From d5d09741df0f938998ab7f7cd117c26e4c593262 Mon Sep 17 00:00:00 2001
From: Mitch Miller <mitch.miller@thinkscience.us>
Date: Wed, 8 May 2024 15:58:06 -0400
Subject: [PATCH] made ringsSearcherSupplier resistent to exceptions thrown by
 AllRingsFinder

---
 .../gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java    |  6 ++++--
 .../org/openscience/cdk/geometry/cip/CIPToolMod.java   |  2 +-
 src/test/java/TestChiralRead.java                      | 10 +++++++++-
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
index 313ee29..5564070 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -449,8 +449,10 @@ public static void setMaxUndefinedStereoCenters(int maxUndefinedStereoCenters) {
 			            }
 					}
 					return 1;
-				} catch (CDKException e) {
-					throw new RuntimeException(e);
+				} catch (CDKException | IllegalArgumentException e) {
+					Logger.getLogger(this.getClass().getName()).fine(String.format("Error processing rings in molecule with formula %s (%s; ring size limit %d)",
+							this.getFormula(), e.getMessage(), Math.min(container.getAtomCount(),12)));
+					return 0;
 				}
 		    	
 
diff --git a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
index 3cffb5b..9a24ed1 100644
--- a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
+++ b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
@@ -300,7 +300,7 @@ public static int getSizeOfLargestRingSystem(CdkChemicalImpl chemical) {
             }
         }
         bondsToRemove.forEach(b-> copy.removeBond(b));
-        
+
         if( copy.getBondCount() == 0) {
             //we have removed all non-ring bonds. When we have no bonds, that means no rings
             return 0;
diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
index 0eab2b8..b3425dd 100644
--- a/src/test/java/TestChiralRead.java
+++ b/src/test/java/TestChiralRead.java
@@ -20,7 +20,9 @@
  */
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.nio.file.Files;
 import java.util.Arrays;
 import java.util.Date;
@@ -28,6 +30,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import com.simolecule.centres.CdkMol;
 import gov.nih.ncats.molwitch.TetrahedralChirality;
 import gov.nih.ncats.molwitch.cdk.CdkChemicalImpl;
 import org.apache.commons.io.IOUtils;
@@ -38,7 +41,13 @@
 import gov.nih.ncats.molwitch.Chirality;
 import gov.nih.ncats.molwitch.Stereocenter;
 import gov.nih.ncats.molwitch.io.ChemicalReaderFactory;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.geometry.cip.CIPToolMod;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IRingSet;
+import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.io.Mol2Reader;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
 
 import static org.junit.Assert.*;
 
@@ -1938,5 +1947,4 @@ public void testRingSystem3() throws Exception {
 
 		assertEquals(5, ringSystemCount);
 	}
-
 }