New Upstream Release - king-probe

Ready changes

Summary

Merged new upstream version: 02.26 (was: 02.23).

Diff

diff --git a/debian/changelog b/debian/changelog
index 979b717..08dfaa0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,16 @@
-king-probe (02.23-1) UNRELEASED; urgency=medium
+king-probe (02.26-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
   * Add license for test data
   TODO: Another change in test result:
      https://github.com/rlabduke/probe/issues/11
      --> Upstream recommends to not upload this version
 
- -- Andreas Tille <tille@debian.org>  Mon, 02 May 2022 13:48:13 +0200
+  [ Debian Janitor ]
+  * New upstream release.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 19 May 2023 19:58:37 -0000
 
 king-probe (02.21-1) unstable; urgency=medium
 
diff --git a/debian/patches/compiler_flags.patch b/debian/patches/compiler_flags.patch
index d9669b4..09366e9 100644
--- a/debian/patches/compiler_flags.patch
+++ b/debian/patches/compiler_flags.patch
@@ -4,8 +4,10 @@ Description: Adding default CFLAGS and LDFLAGS to gcc
   'hardening-no-relro'.
 Author: Malihe Asemani <ml.asemani@gmail.com>
 Origin: upstream, http://kinemage.biochem.duke.edu/software/probe.php
---- king-probe.orig/Makefile.linux
-+++ king-probe/Makefile.linux
+Index: king-probe.git/Makefile.linux
+===================================================================
+--- king-probe.git.orig/Makefile.linux
++++ king-probe.git/Makefile.linux
 @@ -1,5 +1,5 @@
  MACHINEFLAGS = 
 -CFLAGS = $(MACHINEFLAGS)
@@ -13,7 +15,7 @@ Origin: upstream, http://kinemage.biochem.duke.edu/software/probe.php
  LFLAGS = -lm $(MACHINEFLAGS)
  OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
  	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
-@@ -8,7 +8,7 @@
+@@ -8,7 +8,7 @@ OBJLIST = dots.o abin.o readPDBrecs.o ge
  	cc -c $*.c $(CFLAGS)
  
  probe: probe.o $(OBJLIST)
diff --git a/debian/patches/cross.patch b/debian/patches/cross.patch
index 0ffe272..adcc64a 100644
--- a/debian/patches/cross.patch
+++ b/debian/patches/cross.patch
@@ -3,8 +3,10 @@ Date: Sun, 24 May 2020 14:11:49 +0200
 Bug-Debian: https://bugs.debian.org/961467
 Description: Do not hard code the build architecture compiler
 
---- a/Makefile
-+++ b/Makefile
+Index: king-probe.git/Makefile
+===================================================================
+--- king-probe.git.orig/Makefile
++++ king-probe.git/Makefile
 @@ -5,10 +5,10 @@ OBJLIST = dots.o abin.o readPDBrecs.o ge
  	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
  
@@ -18,8 +20,10 @@ Description: Do not hard code the build architecture compiler
  
  clean:
  	@rm -f *.o *.ckp
---- a/Makefile.linux
-+++ b/Makefile.linux
+Index: king-probe.git/Makefile.linux
+===================================================================
+--- king-probe.git.orig/Makefile.linux
++++ king-probe.git/Makefile.linux
 @@ -5,10 +5,10 @@ OBJLIST = dots.o abin.o readPDBrecs.o ge
  	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
  
diff --git a/debian/patches/fix_build_issue.patch b/debian/patches/fix_build_issue.patch
index f3b265c..b8255dd 100644
--- a/debian/patches/fix_build_issue.patch
+++ b/debian/patches/fix_build_issue.patch
@@ -4,9 +4,11 @@ Last-Update: Sat Aug  8 07:28:44 UTC 2015
 Origin: upstream, http://kinemage.biochem.duke.edu/software/probe.php
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- probe.orig/Makefile.linux
-+++ probe/Makefile.linux
-@@ -2,7 +2,7 @@
+Index: king-probe.git/Makefile.linux
+===================================================================
+--- king-probe.git.orig/Makefile.linux
++++ king-probe.git/Makefile.linux
+@@ -2,7 +2,7 @@ MACHINEFLAGS =
  CFLAGS = $(MACHINEFLAGS)
  LFLAGS = -lm $(MACHINEFLAGS)
  OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
@@ -15,7 +17,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  
  .c.o:
  	cc -c $*.c $(CFLAGS)
-@@ -30,9 +30,11 @@
+@@ -30,9 +30,11 @@ parse.o:	./parse.h	./utility.h	parse.c
  probe.o:	./abin.h	./atomprops.h	./autobondrot.h	./dots.h	./geom3d.h \
  		./parse.h	./probe.h	./readPDBrecs.h	./select.h \
  		./stdconntable.h	./utility.h	probe.c
diff --git a/probe.c b/probe.c
index 12556b8..6f923a7 100644
--- a/probe.c
+++ b/probe.c
@@ -51,8 +51,8 @@
 
