class IDCodeParserWithoutCoordinateInvention {
 	private StereoMolecule	mMol;
@@ -69,7 +71,7 @@ public void neglectSpaceDelimitedCoordinates() {
 	/**
 	 * Creates and returns a molecule from the idcode with its atom and bond arrays being
 	 * just as large as needed to hold the molecule. Use this to conserve memory if no
-	 * atoms or bonds are added to the molecule afterwards. This version of the method
+	 * atoms or bonds are added to the molecule afterward. This version of the method
 	 * allows to pass idcode and atom coordinates in one String object.
 	 * @param idcode null or idcode, which may contain coordinates separated by a space character
 	 * @return

src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java

@@ -25,12 +25,42 @@ public class PheSAAlignmentOptimizer {
 	public static final int PMI_OPTIMIZATIONS = 10;
 	private static final double EXIT_VECTOR_WEIGHT = 10.0;
 	private static final int BEST_RESULT_SIZE = 20;
-	
+
+	private final PheSASetting mSettings;
+	private final MolecularVolume mRefVol;
+	private final Coordinates mOrigCOM;
+	private final Rotation mInverseRefRotation;
+
 	public enum SimilarityMode {REFTVERSKY,TVERSKY, TANIMOTO
 		}
 
-	private PheSAAlignmentOptimizer() {}
-	
+	public PheSAAlignmentOptimizer(StereoMolecule refMol, double ppWeight) {
+		mSettings = new PheSASetting();
+		mSettings.setPpWeight(ppWeight);
+		mRefVol = new MolecularVolume(refMol);
+		mOrigCOM = new Coordinates(mRefVol.getCOM());
+		mInverseRefRotation = mRefVol.preProcess(new Conformer(refMol)).getInvert();
+	}
+
+	public double alignMoleculeInPlace(StereoMolecule fitMol, ThreadMaster tm) {
+		MolecularVolume fitVol = new MolecularVolume(fitMol);
+		Conformer fitConf = new Conformer(fitMol);
+		fitVol.preProcess(fitConf);
+
+		AlignmentResult bestSolution = createAlignmentSolutions(Collections.singletonList(mRefVol), Collections.singletonList(fitVol),mSettings, tm).get(0);
+
+		for(int a=0;a<fitMol.getAllAtoms();a++) {
+			fitMol.setAtomX(a, fitConf.getX(a));
+			fitMol.setAtomY(a, fitConf.getY(a));
+			fitMol.setAtomZ(a, fitConf.getZ(a));
+		}
+
+		bestSolution.getTransform().apply(fitMol);
+		mInverseRefRotation.apply(fitMol);
+		fitMol.translate(mOrigCOM.x, mOrigCOM.y, mOrigCOM.z);
+
+		return bestSolution.getSimilarity();
+	}
 
 	public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol, ThreadMaster tm) {
 		return alignTwoMolsInPlace(refMol, fitMol, 0.5, tm);
@@ -39,7 +69,6 @@ public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule f
 	public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol, double ppWeight, ThreadMaster tm) {
 		PheSASetting setting = new PheSASetting();
 		setting.setPpWeight(ppWeight);
-		double similarity = 0.0;
 		MolecularVolume refVol = new MolecularVolume(refMol);
 		MolecularVolume fitVol = new MolecularVolume(fitMol);
 		Coordinates origCOM = new Coordinates(refVol.getCOM());
@@ -49,7 +78,7 @@ public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule f
 		rotation = rotation.getInvert();
 		fitVol.preProcess(fitConf);
 		AlignmentResult bestSolution = createAlignmentSolutions(Collections.singletonList(refVol), Collections.singletonList(fitVol),setting, tm).get(0);
-		similarity = bestSolution.getSimilarity();
+		double similarity = bestSolution.getSimilarity();
 
 		for(int a=0;a<fitMol.getAllAtoms();a++) {
 			fitMol.setAtomX(a, fitConf.getX(a));
@@ -61,9 +90,6 @@ public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule f
 		fitMol.translate(origCOM.x, origCOM.y, origCOM.z);
 
