From 5dd09cf437db4828ea30bf37d4c37329eccebe9a Mon Sep 17 00:00:00 2001
From: Mitch Miller <mitch.miller@thinkscience.us>
Date: Mon, 17 Jun 2024 22:16:51 -0400
Subject: [PATCH] beginning of creating warnings for SGroups with extranous
 atoms within the boundaries of their brackets

---
 pom.xml                                       |  4 +--
 .../ncats/molwitch/cdk/CdkChemicalImpl.java   |  5 +--
 .../cdk/writer/AbstractMdlWriterFactory.java  | 32 +++++--------------
 3 files changed, 13 insertions(+), 28 deletions(-)

diff --git a/pom.xml b/pom.xml
index 7f255ee..c679168 100644
--- a/pom.xml
+++ b/pom.xml
@@ -247,7 +247,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>smsd-core</artifactId>
-            <version>2.2.3</version>
+            <version>2.2.4</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>
@@ -258,7 +258,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>smsd-exec</artifactId>
-            <version>2.2.3</version>
+            <version>2.2.4</version>
         </dependency>
     </dependencies>
 
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 5536e1d..13d1acc 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -46,7 +46,6 @@
 
 import javax.vecmath.Tuple2d;
 
-import org.junit.Assert;
 import org.openscience.cdk.AtomRef;
 import org.openscience.cdk.BondRef;
 import org.openscience.cdk.CDKConstants;
@@ -2489,7 +2488,9 @@ public List<String> getSGroupWarnings() {
 		List<String> messages = new ArrayList<>();
 		AtomicInteger counter = new AtomicInteger(0);
 		this.getSGroups().forEach(sg->{
-			Assert.assertEquals(2, sg.getBrackets().size());
+			if(sg.getBrackets().size() != 2 ){
+				Logger.getLogger(CdkChemicalImpl.class.getName()).warning("Expecting SGroups to have 2 brackets.  This one has " + sg.getBrackets().size());
+			}
 			Logger.getLogger(CdkChemicalImpl.class.getName()).fine(String.format("looking at SGroup %d with %d atoms bracket 0 x: %.2f; y: %.2f; bracket 1 x: %.2f; y: %.2f\n",
 					counter.incrementAndGet(), sg.getAtoms().count(), sg.getBrackets().get(0).getPoint1().getX(), sg.getBrackets().get(0).getPoint1().getY(),
 					 sg.getBrackets().get(1).getPoint1().getX(), sg.getBrackets().get(1).getPoint1().getY()));
diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/writer/AbstractMdlWriterFactory.java b/src/main/java/gov/nih/ncats/molwitch/cdk/writer/AbstractMdlWriterFactory.java
index 289f95f..29c5d96 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/writer/AbstractMdlWriterFactory.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/writer/AbstractMdlWriterFactory.java
@@ -21,35 +21,19 @@
 
 package gov.nih.ncats.molwitch.cdk.writer;
 
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.Arrays;
-import java.util.Properties;
-import java.util.function.Function;
-
-import javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
-
-import gov.nih.ncats.molwitch.cdk.CdkUtil;
-import org.apache.xpath.operations.Bool;
-import org.openscience.cdk.aromaticity.Aromaticity;
-import org.openscience.cdk.aromaticity.ElectronDonation;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.Cycles;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.io.IChemObjectWriter;
-import org.openscience.cdk.io.listener.PropertiesListener;
-
-import gov.nih.ncats.molwitch.io.ChemFormat.AromaticAwareChemFormatWriterSpecification;
 import gov.nih.ncats.molwitch.io.ChemFormat.ChemFormatWriterSpecification;
-import gov.nih.ncats.molwitch.io.ChemFormat.KekulizationEncoding;
 import gov.nih.ncats.molwitch.io.ChemFormat.MolFormatSpecification;
 import gov.nih.ncats.molwitch.io.ChemFormat.MolFormatSpecification.Version;
 import gov.nih.ncats.molwitch.spi.ChemicalWriterImpl;
 import gov.nih.ncats.molwitch.spi.ChemicalWriterImplFactory;
-import org.openscience.cdk.io.setting.IOSetting;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.IChemObjectWriter;
+import org.openscience.cdk.io.listener.PropertiesListener;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Properties;
+import java.util.function.Function;
 
 public abstract class AbstractMdlWriterFactory implements ChemicalWriterImplFactory{