minor improvements

Actelion · Sep 23, 2024 · 1f6142b · 1f6142b
1 parent fc91f65
commit 1f6142b
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Showing 4 changed files with 15 additions and 5 deletions.
diff --git a/src/main/java/com/actelion/research/chem/AromaticityResolver.java b/src/main/java/com/actelion/research/chem/AromaticityResolver.java
@@ -168,7 +168,13 @@ public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond, boolean ma
                     }
                 }
 
-            if (!bondsPromoted) {
+
+			if (bondsPromoted) {
+				promoteObviousBonds();
+				continue;
+				}
+
+			if (!bondsPromoted) {
                 // find and promote one aromatic bond
                 // (should never happen, but to prevent an endless loop nonetheless)
                 for (int bond=0; bond<mMol.getBonds(); bond++) {

diff --git a/src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java b/src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
@@ -786,6 +786,9 @@ public void parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idc
 								mMol.setAtomY(hydrogen, mMol.getAtomY(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
 								if (coordsAre3D)
 									mMol.setAtomZ(hydrogen, mMol.getAtomZ(atom) + (decodeBits(resolutionBits) - binCount / 2.0));
+
+								if (mMol.isSelectedAtom(atom))
+									mMol.setAtomSelection(hydrogen, true);
 								}
 							}
 

diff --git a/src/main/java/com/actelion/research/chem/conf/MolecularFlexibilityCalculator.java b/src/main/java/com/actelion/research/chem/conf/MolecularFlexibilityCalculator.java
@@ -137,7 +137,7 @@ public float[] calculateBondFlexibilities(StereoMolecule mol, boolean[] isRotata
 				}
 
 				if (!mol.isAromaticBond(bond)) {
-					bondFlexibility[bond] = calculateBondFlexibility(torsion, frequency, range);
+					bondFlexibility[bond] = (torsion == null) ? 1f : calculateBondFlexibility(torsion, frequency, range);
 
 					// we need to reduce in rings increasingly with ring size, because flexibility is hampered
 					if (mol.isRingBond(bond))

diff --git a/src/main/java/com/actelion/research/chem/shredder/Fragment3D.java b/src/main/java/com/actelion/research/chem/shredder/Fragment3D.java
@@ -3,9 +3,10 @@
 import com.actelion.research.chem.conf.TorsionDescriptor;
 
 public class Fragment3D implements Comparable<Fragment3D> {
-	private String mIDCode,mIDCoords;
-	private TorsionDescriptor mTorsions;
-	private int[] mExitAtoms;
+	private final String mIDCode;
+	private String mIDCoords;
+	private final TorsionDescriptor mTorsions;
+	private final int[] mExitAtoms;
 
 	public Fragment3D(String idcode, String coords, TorsionDescriptor td, int[] exitAtoms) {
 		this.mIDCode = idcode;