 #define INLINE_FOR_SPEED 1
 
-static char* versionString = "probe: version 2.23.040422, Copyright 1996-2016, J. Michael Word; 2021-2022 Richardson Lab";
-static char* shortVersionStr = "probe.2.23.040422";
+static char* versionString = "probe: version 2.26.021123, Copyright 1996-2016, J. Michael Word; 2021-2023 Richardson Lab";
+static char* shortVersionStr = "probe.2.26.021123";
 static char *referenceString = "Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733.";
 static char *electronicReference = "http://kinemage.biochem.duke.edu/";
 
@@ -5573,7 +5573,14 @@ dotNode * Condense(dotNode * head, int conFlag)
 			 	 sprintf(jTarget,"%s%4.4s%c%s %s%c",target->r->chain,target->r->Hy36resno,
 			 	 	target->r->resInsCode,target->r->resname,target->atomname,target->altConf);
 			 	 //jTarget[17]='\0';
-			 	 if(strcmp(jTarget,minTarget) < 0) // if the target atom of j is less than that of the min then swap it
+                 // if the target atom of j is less than that of the min then swap it:
+                 // also swap if the names are the same but the gap is less so that we
+                 // get the list sorted from smallest (most negative) to largest gap.
+                 // This will be important when we are using condensed output so that we
+                 // pick the node with the smallest gap.
+                 if ( (strcmp(jTarget,minTarget) < 0) ||
+                     ((strcmp(jTarget, minTarget) == 0) && (j->gap < minNode->gap) )
+                    )
 			 	 {
 			 	 	 strcpy(minTarget,jTarget);
 			 	 	 minNode = j;
@@ -6517,7 +6524,10 @@ fprintf(outf,"12/21/2021 - RMT Version 2.20 dumps atom information after hydroge
 fprintf(outf,"12/21/2021 - RMT Version 2.21 does not dump Phantom Hydrogen information.\n");
 fprintf(outf,"03/31/2022 - RMT Version 2.22 does not mark Nitrogens in the HIS ring or atoms in the\n");
 fprintf(outf,"   TRP 5-membered ring as acceptors.  Too many side contacts are made to these rings.\n");
-fprintf(outf,"04/04/2022 - RMT Version 2.22 fixes copy/paste bug to allow F and G pointmasters.\n");
+fprintf(outf,"04/04/2022 - RMT Version 2.23 fixes copy/paste bug to allow F and G pointmasters.\n");
+fprintf(outf,"09/29/2022 - RMT Version 2.24 sorts raw dots by increasing gap, providing smallest for condensed output.\n");
+fprintf(outf,"02/08/2023 - RMT Version 2.25 makes the Nitrogens in TRP and HIS 5-membered rings acceptors.\n");
+fprintf(outf,"02/11/2023 - RMT Version 2.26 makes the Nitrogen in TRP not an acceptor.\n");
 
 exit(0);
 
diff --git a/select.c b/select.c
index 86a98ab..bf6894e 100644
--- a/select.c
+++ b/select.c
@@ -64,7 +64,7 @@ static ResidueAndAtomPair AromaticAtomsTbl[] = {
 ":HIS:", ": ND1: CD2: CE1: NE2: CG :", 0,
 ":TYR:", ": CG : CD1: CD2: CE1: CE2: CZ :",                TEST_ACCEPT_ANGLE_PROP,
 // The 5-membered ring is not treated as an aromatic acceptor face, but the 6-membered
-// ring is.
+// ring is. The Nitrogen is not an acceptor because it is protonated.
 //":TRP:", ": CG : CD1: CD2: NE1: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP,
 ":TRP:", ": CG : CD1: NE1:", 0,
 ":TRP:", ": CD2: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP,
@@ -274,9 +274,10 @@ static ResidueAndAtomPair DonorAcceptorAtomTbl[] = {
 				       DONOR_PROP,
 
 // The Nitrogens on Histidine's ring are not marked as acceptors just because of their
-// status as being on the ring.
-//":HIS:", ": ND1: NE2:",                DONOR_PROP | ACCEPTOR_PROP,
-":HIS:", ": ND1: NE2:",                DONOR_PROP,
+// status as being on the ring, but they remain acceptors because they might be
+// unprotonated.
+":HIS:", ": ND1: NE2:",                DONOR_PROP | ACCEPTOR_PROP,
+//":HIS:", ": ND1: NE2:",                DONOR_PROP,
 ":HIS:", ": HD1: HE2: DD1: DE2:",      DONOR_PROP,
 ":HIS:", ": HD2: HE1: DD2: DE1:",      DONOR_PROP|CH_DONOR_PROP,
 ":SER:", ": OG :",                     DONOR_PROP|ACCEPTOR_PROP,

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