[med-svn] [Git][med-team/king-probe][master] 8 commits: Upstream is now using release tags - adapt watch file
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Oct 6 08:14:31 BST 2021
Andreas Tille pushed to branch master at Debian Med / king-probe
Commits:
61deba08 by Andreas Tille at 2021-10-06T09:03:36+02:00
Upstream is now using release tags - adapt watch file
- - - - -
69dfa6ed by Andreas Tille at 2021-10-06T09:05:09+02:00
New upstream version 02.18
- - - - -
f8b8b1ec by Andreas Tille at 2021-10-06T09:05:09+02:00
routine-update: New upstream version
- - - - -
863d396f by Andreas Tille at 2021-10-06T09:05:10+02:00
Update upstream source from tag 'upstream/02.18'
Update to upstream version '02.18'
with Debian dir b88614e5a9c71a9c699b4574b7fd608e6727faf9
- - - - -
6e14728d by Andreas Tille at 2021-10-06T09:05:10+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
0c74123e by Andreas Tille at 2021-10-06T09:05:16+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
df761e35 by Andreas Tille at 2021-10-06T09:11:46+02:00
Do not mention reference data in include-binaries any more
- - - - -
429b9ff7 by Andreas Tille at 2021-10-06T09:12:37+02:00
Upload to unstable
- - - - -
9 changed files:
- + CMakeLists.txt
- atomprops.h
- autobondrot.c
- debian/changelog
- debian/control
- debian/source/include-binaries
- debian/upstream/metadata
- debian/watch
- probe.c
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -0,0 +1,40 @@
+cmake_minimum_required(VERSION 3.10.0)
+project(probe)
+
+if (WIN32)
+ add_definitions(-D_CRT_SECURE_NO_WARNINGS)
+endif ()
+
+set(probe_SOURCES
+ abin.c
+ atomprops.c
+ autobondrot.c
+ dots.c
+ geom3d.c
+ hybrid_36_c.c
+ readPDBrecs.c
+ parse.c
+ select.c
+ stdconntable.c
+ utility.c
+ probe.c
+)
+
+set(probe_HEADERS
+ abin.h
+ atomprops.h
+ autobondrot.h
+ dots.h
+ geom3d.h
+ hybrid_36_c.h
+ parse.h
+ readPDBrecs.h
+ select.h
+ stdconntable.h
+ utility.h
+)
+
+add_executable(probe ${probe_SOURCES} ${probe_HEADERS})
+if (NOT WIN32)
+ target_link_libraries(probe m)
+endif()
=====================================
atomprops.h
=====================================
@@ -93,6 +93,9 @@ enum atomIdentifiers {
#define METALIC_ATOM_FLAG (1 << 0) /*atomProp AtomTbl flags: element features*/
#define IONIC_ATOM_FLAG (1 << 1) /*dcr041007 partial, now on halides*/
+/* Explicit vdW radius of carbonyl (C=O, atomC) entry. */
+#define ATOMC_EXPLICIT_VDW (1.70)
+
#ifdef INIT_ATOM_TABLE
/* For non-metals, explicit VDW radii from */
/* Gavezzotti, J. Am. Chem. Soc. (1983) 105, 5220-5225. */
@@ -120,7 +123,7 @@ atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */
{atomHarom, 1, "Har", 1.05, 1.00, 0.00, 0.30, "grey", 0},
{atomHpolar, 1, "Hpol", 1.05, 1.00, 0.00, 0.30, "grey", 0},
{atomHOd, 1, "HOd", 1.05, 1.00, 0.00, 0.30, "grey", 0},/*hb-only-dummy*/
- {atomC, 6, "C", 1.70, 1.70, 1.90, 0.77, "white", 0},
+ {atomC, 6, "C", ATOMC_EXPLICIT_VDW, ATOMC_EXPLICIT_VDW, 1.90, 0.77, "white", 0},
{atomCarom, 6, "Car", 1.75, 1.75, 1.90, 0.77, "white", 0},
{atomN, 7, "N", 1.55, 1.55, 1.70, 0.70, "sky", 0},
{atomO, 8, "O", 1.40, 1.40, 1.50, 0.66, "red", 0},
=====================================
autobondrot.c
=====================================
@@ -140,7 +140,7 @@ void scanXDBinputText(xformDatabase* xdb, FILE *inf, FILE *outf,
}
else if (s[0] == '@') { /* include file */
FILE *if2 = NULL;
- if2 = fopen(s+1, "r");
+ if2 = fopen(s+1, "rb");
if (if2) { /* recursive call */
fprintf(outf, "%s%s\n", cch, s);
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+king-probe (02.18-1) unstable; urgency=medium
+
+ * Upstream is now using release tags - adapt watch file
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+ * Do not mention reference data in include-binaries any more
+
+ -- Andreas Tille <tille at debian.org> Wed, 06 Oct 2021 09:11:54 +0200
+
king-probe (2.16.160404+git20200121.9b198c1-3) unstable; urgency=medium
* Add test and reference data
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Uploaders: Malihe Asemani <ml.asemani at gmail.com>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.0
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/king-probe
Vcs-Git: https://salsa.debian.org/med-team/king-probe.git
Homepage: http://kinemage.biochem.duke.edu/software/probe.php
=====================================
debian/source/include-binaries
=====================================
@@ -1,8 +1,2 @@
debian/tests/data/1zni.pdb1.gz
debian/tests/data/6ins.pdb1.gz
-debian/tests/ref/6ins_1zni.kin.gz
-debian/tests/ref/6ins.dotinfo.table.gz
-debian/tests/ref/6insEF.kin.gz
-debian/tests/ref/6ins.kin.gz
-debian/tests/ref/6ins.rawinfo.table.gz
-debian/tests/ref/6ins.surfacedots.kin.gz
\ No newline at end of file
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,3 @@
-Name: probe
Bug-Database: https://github.com/rlabduke/probe/issues
Bug-Submit: https://github.com/rlabduke/probe/issues/new
Reference:
=====================================
