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 <[email protected]> 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 <[email protected]>, Michael Prisant <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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