From 42b33166cdf6851312e24090a3a0020bfe8c1022 Mon Sep 17 00:00:00 2001
From: Dan Vasilescu <vasilescu@uchc.edu>
Date: Wed, 20 May 2026 14:34:19 -0400
Subject: [PATCH] in bngl input file, replace ~<digit>   with   ~s<digit>

---
 vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java b/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
index 4585987aa5..80e5ae1172 100644
--- a/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
+++ b/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
@@ -1261,6 +1261,9 @@ public static String applySyntaxCorrections(String line) {
 		if( (line.startsWith("begin reaction_rules") ) || (line.startsWith("end reaction_rules")) ) {
 			line = line.replace("reaction_rules", "reaction rules");
 		}
+		// replace ~<digit>   with   ~s<digit>
+		// ex: A(site2~0) -> A(site2~1)   becomes:    A(site2~s0) -> A(site2~s1)
+		line = line.replaceAll("~(?=\\d)", "~s");
 		return line;
 	}