debian/watch
=====================================
@@ -1,7 +1,11 @@
version=4
-opts="mode=git,pretty=2.16.160404+git%cd.%h" \
- https://github.com/rlabduke/probe.git HEAD
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+ https://github.com/rlabduke/probe/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+
+#opts="mode=git,pretty=2.16.160404+git%cd.%h" \
+# https://github.com/rlabduke/probe.git HEAD
# asked for release tags in
# https://github.com/rlabduke/probe/issues/4
+# closed. :-)
=====================================
probe.c
=====================================
@@ -51,7 +51,8 @@
#define INLINE_FOR_SPEED 1
-static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J. Michael Word";
+static char* versionString = "probe: version 2.18.211005, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab";
+/*static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J. Michael Word";*/
/*static char *versionString = "probe: version 2.16.130520, Copyright 1996-2013, J. Michael Word";*/
/*"probe: version 2.15.130427, merged probeVector, Copyright 1996-2013, J. Michael Word";*/
/*"probe: version 2.14.130116, Copyright 1996-2013, J. Michael Word";*/
@@ -70,7 +71,8 @@ static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J
/*"probe: version 2.10.031014dcr041101, Copyright 1996-2004, J. Michael Word";*/
/*"probe: version 2.10 10/14/2003, Copyright 1996-2003, J. Michael Word";*/
/*jmw & dcr agreement on version name and maintenance by dcr 041110*/
-static char *shortVersionStr = "probe.2.16.160404";
+static char* shortVersionStr = "probe.2.18.211005";
+/*static char *shortVersionStr = "probe.2.16.160404";*/
/*static char *shortVersionStr = "probe.2.16.130520";*/
/*static char *shortVersionStr = "probe.2.15.130427";*/
/*static char *shortVersionStr = "probe.2.14.130116";*/
@@ -149,7 +151,7 @@ static float Min_regular_hb_cutoff=0.6; /* globals controling hbond cutoff */
static float Min_charged_hb_cutoff=0.8; /* defaults set in processCommandline() */
static float RadScaleFactor =1.0; /* global VDW radius scale Factor r*f */
static float RadScaleOffset =0.0; /* global VDW radius scale Offset r+o */
-static float CORadScale =(1.65/1.75); /* global VDW radius scale Factor for C=O */
+static float CORadScale =(1.65/ATOMC_EXPLICIT_VDW); /* global VDW radius scale Factor for C=O */
static float GAPweight =0.25;/* global raw GAP score weight */
static float BUMPweight =10.0;/* global raw BUMP score scale Factor */
static float HBweight = 4.0;/* global raw HBond score scale Factor */
@@ -297,7 +299,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf)
note(message);
}
sprintf(message, "C=O carbon VDW scaled by %.3f to a radius of %g A",
- CORadScale, CORadScale*1.75);
+ CORadScale, CORadScale* ATOMC_EXPLICIT_VDW);
note(message);
if (rawOutput || countDots) {
sprintf(message, "Score Weights: gapWt=%g, bumpWt=%g, HBWt=%g",
@@ -1899,7 +1901,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
}
else {
file++;
- inf = fopen(p, "r"); /*p holds autobondrot input file name*/
+ inf = fopen(p, "rb"); /*p holds autobondrot input file name*/
if (inf) {
if (mabip) {
mabip->filenum = file;
@@ -1965,7 +1967,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
else
{
file++;
- inf = fopen(p, "r");
+ inf = fopen(p, "rb");
if (inf)
{
strcpy(inputfilename,p); /*dcr041023*/
@@ -1992,7 +1994,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
DoMcMc = TRUE;
DoHet = TRUE;
file++;
- inf = fopen(p, "r");
+ inf = fopen(p, "rb");
if (inf)
{
strcpy(inputfilename,p); /*dcr041023*/
@@ -2242,7 +2244,7 @@ void ProcessResInfo(chainEndData_t *ed, atom *a)
if (!strcmp(a->atomname, " O ")) { /* last Os[0-7] (cleared each res)*/
for (i = 0; i < 8; i++) {
if (ed->ambigO[i] == NULL) {
- if ((i == 0)|| (ed->ambigN[i-1]->r == a->r)) {
+ if ((i == 0)|| (ed->ambigO[i-1]->r == a->r)) {
ed->ambigO[i] = a;
}
break;
@@ -6516,6 +6518,8 @@ fprintf(outf,"2.15.130427 version number change for merged code! \n");
fprintf(outf,"2.16.130509 jjh added support for segid instead of chaind\n");
fprintf(outf,"2.16.130520 jjh fixed bug in segid handling\n");
fprintf(outf,"04/16/2015 - SJ added the -sepworse flag, if true will seperate the overlaps of >= 0.4 and overlaps of >=0.5. This is default by false. Had to change NODEWIDTH value (see probe.h)\n One can change the 0.5 cutoff for worse overlap by specifying the flag DIVWorse\n");
+fprintf(outf,"09/24/2021 - RMT Version 2.17 Fixed crash when finding ambiguous Oxygens\n");
+fprintf(outf,"10/05/2021 - RMT Version 2.18 Makes default C=O radius scale depend on table value\n");
exit(0);
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/d8b145dc2a9d6cf2dc305b9fce70aeec00e22fa6...429b9ff70c0d74dacb87585ae53310332b1edb65
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/d8b145dc2a9d6cf2dc305b9fce70aeec00e22fa6...429b9ff70c0d74dacb87585ae53310332b1edb65
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