From e5a02b5d2b89ba21bb466980e2d0bd0ae5eabb95 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:06:57 -0500
Subject: [PATCH 1/3] updated stereo definitions

---
 pom.xml                                       |  2 +-
 .../java/gov/nih/ncats/molwitch/Bond.java     |  4 +++
 .../gov/nih/ncats/molwitch/Chirality.java     | 26 ++++++++++++++++---
 3 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index 81fe746..9108547 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,7 +24,7 @@
 
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch</artifactId>
-    <version>0.6.3-SNAPSHOT</version>
+    <version>0.6.5-SNAPSHOT</version>
 
     <name>ncats-molwitch</name>
 
diff --git a/src/main/java/gov/nih/ncats/molwitch/Bond.java b/src/main/java/gov/nih/ncats/molwitch/Bond.java
index 3e4f356..f131089 100644
--- a/src/main/java/gov/nih/ncats/molwitch/Bond.java
+++ b/src/main/java/gov/nih/ncats/molwitch/Bond.java
@@ -250,6 +250,10 @@ public enum DoubleBondStereo {
 		 *  Z (from zusammen, the German word for "together").
 		 */
 		Z_CIS;
+
+		public boolean isDefined() {
+			return this == Z_CIS || this == E_TRANS;
+		}
 		
     }
 
diff --git a/src/main/java/gov/nih/ncats/molwitch/Chirality.java b/src/main/java/gov/nih/ncats/molwitch/Chirality.java
index 49f8010..54b3986 100644
--- a/src/main/java/gov/nih/ncats/molwitch/Chirality.java
+++ b/src/main/java/gov/nih/ncats/molwitch/Chirality.java
@@ -32,7 +32,15 @@ public enum Chirality {
 	 * Sinister (left, even). priority decreases in counterclockwise direction.
 	 */
 	S(2),
-	Parity_Either(3);
+	Parity_Either(3),
+	/**
+	 * Psuedo-Rectus (right, odd). Priority decreases in clockwise direction.
+	 */
+	r(4),
+	/**
+	 * Psuedo-Sinister (left, even). priority decreases in counterclockwise direction.
+	 */
+	s(5);
 	
 	
 	
@@ -42,8 +50,8 @@ public enum Chirality {
 	private static final Chirality[] VALUES;
 	private static final Chirality[] INVERTED;
 	static {
-		VALUES = new Chirality[] {Non_Chiral, R, S, Parity_Either};
-		INVERTED = new Chirality[] {Unknown,Non_Chiral, S, R, Parity_Either};
+		VALUES = new Chirality[] {Non_Chiral, R, S, Parity_Either, r, s};
+		INVERTED = new Chirality[] {Unknown,Non_Chiral, S, R, Parity_Either, s, r};
 		
 	}
 	Chirality(int v){
@@ -65,9 +73,19 @@ public boolean isEither(){
 	public int getParity(){
 		return parity;
 	}
+	public boolean isRForm() {
+		return parity==1 || parity==4;
+	}
+	public boolean isSForm() {
+		return parity==2 || parity==5;
+	}
+	
+	public boolean isDefined() {
+		return parity==2 || parity==1 || parity==4 || parity==5;
+	}
 	
 	public static Chirality valueByParity(int parity) {
-		if(parity <0 || parity > 3) {
+		if(parity <0 || parity > 5) {
 			return Unknown;
 		}
 		return VALUES[parity];

From dbe64c71657e4c103e701bdf1756bb885595bfe4 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:19:46 -0500
Subject: [PATCH 2/3] incremented version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a2d10da..d0f01e3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,7 +24,7 @@
 
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch</artifactId>
-    <version>0.6.5</version>
+    <version>0.6.6-SNAPSHOT</version>
 
     <name>ncats-molwitch</name>
 

From f302d8f4ae0ad52f9bbbb970dc2b43b4bac0c517 Mon Sep 17 00:00:00 2001
From: Mitch Miller <mitch.miller@thinkscience.us>
Date: Fri, 19 Jan 2024 13:33:36 -0500
Subject: [PATCH 3/3] bumped version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index d0f01e3..d50874b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,7 +24,7 @@
 
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch</artifactId>
-    <version>0.6.6-SNAPSHOT</version>
+    <version>0.6.6</version>
 
     <name>ncats-molwitch</name>