[med-svn] [Git][med-team/king-probe][master] 10 commits: New upstream version 2.16.160404+git20200121.9b198c1
Steffen Möller
gitlab at salsa.debian.org
Sat May 23 16:32:51 BST 2020
Steffen Möller pushed to branch master at Debian Med / king-probe
Commits:
457acc77 by Steffen Moeller at 2020-05-23T17:23:47+02:00
New upstream version 2.16.160404+git20200121.9b198c1
- - - - -
ca579180 by Steffen Moeller at 2020-05-23T17:23:47+02:00
routine-update: New upstream version
- - - - -
9cf78952 by Steffen Moeller at 2020-05-23T17:23:48+02:00
Update upstream source from tag 'upstream/2.16.160404+git20200121.9b198c1'
Update to upstream version '2.16.160404+git20200121.9b198c1'
with Debian dir 05e0a5537a7791043e48f78b7261d59f2ca85ab0
- - - - -
c299c086 by Steffen Moeller at 2020-05-23T17:23:48+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
9d777c50 by Steffen Moeller at 2020-05-23T17:23:48+02:00
routine-update: debhelper-compat 12
- - - - -
def79bc2 by Steffen Moeller at 2020-05-23T17:23:51+02:00
routine-update: Secure URI in copyright format
- - - - -
b9d08500 by Steffen Moeller at 2020-05-23T17:23:51+02:00
routine-update: Add salsa-ci file
- - - - -
f2b534f6 by Steffen Moeller at 2020-05-23T17:23:51+02:00
routine-update: Rules-Requires-Root: no
- - - - -
e45c8834 by Steffen Moeller at 2020-05-23T17:24:01+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
1c1e8e73 by Steffen Moeller at 2020-05-23T17:24:10+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/salsa-ci.yml
- debian/upstream/metadata
- readPDBrecs.c
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+king-probe (2.16.160404+git20200121.9b198c1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 12 (routine-update)
+ * Secure URI in copyright format (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 23 May 2020 17:24:01 +0200
+
king-probe (2.16.160404+git20180613.a09b012-1) unstable; urgency=medium
* Use git mode in watch file
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,11 +5,12 @@ Uploaders: Malihe Asemani <ml.asemani at gmail.com>,
Michael Prisant <michael.prisant at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.5
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.5.0
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
+Rules-Requires-Root: no
Package: king-probe
Architecture: any
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: probe
Source: https://github.com/rlabduke/probe/
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/rlabduke/probe/issues
+Bug-Submit: https://github.com/rlabduke/probe/issues/new
Reference:
- Author: >
J. Michael Word and Simon C. Lovell and Thomas H. LaBean and
=====================================
readPDBrecs.c
=====================================
@@ -44,6 +44,8 @@ int readRecord(FILE *inf, char buffer[], int maxChars) {
register int count = 0;
register int done = 0;
int makeUpperCase = 1;
+ int setCase = 0;
+ char linecard[5];
if (!inf || feof(inf)) {
count = -1; /* signal end-of-file */
@@ -52,15 +54,46 @@ int readRecord(FILE *inf, char buffer[], int maxChars) {
else {
while(!done) {
ch = getc(inf);
- if ((ch == '@') || (ch == '#')) {
- /* special codes turn off forced uppercase */
- /* "at sign" used for commands */
- /* "hash" used for comments */
- makeUpperCase = 0;
- }
- if (makeUpperCase) {
- ch = toupper(ch);
- }
+ // This block added by cjw, 01-21-2020
+ // Forces uppercase on record type, resname, and atomname fields
+ // Preserves existing case for all other fields, assumes internal file
+ // consistency.
+ if (count < 6){
+ //set 6-char line identifier (REMARK, ATOM) to uppercase
+ ch = toupper(ch);
+ if (count < 4){
+ //build short record type from first 4 chars
+ linecard[count] = ch;
+ }
+ else if (count ==4){
+ linecard[count] = '\0'; //finish linecard string
+ //setCase if line is applicable record
+ if ((strncmp(linecard, "ATOM", 4) == 0) || (strncmp(linecard, "HETA", 4) == 0) || (strncmp(linecard, "TER", 3) == 0)){
+ setCase = 1;
+ }
+ }
+ }
+//0123456789*123456789*123456789*123456789*123456789*123456789*123456789*1234567
+//ATOM 1568 CE2 TYR B 90 0.565 40.044 57.767 1.00 16.94 C
+ else if (setCase && count >= 12 && count < 20 && count != 16){
+ //fix case for atom (12-15) and resname (17-19)
+ ch = toupper(ch);
+ }
+
+ // This block removed by cjw, 12-09-2019
+ // It appears to convert PDB lines to all-uppercase on read-in
+ // Some large files use lowercase chain IDs, which *must* be preserved
+ // Be warned that its removal allows past unsupported lower case chars in
+ // atomnames, etc
+ //if ((ch == '@') || (ch == '#')) {
+ // /* special codes turn off forced uppercase */
+ // /* "at sign" used for commands */
+ // /* "hash" used for comments */
+ // makeUpperCase = 0;
+ //}
+ //if (makeUpperCase) {
+ // ch = toupper(ch);
+ //}
if ((ch == EOF) || (ch == '\n')) {
done = 1;
}
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf
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