From 1f6142b8260a26c1df45093580ba9b37049463b4 Mon Sep 17 00:00:00 2001
From: thomas <thomas@openmolecules.org>
Date: Mon, 23 Sep 2024 15:49:26 +0200
Subject: [PATCH] minor improvements

---
 .../com/actelion/research/chem/AromaticityResolver.java   | 8 +++++++-
 .../chem/IDCodeParserWithoutCoordinateInvention.java      | 3 +++
 .../chem/conf/MolecularFlexibilityCalculator.java         | 2 +-
 .../com/actelion/research/chem/shredder/Fragment3D.java   | 7 ++++---
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/main/java/com/actelion/research/chem/AromaticityResolver.java b/src/main/java/com/actelion/research/chem/AromaticityResolver.java
index ca0db78c..12775ea6 100644
--- 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
index 088d9602..5e043e03 100644
--- 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
index 86d36cca..6eae8f26 100644
--- 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
index 71d1b3b3..3f5d0e4c 100644
--- 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;