[med-svn] [Git][med-team/king-probe][master] 5 commits: Cleanup watch file
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 28 16:02:57 GMT 2022
Andreas Tille pushed to branch master at Debian Med / king-probe
Commits:
9a897e6e by Andreas Tille at 2022-01-28T16:54:31+01:00
Cleanup watch file
- - - - -
0b94e5e4 by Andreas Tille at 2022-01-28T16:54:48+01:00
New upstream version 02.21
- - - - -
c1fa8080 by Andreas Tille at 2022-01-28T16:54:48+01:00
routine-update: New upstream version
- - - - -
fb29eaf3 by Andreas Tille at 2022-01-28T16:54:49+01:00
Update upstream source from tag 'upstream/02.21'
Update to upstream version '02.21'
with Debian dir ef09dce3d690371cf8d56b411d75a57aaadf5f46
- - - - -
9e95fd71 by Andreas Tille at 2022-01-28T16:55:36+01:00
routine-update: Ready to upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/watch
- probe.c
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+king-probe (02.21-1) unstable; urgency=medium
+
+ * Cleanup watch file
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Fri, 28 Jan 2022 16:54:59 +0100
+
king-probe (02.18-2) unstable; urgency=medium
* Fix autopkgtest to reflect the result of using the proper radius for
=====================================
debian/watch
=====================================
@@ -2,10 +2,3 @@ version=4
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
=====================================
@@ -51,43 +51,8 @@
#define INLINE_FOR_SPEED 1
-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";*/
-/*"probe: version 2.13.120907, Copyright 1996-2012, J. Michael Word";*/
-/*"probe: version 2.14.120109, Copyright 1996-2011, J. Michael Word";probeVector version*/
-/*"probe: version 2.13.110909, Copyright 1996-2011, J. Michael Word";*/
-/*"probe: version 2.13.110830, Copyright 1996-2011, J. Michael Word";*/
-/*"probe: version 2.12.110413, Copyright 1996-2007, J. Michael Word";*/
-/*"probe: version 2.12.070821, Copyright 1996-2007, J. Michael Word";*/
-/*"probe: version 2.11.061018, Copyright 1996-2006, J. Michael Word";*/
-/*"probe: version 2.11.060831, Copyright 1996-2006, J. Michael Word";*/
-/*minor work: 2.11.060212*/
-/*"probe: version 2.11.060129, Copyright 1996-2006, J. Michael Word";*/
-/*"probe: version 2.11.050121, Copyright 1996-2005, J. Michael Word";*/
-/*"probe: version 2.11.041112, Copyright 1996-2004, J. Michael Word";*/
-/*"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.2.18.211005";
-/*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";*/
-/*static char *shortVersionStr = "probe.2.13.120907"; gjk changed %s for OUTCOLor to make -OUT work again*/
-/*static char *shortVersionStr = "probe.2.14.120109";probeVector version*/
-/*static char *shortVersionStr = "probe.2.13.110909";*/
-/*static char *shortVersionStr = "probe.2.13.110830";*/
-/*static char *shortVersionStr = "probe.2.12.110413";*/
-/*static char *shortVersionStr = "probe.2.11.061018";*/
-/*static char *shortVersionStr = "probe.2.11.060831";*/
-/*static char *shortVersionStr = "Probe V2.11.060129";*/
-/*static char *shortVersionStr = "Probe V2.11.050121";*/
-/*static char *shortVersionStr = "Probe V2.11.041112";*/ /*041112 version change*/
-/*static char *shortVersionStr = "Probe V2.10.031014dcr041101";*/
-/*static char *shortVersionStr = "Probe V2.9 ( 10/14/2003)";*/
+static char* versionString = "probe: version 2.21.211221, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab";
+static char* shortVersionStr = "probe.2.21.211221";
static char *referenceString = "Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733.";
