From 9856e1cdf0abde6e5666b59920d208cbd7e202e6c80511da7edfd6f4feca68fb Mon Sep 17 00:00:00 2001 From: Jan Engelhardt Date: Sat, 28 May 2016 17:35:14 +0000 Subject: [PATCH] Accepting request 398617 from home:ithod Update jmol to the current stable version 14.6.0 and some minor improvements (see diff). OBS-URL: https://build.opensuse.org/request/show/398617 OBS-URL: https://build.opensuse.org/package/show/science/jmol?expand=0&rev=7 --- Jmol-14.5.0_2015.11.06-binary.zip | 3 - _service | 7 ++ ...load_url:Jmol-14.6.0_2016.05.24-binary.zip | 3 + fsf-adress.patch | 13 ++++ jmol.changes | 33 +++++++++ jmol.desktop | 9 +++ jmol.man | 67 +++++++++++++++++++ jmol.spec | 43 ++++++------ 8 files changed, 156 insertions(+), 22 deletions(-) delete mode 100644 Jmol-14.5.0_2015.11.06-binary.zip create mode 100644 _service create mode 100644 _service:download_url:Jmol-14.6.0_2016.05.24-binary.zip create mode 100644 fsf-adress.patch create mode 100644 jmol.desktop create mode 100644 jmol.man diff --git a/Jmol-14.5.0_2015.11.06-binary.zip b/Jmol-14.5.0_2015.11.06-binary.zip deleted file mode 100644 index 2703676..0000000 --- a/Jmol-14.5.0_2015.11.06-binary.zip +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:39bcfc2138f631973471466f5a649639421571a65178315e3a4ab8561f9d817e -size 60762047 diff --git a/_service b/_service new file mode 100644 index 0000000..56947be --- /dev/null +++ b/_service @@ -0,0 +1,7 @@ + + + downloads.sf.net + http + /jmol/Jmol-14.6.0_2016.05.24-binary.zip + + \ No newline at end of file diff --git a/_service:download_url:Jmol-14.6.0_2016.05.24-binary.zip b/_service:download_url:Jmol-14.6.0_2016.05.24-binary.zip new file mode 100644 index 0000000..1ac0446 --- /dev/null +++ b/_service:download_url:Jmol-14.6.0_2016.05.24-binary.zip @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6b63fa63b45fadc82171dd651531a72905fdef6aa8b8364696ac682c53bc8f5c +size 66473417 diff --git a/fsf-adress.patch b/fsf-adress.patch new file mode 100644 index 0000000..a1433b0 --- /dev/null +++ b/fsf-adress.patch @@ -0,0 +1,13 @@ +--- /usr/share/doc/packages/jmol/COPYRIGHT.txt 2014-04-29 22:01:17.000000000 +0200 ++++ COPYRIGHT.txt 2014-05-24 12:33:40.982788719 +0200 +@@ -13,8 +13,8 @@ + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software +-Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA +-02111-1307 USA. ++Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA ++02110-1301, USA. + + + Complete source code for the Jmol application, the Jmol applet, and diff --git a/jmol.changes b/jmol.changes index 24c58ab..13eeef5 100644 --- a/jmol.changes +++ b/jmol.changes @@ -1,3 +1,36 @@ +------------------------------------------------------------------- +Sat May 28 16:18:55 UTC 2016 - thod_@gmx.de + +- Add manual +- Split desktop file +- update to version 14.6.0 + selected new feature: + * CONNECT {pair1} {pair2} ATROPISOMER + * C13 NMR prediction from http://www.nmrdb.org/service/jsmol13c?smiles=CCCC + * Jmol SMILES bond atropisomerism ^nm- and ^^nm- + * SMILES/nonaromatic same as SMILES/noaromatic + * adds SHOW SMILES/bio and {*}.find("SMILES/bio") options: + * print {*}.find("SMILES/hydrogen/") adds hydrogen atoms + * Jmol now implements a way of indicating atropisomer chirality. + * full implementation of OpenSMILES and OpenSMARTS in Jmol + * Polyhedra command allows for min and max radius + * draw POINTGROUP SPACEGROUP + * draw SPACEGROUP + * print pointgroup("spacegroup", @1) + * show spacegroup/xxxxx + * show symop 3 @3 "atom" + * show/draw symop @1 @2 + * show/draw symop @1 @2 n + * symop() options + * symop(3,@3,"atom") + * getProperty("shapeInfo.echo") + * preliminary MMTF reader + * set window width height + * set window "xxx.png" + * setting DSSR on the fly + * show chemical xxx where xxx is a file type + and many bug fixes + ------------------------------------------------------------------- Sun Mar 13 10:24:28 UTC 2016 - jengelh@inai.de diff --git a/jmol.desktop b/jmol.desktop new file mode 100644 index 0000000..8520d15 --- /dev/null +++ b/jmol.