From 9505bc9b1eb6381ab2074586be5ec38b67a0d48e Mon Sep 17 00:00:00 2001
From: Steffen Moeller <steffen_moeller@gmx.de>
Date: Fri, 5 Jun 2015 14:49:29 +0200
Subject: [PATCH 1/3] Hydroxyproline is an amino acid

---
 source/KERNEL/residue.C     |  8 ++++++++
 source/STRUCTURE/peptides.C | 11 +++++++++--
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/source/KERNEL/residue.C b/source/KERNEL/residue.C
index f2bbe1afa4..95cd071c64 100644
--- a/source/KERNEL/residue.C
+++ b/source/KERNEL/residue.C
@@ -163,6 +163,10 @@ namespace BALL
 				Log.error() << "No next residue!" << endl;
 			}
 		}
+		else
+		{
+			Log.error() << "Has no torsion Psi! (" << getFullName() << ")" << endl;
+		}
 
 		return result;
 	}
@@ -227,6 +231,10 @@ namespace BALL
 				Log.error() << "No previous residue!" << endl;
 			}
 		}
+		else
+		{
+			Log.error() << "Has no torsion Phi! (" << getFullName() << ")" << endl;
+		}
 
 		return result;
 	}
diff --git a/source/STRUCTURE/peptides.C b/source/STRUCTURE/peptides.C
index 35378aef04..afec083480 100644
--- a/source/STRUCTURE/peptides.C
+++ b/source/STRUCTURE/peptides.C
@@ -19,8 +19,15 @@ namespace BALL
 	namespace Peptides
 	{
 
-		const String one_letter_codes = "ARNDCQEGHILKMFPSTWYV";
-		const String three_letter_codes = "ALA@ARG@ASN@ASP@CYS@GLN@GLU@GLY@HIS@ILE@LEU@LYS@MET@PHE@PRO@SER@THR@TRP@TYR@VAL@";
+		const String one_letter_codes = "ARNDCQEGHILKMFPSTWYVBZ";
+		/**
+		 * http://www.apsstylemanual.org/oldmanual/reference/amino-acids.htm also defines Cit, Hey, Hyp, Orn, Thx
+		 * somewhat exceptional is Xaa and the ambiguity codes like Asx and Glx"
+		 * http://www.fao.org/docrep/004/y2775e/y2775e0e.htm has single letter for GLX and ASX
+		 * Instead of UNK one might possibly better use "Xaa" as long as one is confident that an AA is meant.
+		 * It may also be preferable to have another character than '?' as the representation of unknown, e.g. 'X'.
+		 */
+		const String three_letter_codes = "ALA@ARG@ASN@ASP@CYS@GLN@GLU@GLY@HIS@ILE@LEU@LYS@MET@PHE@PRO@SER@THR@TRP@TYR@VAL@ASX@GLX@CIT@HEY@HYP@ORN@THX@";
 
 		char OneLetterCode(const String& aa)
 		{

From 97dc1d09d1706732c66848c5af9c7da656600338 Mon Sep 17 00:00:00 2001
From: Steffen Moeller <steffen_moeller@gmx.de>
Date: Fri, 5 Jun 2015 15:03:54 +0200
Subject: [PATCH 2/3] Set is_proline also for HYP

---
 include/BALL/STRUCTURE/peptideBuilder.h | 9 ++++++---
 source/STRUCTURE/peptideBuilder.C       | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/include/BALL/STRUCTURE/peptideBuilder.h b/include/BALL/STRUCTURE/peptideBuilder.h
index 4e1c29cb29..18ae645d81 100644
--- a/include/BALL/STRUCTURE/peptideBuilder.h
+++ b/include/BALL/STRUCTURE/peptideBuilder.h
@@ -159,9 +159,12 @@ namespace BALL
 	   String chainname_;
 	   String proteinname_;
 	   
-		 /// The proline flag
-		 bool is_proline_;
-		 FragmentDB* fragment_db_;
+	   /** The proline flag is set for side chains that
+	    * are covalently bound to the backbone. Proline
+	    * and hydroxyproline are among them.
+	    */
+	   bool is_proline_;
+	   FragmentDB* fragment_db_;
 
 	   /** some helper functions for the construction of the residue; for internal use only
 	    * omega is not yet implemented
diff --git a/source/STRUCTURE/peptideBuilder.C b/source/STRUCTURE/peptideBuilder.C
index 00fda1c02d..b8d923c5bc 100644
--- a/source/STRUCTURE/peptideBuilder.C
+++ b/source/STRUCTURE/peptideBuilder.C
@@ -226,7 +226,7 @@ namespace BALL
 				// special case: residue is a proline
 				type = i->getType();
 				type.toUpper();
-				is_proline_ = (type == "PRO") ? true : false;
+				is_proline_ = ("PRO" == type || "HYP" == type) ? true : false;
 
 				Residue* residue2 = createResidue_(i->getType(), id);
 

From 76ce286c7c1c3d7f55e385138ac4bad3e009d719 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Steffen=20M=C3=B6ller?= <moeller@debian.org>
Date: Mon, 8 Jun 2015 14:31:59 +0200
Subject: [PATCH 3/3] Attempt to describe HYP structure

---
 data/fragments/PRO.db | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/data/fragments/PRO.db b/data/fragments/PRO.db
index 5da753ffa9..4ba0fb2ddc 100644
--- a/data/fragments/PRO.db
+++ b/data/fragments/PRO.db
@@ -14,6 +14,8 @@
 		<node>CB<value>C 1.34565 1.283736 -2.23033</value></node>
 		<node>1HB<value>H 2.062533 0.6767905 -2.785621</value></node>
 		<node>2HB<value>H 0.7182986 1.840951 -2.927554</value></node>
+		<node>1OB<value>O 0.7182986 1.840951 -2.927554</value></node>
+		<node>1OH<value>H 1.4182986 2.440951 -2.927554</value></node>
 		<node>CG<value>C 2.02933 2.275858 -1.278275</value></node>
 		<node>1HG<value>H 3.057449 1.966999 -1.081919</value></node>
 		<node>2HG<value>H 2.018846 3.280874 -1.702292</value></node>
@@ -42,6 +44,8 @@
     <node>32<value>OXT C s</value></node>
     <node>33<value>1H N s</value></node>
     <node>34<value>2H N s</value></node>
+    <node>40<value>2OB CB s</value></node>
+    <node>41<value>2OH 2OB s</value></node>
   </node>
 	<node>Connections
 		<node>N-term<value>N C-term s 1.33 0.5</value></node>
@@ -56,9 +60,22 @@
 				<node>OXT</node>
 				<node>1H</node>
 				<node>2H</node>
+				<node>2OB</node>
+				<node>2OH</node>
 			</node>
 		</node>
+		<node>HYP
+			<node>Delete
+				<node>2HB</node>
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
 		<node>PRO-M
+			<node>Delete
+				<node>2OB</node>
+				<node>2OH</node>
+			</node>
 			<node>Properties
 				<node>C_TERMINAL</node>
 				<node>N_TERMINAL</node>
@@ -66,6 +83,8 @@
 		</node>
 		<node>PRO-C
 			<node>Delete
+				<node>2OB</node>
+				<node>2OH</node>
 				<node>1H</node>
 				<node>2H</node>
 			</node>
@@ -75,6 +94,8 @@
 		</node>
  		<node>PRO-N
  			<node>Delete
+				<node>2OB</node>
+				<node>2OH</node>
 	 			<node>OXT</node>
  			</node>
  			<node>Properties