static char *electronicReference = "http://kinemage.biochem.duke.edu/";
@@ -147,21 +112,21 @@ static int OutputVDWs = TRUE; /* global controling display of contact categor
static int OnlyBadOut = FALSE; /* global controling display of contact categories dcr041010*/
static int ContactSUMMARY = FALSE; /* global controling output of contact summaries dcr041101*/
-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 Min_regular_hb_cutoff=0.6f; /* globals controling hbond cutoff */
+static float Min_charged_hb_cutoff=0.8f; /* 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/ATOMC_EXPLICIT_VDW); /* global VDW radius scale Factor for C=O */
+static float CORadScale =(float)(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 */
static float CHOHBfactor = 0.5;/* global CH..O HBond score scale Factor */
-static float LowGoodCut =-0.4;/* global cutoff for good bin */
+static float LowGoodCut =-0.4f;/* global cutoff for good bin */
static float HighGoodCut = 0.25;/* global cutoff for good bin */
static float WorseBumpCut =-0.5; /* SJ 04/10/2015 - global cutoff for worse overlap*/
-static float OccupancyCutoff =0.02; /* global occupancy below which atom has presence but no clashes */
+static float OccupancyCutoff =0.02f; /* global occupancy below which atom has presence but no clashes */
/*unfortunately, one needs intervening atoms to avoid clashes between atoms*/
/*that are separated by <= Maxbonded, which thus needs to pass through any*/
/*atom no matter what it's own occupancy happens to be */
@@ -200,6 +165,8 @@ static int modelSrc = 0; /*global model specified for source 041114*/
static int modelTarg = 0; /*global model specified for target 041114*/
static int modelToProcess = 0; /*global model specified for processing 041114*/
+static char* dumpFileName = 0; /* global name of file to dump atom info to (default none) */
+
#define ATOMS_IN_THE_SAME_RES(aa, bb) IS_THE_SAME_RES((aa)->r, (bb)->r)
/*041112 IS_THE_SAME_RES() cannot avoid modeltest, i.e. implied Lmodeltest==1*/
#define IS_THE_SAME_RES(ra, rb) \
@@ -431,7 +398,27 @@ int mainProbeProc(int argc, char **argv, FILE *outf)
/*(returned param used on separate call for autobondrot processing)*/
/*e.g. creates: newH->elem = atomHOd , dummy Hydrogen to make an H-Bond*/
}
- /*now do the real work: */
+
+ /* Dump the atom information if we've been asked to. */
+ if (dumpFileName) {
+ FILE* dumpFile = 0;
+ dumpFile = fopen(dumpFileName, "wb");
+ for (atom* a = allMainAtoms; a; a = a->next) {
+ /* Don't dump Phantom Hydrogen information. */
+ if (a->elem != atomHOd) {
+ fprintf(dumpFile, "%s %s %3d %-4s %c %7.3f %7.3f %7.3f %5.2f %s %s %s\n",
+ a->r->chain, a->r->resname, a->r->resid, a->atomname,
+ a->altConf == ' ' ? '-' : a->altConf,
+ a->loc.x, a->loc.y, a->loc.z, a->radius,
+ a->props & ACCEPTOR_PROP ? "isAcceptor" : "noAcceptor",
+ a->props & DONOR_PROP ? "isDonor" : "noDonor",
+ a->props & METAL_PROP ? "isMetallic" : "noMetallic");
+ }
+ }
+ fclose(dumpFile);
+ }
+
+ /*now do the real work: */
doCommand(outf, method,
allMainAtoms, abins, NULL, NULL,
dots, probeRad, density, spikelen,
@@ -1328,6 +1315,7 @@ else { /*longlist option*/
fprintf(stderr, " -OLDU generate old style -u output: kissEdge2BullsEye, etc\n");
fprintf(stderr, " -VErbose verbose mode (default)\n");
fprintf(stderr, " -DOTDUMP dump dot info while doing examineDots()\n");
+ fprintf(stderr, " -DUMPATOMS filename dump atom information to filename for regression testing\n");
fprintf(stderr, " -REFerence display reference string\n");
