From c94f33c3aaaaef55fe8879e3aae8ef29e91e7396 Mon Sep 17 00:00:00 2001
From: toshinagata1964 <toshinagata1964@a2be9bc6-48de-4e38-9406-05402d4bc13c>
Date: Mon, 14 Oct 2013 11:15:15 +0000
Subject: [PATCH] Exclusion of non-bonding interaction in pi-metal systems were
 not working. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@401 a2be9bc6-48de-4e38-9406-05402d4bc13c
---
 MolLib/MD/MDCore.c | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/MolLib/MD/MDCore.c b/MolLib/MD/MDCore.c
index daf2731..88bff3a 100644
--- a/MolLib/MD/MDCore.c
+++ b/MolLib/MD/MDCore.c
@@ -279,11 +279,12 @@ s_register_missing_parameters(Int **missing, Int *nmissing, Int type, Int t1, In
 static int
 s_check_bonded(Molecule *mol, Int idx, Int *results)
 {
-	Int i, n, *ip;
+	Int i, j, n, *ip;
 	const Int *cp;
 	Atom *ap = ATOM_AT_INDEX(mol->atoms, idx);
 	cp = AtomConnectData(&ap->connect);
 	for (i = 0; i < ap->connect.count; i++, cp++) {
+		Atom *api;
 		n = *cp;
 		for (ip = results; *ip >= 0; ip++) {
 			if (n == *ip)
@@ -293,6 +294,35 @@ s_check_bonded(Molecule *mol, Int idx, Int *results)
 			*ip++ = n;
 			*ip = -1;
 		}
+		api = ATOM_AT_INDEX(mol->atoms, n);
+		if (api->anchor != NULL) {
+			const Int *cpi = AtomConnectData(&api->anchor->connect);
+			for (j = 0; j < api->anchor->connect.count; j++, cpi++) {
+				n = *cpi;
+				for (ip = results; *ip >= 0; ip++) {
+					if (n == *ip)
+						break;
+				}
+				if (*ip < 0) {
+					*ip++ = n;
+					*ip = -1;
+				}
+			}
+		}
+	}
+	if (ap->anchor != NULL) {
+		cp = AtomConnectData(&ap->anchor->connect);
+		for (i = 0; i < ap->anchor->connect.count; i++, cp++) {
+			n = *cp;
+			for (ip = results; *ip >= 0; ip++) {
+				if (n == *ip)
+					break;
+			}
+			if (*ip < 0) {
+				*ip++ = n;
+				*ip = -1;
+			}
+		}
 	}
 	for (ip = results; *ip >= 0; ip++)
 		;
-- 
2.11.0