 		return similarity;
-		
-		
-		
 	}
 
 	public static List<AlignmentResult> alignToNegRecImg(ShapeVolume ref,

src/main/java/com/actelion/research/chem/conf/BondRotationHelper.java

@@ -56,16 +56,16 @@ public class BondRotationHelper {
 	private int[] mRotationCenters;
 	private int[] mRotationCentersBig;
 	private String[] mTorsionIDs;
-	private boolean includeTerminalPolarH;
-	private int[] terminalPolarHBond;
+	private final boolean mIncludeTerminalPolarH;
+	private int[] mTerminalPolarHBond;
 
 	public BondRotationHelper(StereoMolecule mol) {
 		this(mol,false);
 	}
 
 	public BondRotationHelper(StereoMolecule mol, boolean includeTerminalPolarH) {
 		mMol = mol;
-		this.includeTerminalPolarH = includeTerminalPolarH;
+		mIncludeTerminalPolarH = includeTerminalPolarH;
 		initialize();
 	}
 
@@ -77,8 +77,8 @@ public void initialize() {
 			disconnectedFragmentSize[disconnectedFragmentNo[atom]]++;
 		mIsRotatableBond = new boolean[mMol.getBonds()];
 		TorsionDB.findRotatableBonds(mMol,true, mIsRotatableBond);
-		if(includeTerminalPolarH)
-			terminalPolarHBond = findTerminalBondsPolarHs(mIsRotatableBond);
+		if(mIncludeTerminalPolarH)
+			mTerminalPolarHBond = findTerminalBondsPolarHs(mIsRotatableBond);
 		List<Integer> rotBonds = new ArrayList<Integer>();
 		IntStream.range(0, mIsRotatableBond.length).forEach(e -> {
 			if(mIsRotatableBond[e])
@@ -96,8 +96,8 @@ public void initialize() {
 		for(int i=0;i<mRotatableBonds.length;i++) {
 			int bond = mRotatableBonds[i];
 			boolean isSpecialBond = false;
-			if(terminalPolarHBond!=null) {
-				for(int b : terminalPolarHBond) {
+			if(mTerminalPolarHBond!=null) {
+				for(int b : mTerminalPolarHBond) {
 					if(b==bond)
 						isSpecialBond=true;
 				}

src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java

@@ -275,7 +275,7 @@ private double getFGValueOverlap(double[] grad,List<AtomicGaussian> refMolGauss,
 				double dy = refAt.getCenter().y-fitCenterModCoord.y;
 				double dz = refAt.getCenter().z-fitCenterModCoord.z;
 				double Rij2 = dx*dx + dy*dy + dz*dz;
-				if(Rij2>=Gaussian3D.DIST_CUTOFF) 
+				if(Rij2>=Gaussian3D.SQUARE_DIST_CUTOFF)
 					continue;
 				atomOverlap = refAt.getHeight()*fitAt.getHeight()*QuickMathCalculator.getInstance().quickExp(-( refAt.getWidth() * fitAt.getWidth()* Rij2)/alphaSum) *
 							QuickMathCalculator.getInstance().getPrefactor(refAt.getAtomicNo(),fitAt.getAtomicNo());
@@ -310,7 +310,7 @@ private double getFGValueOverlap(double[] grad,List<AtomicGaussian> refMolGauss,
 					double dz = refVol.getCenter().z-fitCenterModCoord.z;
 					double Rij2 = dx*dx + dy*dy + dz*dz;
 
-					if(Rij2>=Gaussian3D.DIST_CUTOFF) 
+					if(Rij2>=Gaussian3D.SQUARE_DIST_CUTOFF)
 						continue;
 					atomOverlap = refVol.getRole()*refVol.getHeight()*fitAt.getHeight()*QuickMathCalculator.getInstance().quickExp(-( refVol.getWidth() * fitAt.getWidth()* Rij2)/alphaSum) *
 								QuickMathCalculator.getInstance().getPrefactor(refVol.getAtomicNo(),fitAt.getAtomicNo());
@@ -369,7 +369,7 @@ private double getFGValueOverlapPP(double[] grad, List<PPGaussian> refMolGauss,L
 					double dz = refAt.getCenter().z-fitCenterModCoord.z;
 					double Rij2 = dx*dx + dy*dy + dz*dz;
 