fprintf(stderr, " -CHANGEs display a list of program changes\n");
fprintf(stderr, " -Quiet quiet mode\n");
@@ -1496,6 +1484,13 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
}
else if(compArgStr(p+1, "DOTDUMP", 7)){
Ldotdump = TRUE; /*111202dcr Ldotdump in examineOneDotEach() */
+ }
+ else if(compArgStr(p+1, "DUMPATOMS", 9)){
+ if (++i < argc) {
+ dumpFileName = argv[i];
+ } else {
+ halt("no filename after -DUMPATOMS flag");
+ }
}
else if(compArgStr(p+1, "QUIET", 1)){
Verbose = FALSE;
@@ -1633,14 +1628,14 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
argcnt = 1;
* srcArg = "not water";
*keepUnselected = FALSE;
- *probeRad = 1.4;
+ *probeRad = 1.4f;
*groupLabel = "SCS";
}
else if(compArgStr(p+1, "EXPOSED", 4)){
*method = EXTERNALSURFACE;
nargs = 1;
*keepUnselected = FALSE;
- *probeRad = 1.4;
+ *probeRad = 1.4f;
*groupLabel = "SCS";
}
else if(compArgStr(p+1, "ASURFACE", 2)){
@@ -1649,7 +1644,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
argcnt = 1;
* srcArg = "not water";
*keepUnselected = FALSE;
- RadScaleOffset = 1.4;
+ RadScaleOffset = 1.4f;
*probeRad = 0.0;
*groupLabel = "AS";
}
@@ -1657,7 +1652,7 @@ atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
*method = EXTERNALSURFACE;
nargs = 1;
*keepUnselected = FALSE;
- RadScaleOffset = 1.4;
+ RadScaleOffset = 1.4f;
*probeRad = 0.0;
*groupLabel = "AS";
}
@@ -2412,7 +2407,7 @@ atomBins* binAtoms(atom *theAtoms, region *boundingBox, char serialNum,
atomBins *bins = NULL;
bins = initBins(serialNum, boundingBox,
- 2.0*(getMaxRadius(ImplicitH)+probeRad)+0.2);
+ 2.0f*(getMaxRadius(ImplicitH)+probeRad)+0.2f);
if (bins) {
for(a = theAtoms; a; a = a->next) {
if (keepUnselected || (a->flags & selflags)) {
@@ -2708,7 +2703,7 @@ int atomsClose(atom *a, atom *b, float probeRad)
lim = a->radius + b->radius + probeRad + probeRad;
- dsq = v3distanceSq(&(a->loc), &(b->loc));
+ dsq = (float)v3distanceSq(&(a->loc), &(b->loc));
/* if too close they must be the same atom...dummy atom?? */
@@ -3012,15 +3007,13 @@ void examineOneDotEach(atom *src, int type, atom *scratch,
/*called from genDotIntersect() with same names except scratch==atomList2 */
/*cloned and modified from examineDots to do only the OneDotEach option 111205*/
/*111013 switch to dump details... 111202 now input param: -dotdump */
- float neighborhoodsq,neighbor2dotsq;
atom *holdsrc;
atom *holdcause;
int holdtype;
point3d holddotloc;
point3d holdspikeloc;
- dotNode *holdresults;
int holdovrlaptype;
- float holdmingap = 999.9;
+ float holdmingap = 999.9f;
char holdptmaster;
int Lholdingdot = FALSE; /*111021dcr src and targ can have diff patterns*/
int Lbetweenatoms = FALSE; /*111202dcr*/
@@ -3036,13 +3029,12 @@ void examineOneDotEach(atom *src, int type, atom *scratch,
point3d targetloc, dotloc, dotvect, exploc, spikeloc;
point3d gapvect, gaploc;
point3d perploc; /*LOneDotEach occluder perpendicular to src-targ 111018*/
- point3d distalloc,distalvec; /*point across gap from source dot 111024dcr*/
pointSet *srcDots = NULL;
char ptmaster = ' '; /*pointmaster character dcr041009*/
int idx = 0; /*dcr041020*/
atom *parent = NULL; /*dcr20120120*/
/*int LXHvector = TRUE;*/ /*dcr20120120 eventually commandline param*/
- float XHdistance = 99.9; /*dcr20120120*/
+ float XHdistance = 99.9f; /*dcr20120120*/
float XHTangle = 0.0; /*dcr20120120*/
if (src->elem == ignoreAtom)
@@ -3117,7 +3109,7 @@ void examineOneDotEach(atom *src, int type, atom *scratch,
