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,