[med-svn] [Git][med-team/king-probe][master] 5 commits: routine-update: New upstream version
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon May 2 13:42:25 BST 2022
Andreas Tille pushed to branch master at Debian Med / king-probe
Commits:
d9aa30e1 by Andreas Tille at 2022-05-02T13:48:13+02:00
routine-update: New upstream version
- - - - -
873d4f7b by Andreas Tille at 2022-05-02T13:48:14+02:00
New upstream version 02.23
- - - - -
d207ae2b by Andreas Tille at 2022-05-02T13:48:14+02:00
Update upstream source from tag 'upstream/02.23'
Update to upstream version '02.23'
with Debian dir c880514522be8b4557f1c77d5e8eac7b78b2068f
- - - - -
170b90e1 by Andreas Tille at 2022-05-02T13:59:49+02:00
Add license for test data
- - - - -
9bc10c39 by Andreas Tille at 2022-05-02T14:41:19+02:00
Another change in test result
- - - - -
4 changed files:
- debian/changelog
- debian/copyright
- probe.c
- select.c
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+king-probe (02.23-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Add license for test data
+ TODO: Another change in test result
+
+ -- Andreas Tille <tille at debian.org> Mon, 02 May 2022 13:48:13 +0200
+
king-probe (02.21-1) unstable; urgency=medium
* Cleanup watch file
=====================================
debian/copyright
=====================================
@@ -12,9 +12,11 @@ License: probe
Files: debian/tests/data/6ins.pdb1.gz
Source: https://www.rcsb.org/structure/6INS
+License: public_domain
Files: debian/tests/data/1zni.pdb1.gz
Source: https://www.rcsb.org/structure/1ZNI
+License: public_domain
License: probe
This is free software and the source code is freely
@@ -34,4 +36,8 @@ License: probe
the program are also available for free."
.
Simply put: we would like our software to be used as widely as possible,
- and we would appreciate attribution.
\ No newline at end of file
+ and we would appreciate attribution.
+
+License: public_domain
+ The test data are published as public domain.
+
=====================================
probe.c
=====================================
@@ -51,8 +51,8 @@
#define INLINE_FOR_SPEED 1
-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* 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 *referenceString = "Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733.";
static char *electronicReference = "http://kinemage.biochem.duke.edu/";
@@ -204,7 +204,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf)
int method;
int keepUnselected;
region boundingBoxA;
- atom *allMainAtoms = NULL;
+ atom *a, *allMainAtoms = NULL;
atomBins *abins = NULL;
pointSet dots[NUMATOMTYPES];
char *srcArg=NULL, *targArg=NULL, *extraArg=NULL, *ignoreArg=NULL; /* extraArg dcr 111022*/
@@ -215,6 +215,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf)
char message[200];
movingAtomBuildInfo mabis;
residue *resLst = NULL;
+ FILE* dumpFile = NULL;
/*mabis moving atom build info structure */
/*buffer to pass data to newMovingAtom for autobondrot*/
@@ -401,9 +402,8 @@ int mainProbeProc(int argc, char **argv, FILE *outf)
/* 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) {
+ for (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",
@@ -5219,6 +5219,7 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int
{/*kinemage point or point-line for each node in (ij)th dot-node list*/
a = node->a; /*owner of dot*/
t = node->t; /*cause of dot, use for OneDotEach 111013dcr*/
+ /* Slow way to determine integer truncation of k/5 with a maximum of 9. */
for(k=0; k<10; k++){if(a->bval < k*5) {break;}}
/*2:10A,3:15B,4:20C,5:25D,6:30E,8:40F,10:50G*/
if(k<=2){ptm[0] = 'A';}
@@ -5226,8 +5227,8 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int
else if(k<=4){ptm[0] = 'C';}
else if(k<=5){ptm[0] = 'D';}
else if(k<=6){ptm[0] = 'E';}
- else if(k<=2){ptm[0] = 'F';}
- else if(k<=2){ptm[0] = 'G';}
+ else if(k<=7){ptm[0] = 'F';}
+ else if(k<=8){ptm[0] = 'G';}
else{ptm[0] = 'H';}
/*Note first nemdstr char of inputfilename 20120120dcr*/
fprintf(outf,"{%6s %s%c%s%s%c%s:O=%4.2f, B=%6.2f; %s%c%s%s%c%s:O=%4.2f, B=%6.2f; GAP %6.3f}'%s' %8.3f, %8.3f , %8.3f\n",
@@ -6509,11 +6510,14 @@ 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");
-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");
+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");
+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");
exit(0);
=====================================
select.c
=====================================
@@ -63,7 +63,11 @@ static ResidueAndAtomPair AromaticAtomsTbl[] = {
":PHE:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP,
":HIS:", ": ND1: CD2: CE1: NE2: CG :", 0,
":TYR:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP,
-":TRP:", ": CG : CD1: CD2: NE1: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP,
+// The 5-membered ring is not treated as an aromatic acceptor face, but the 6-membered
+// ring is.
+//":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,
": U:URA:UTP:UDP:UMP:PSU: UR:",
": N1 : C2 : N3 : C4 : C5 : C6 :", TEST_ACCEPT_ANGLE_PROP,
": T:THY:TTP:TDP:TMP:5MU: DT: TR:",
@@ -269,7 +273,10 @@ static ResidueAndAtomPair DonorAcceptorAtomTbl[] = {
: DE :1DH1:2DH1:1DH2:2DH2:DH11:DH12:DH21:DH22:",
DONOR_PROP,
-":HIS:", ": ND1: NE2:", DONOR_PROP|ACCEPTOR_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,
":HIS:", ": HD1: HE2: DD1: DE2:", DONOR_PROP,
":HIS:", ": HD2: HE1: DD2: DE1:", DONOR_PROP|CH_DONOR_PROP,
":SER:", ": OG :", DONOR_PROP|ACCEPTOR_PROP,
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/9e95fd7149540bbe218862af5b8a7bfbaa09b35b...9bc10c39cdc5967cbd395bc3b31a2ef27735eb1c
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/9e95fd7149540bbe218862af5b8a7bfbaa09b35b...9bc10c39cdc5967cbd395bc3b31a2ef27735eb1c
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220502/7757856d/attachment-0001.htm>
More information about the debian-med-commit
mailing list