fprintf(stderr,"[src %s %s %s] DOT [%s %s %s] dotloc:%7.3f,%7.3f,%7.3f DOT\n",src->atomname,src->r->resname,src->r->Hy36resno,extratarg->atomname,extratarg->r->resname,extratarg->r->Hy36resno,dotloc.x,dotloc.y,dotloc.z);
/* */
- mingap = 999.9;
+ mingap = 999.9f;
isaHB = tooCloseHB = FALSE;
hbondbumpgap = 0.0;
ok = FALSE; /*expect dot to be rejected*/
@@ -3463,8 +3455,8 @@ fprintf(stderr," NEIGHBOR [%s %s %s] BENIGN for src---targ interaction\n",targ->
if(nearpt == 2) /*disasterously near, i.e. on top of each other*/
{
- sl = -((src->radius) + (extratarg->radius))/2.0;
- mingap = 2.0*LowGoodCut; /*force arbitrary bad clash*/
+ sl = -((src->radius) + (extratarg->radius))/2.0f;
+ mingap = 2.0f*LowGoodCut; /*force arbitrary bad clash*/
ovrlaptype =-1; /*disaster overlap == clash!! */
/*spikeloc calc from src->radius + sl, sl=spikelen*mingap,*/
/*spikelen = 0.50 OR input param*/
@@ -3680,7 +3672,7 @@ fprintf(stderr," NEIGHBOR [%s %s %s] BENIGN for src---targ interaction\n",targ->
if(XHdistance < 1.2 && XHdistance > 0.1 )
{/*parent atom for this Hydrogen*/
XHTangle = v3angle(&(parent->loc), &(src->loc), &(holdcause->loc));
- XHTangle = XHTangle*360/(2*3.14159265);
+ XHTangle = XHTangle*360/(2*3.14159265f);
if(Ldotdump)
fprintf(stderr,"[src %s %s %s] :: [parent %s %s %s]*YES**about to saveDot:: mingap %8.3f, XHdistance: %8.3f, XHTangle: %8.3f HOLD\n",holdsrc->atomname,holdsrc->r->resname,holdsrc->r->Hy36resno,parent->atomname,parent->r->resname,parent->r->Hy36resno,holdmingap,XHdistance,XHTangle);
@@ -3754,7 +3746,7 @@ void examineDots(atom *src, int type, atom *scratch,
v3add(&(src->loc), &dotvect, &exploc);
ok = FALSE;
- mingap = 999.9;
+ mingap = 999.9f;
isaHB = tooCloseHB = FALSE;
hbondbumpgap = 0.0;
@@ -4670,7 +4662,6 @@ void freeResults(dotNode *results[][NODEWIDTH])
{
int i, j;
dotNode *node, *next;
- atom * a;
for (i = 0; i < NUMATOMTYPES; i++) {
for (j = 0; j < NODEWIDTH; j++) {
@@ -4800,7 +4791,7 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int
{'z','y','x','w','v','u','t','g','r','q','f','F','Q','R','G','T','U','V','W','X','Y','Z'};
/*0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ,10 ,11 ,12 ,13 ,14 ,15 ,16 ,17 ,18 ,19 ,20 ,21*/
/*std gapbins scope at least -.5 to +.5, wider if probeRad > 0.25 standard*/
- int gaplimit = ((2*(probeRad>0.25?probeRad:0.25) +0.5)/0.05)+2; /*20111220dcr*/
+ int gaplimit = ((2*(probeRad>0.25f?probeRad:0.25f) +0.5f)/0.05f)+2; /*20111220dcr*/
long *gapcounts = (long *) malloc(gaplimit * sizeof(long));
long maxgapcounts = 0;
int Lgotgapbin = FALSE;
@@ -6210,7 +6201,7 @@ atom* updateHydrogenInfo(FILE *outf, atom *allMainAtoms, atomBins *abins,
{
if (a->props & ACCEPTOR_PROP)
{/* bgn: if acceptor_prop */
- float hbgap = gapSize(&(a->loc), &(orig->loc), a->radius + 2.0);
+ float hbgap = gapSize(&(a->loc), &(orig->loc), a->radius + 2.0f);
int foundAromRingAtom = FALSE;
if (a->props & AROMATIC_PROP)
@@ -6520,6 +6511,9 @@ 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");
+fprintf(outf,"12/09/2021 - RMT Version 2.19 Adds commend-line argument to dump atom info\n");
+fprintf(outf,"12/21/2021 - RMT Version 2.20 Dumps atom information after hydrogens have been updated.\n");
+fprintf(outf,"12/21/2021 - RMT Version 2.21 Does not dump Phantom Hydrogen information.\n");
exit(0);
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/8a4396a191eae197f387e007c4c8355a73b70c46...9e95fd7149540bbe218862af5b8a7bfbaa09b35b
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/8a4396a191eae197f387e007c4c8355a73b70c46...9e95fd7149540bbe218862af5b8a7bfbaa09b35b
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