-					if(Rij2>=Gaussian3D.DIST_CUTOFF) {
+					if(Rij2>=Gaussian3D.SQUARE_DIST_CUTOFF) {
 						continue;
 					}
 

src/main/java/com/actelion/research/chem/phesa/Gaussian3D.java

@@ -1,28 +1,20 @@
 package com.actelion.research.chem.phesa;
 
-import com.actelion.research.util.EncoderFloatingPointNumbers;
-
-import java.io.IOException;
-import java.nio.ByteBuffer;
-import java.util.Arrays;
-
+import com.actelion.research.chem.Coordinates;
 import com.actelion.research.chem.PeriodicTable;
-import com.actelion.research.chem.StereoMolecule;
 import com.actelion.research.chem.alignment3d.transformation.Transformation;
-import com.actelion.research.chem.conf.Conformer;
-import com.actelion.research.chem.Coordinates;
 
 /** 
  * @version: 1.0, February 2018
  * Author: J. Wahl
  * basic class to describe Gaussian functions used for the calculation of Molecular Volumes
  * Gaussian functions have a center (3D coordinates), a width and a height 
  * this class provides functionalities for calculating higher order overlaps of Gaussians
-
 */
 
 public abstract class Gaussian3D {
-	public static final double DIST_CUTOFF = 10.0;
+	public static final double DISTANCE_CUTOFF = 3.2;
+	public static final double SQUARE_DIST_CUTOFF = DISTANCE_CUTOFF * DISTANCE_CUTOFF;
 	protected int atomId;
 	protected int atomicNo;
 	protected Coordinates center;
@@ -53,9 +45,7 @@ public Gaussian3D(Gaussian3D original){
 	}
 
 	public Gaussian3D() {}
-	
 
-	
 	public abstract double calculateHeight();
 
 	public abstract double calculateWidth();
@@ -77,13 +67,11 @@ public void setHeight(double height) {
 	public double getWidth() {
 		return this.alpha;
 	}
-
 
 	public double getVolume() {
 		return this.volume;
 	}
 
-	
 	public Coordinates getCenter() {
 		return this.center;
 	}
@@ -118,15 +106,11 @@ public double getWeight() {
 	public void setWeight(double weight) {
 		this.weight = weight;
 	}
-	
-	
+
 	public void transform(Transformation transform) {
 		transform.apply(center);
 	}
 
-		
-
-	
 	public final double getVolumeOverlap(Gaussian3D g2,Coordinates c2, double distCutoff) {
 		double alphaSum = getWidth() + g2.getWidth();
 		double Vij = 0.0;
@@ -141,13 +125,12 @@ public final double getVolumeOverlap(Gaussian3D g2,Coordinates c2, double distCu
 			Kij = getHeight()*g2.getHeight()*QuickMathCalculator.getInstance().quickExp(c); 
 			double factor = QuickMathCalculator.getInstance().getPrefactor(getAtomicNo(),g2.getAtomicNo());
 			Vij = weight*factor*Kij;
-			
 		}
 		return Vij;
 	}
 
 	public final double getVolumeOverlap(Gaussian3D g2) {
-		return getVolumeOverlap(g2,DIST_CUTOFF);
+		return getVolumeOverlap(g2, SQUARE_DIST_CUTOFF);
 	}
 
 	public final double getVolumeOverlap(Gaussian3D g2, double distCutoff) {
@@ -157,15 +140,11 @@ public final double getVolumeOverlap(Gaussian3D g2, double distCutoff) {
 	public void updateCoordinates(Coordinates[] coords) {
 		center = new Coordinates(coords[atomId]);
 	}
-	
-	
+
 	public void updateAtomIndeces(int[] map) {
 		atomId = map[atomId];
 	}
 
 	abstract public String encode();
-	
-
-	
 }