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Name=Jmol +Comment=An open-source Java viewer for chemical structures in 3D +GenericName=Jmol +Exec=jmol +Icon=jmol +Terminal=0 +Categories=Education;Science;Chemistry;Physics; +Type=Application diff --git a/jmol.man b/jmol.man new file mode 100644 index 0000000..3bcf817 --- /dev/null +++ b/jmol.man @@ -0,0 +1,67 @@ +.\" Manpage for jmol. +.\" Contact thod_@gmx.de to correct errors or typos. +.TH man 1 "24 May 2015" "INST_VERSION" "jmol man page" +.SH NAME +jmol \- INST_SUMMARY +.SH SYNOPSIS +jmol [options] +.SH DESCRIPTION +Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. +.SH OPTIONS + -o,--noconsole no console -- all output to sysout + -c,--check check script syntax only - no file loading + -k,--kiosk kiosk mode -- no frame + -C,--checkload check script syntax only - with file loading + -s,--script script file to execute or '-' for System.in + -q,--quality JPG image quality (1-100; default 75) or PNG + image compression (0-9; default 2, maximum compression 9) + -g,--geometry window width x height, e.g. -g500x500 + -p,--printOnly send only output from print messages to + console (implies -i) + -x,--exit exit after script (implicit with -n) + -j,--jmolscript2 Jmol script to execute AFTER -s option + -J,--jmolscript1 Jmol script to execute BEFORE -s option + -P,--port port for JSON/MolecularPlayground-style + communication + -D supported options are given below + -I,--input allow piping of input from System.Input + -L,--nosplash start with no splash screen + -M,--multitouch use multitouch interface (requires + "sparshui" parameter + -R,--restricted restrict local file access + -T,--headlessmaxtime headless max time (sec) + -b,--backgroundtransparent transparent background + -d,--debug debug + -h,--help give this help page + -i,--silent silent startup operation + -l,--list list commands during script execution + -m,--menu menu file to use + -n,--nodisplay no display (and also exit when done) + -r,--restrictSpt restrict local file access (allow reading of + SPT files) + -t,--threaded independent command thread + -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename +.SH EXAMPLES +Jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt + +The -D options are as follows (defaults in parenthesis) and must be called preceding '-jar Jmol.jar': + + cdk.debugging=[true|false] (false) + cdk.debug.stdout=[true|false] (false) + display.speed=[fps|ms] (ms) + logger.debug=[true|false] (false) + logger.error=[true|false] (true) + logger.fatal=[true|false] (true) + logger.info=[true|false] (true) + logger.logLevel=[true|false] (false) + logger.warn=[true|false] (true) + plugin.dir (unset) + user.language=[ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW] (en_US) +.SH SEE ALSO +java(1) + +For more information, see also +.SH BUGS +No known bugs. +.SH AUTHOR +Jmol authors (jmol-developers@lists.sf.net) diff --git a/jmol.spec b/jmol.spec index 12044a7..7ea55ff 100644 --- a/jmol.spec +++ b/jmol.spec @@ -17,9 +17,9 @@ Name: jmol -Version: 14.5.0 +Version: 14.6.0 Release: 0 -%define date 2015.11.06 +%define date 2016.05.24 Summary: 3D Viewer for chemical structures License: LGPL-2.1 Group: Productivity/Scientific/Chemistry @@ -28,57 +28,62 @@ Url: http://jmol.sf.net/ Source: http://downloads.sf.net/jmol/Jmol-%{version}_%date-binary.zip Source2: Jmol_icon13.png #Source2-Orig: http://wiki.jmol.org/index.php/File:Jmol_icon13.png +Source3: %{name}.man +Source4: %{name}.desktop Patch1: datadir.diff +Patch2: fsf-adress.patch BuildArch: noarch BuildRoot: %{_tmppath}/%{name}-%{version}-build BuildRequires: dos2unix BuildRequires: unzip +BuildRequires: desktop-file-utils +BuildRequires: update-desktop-files Requires: java %description -Jmol is a Java-based viewer for chemical structures in 3D with +Jmol is an open-source Java-based viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. %prep %setup -qn %name-%{version}_%date %patch -P 1 -p1 +%patch -P 2 -p0 cp %{S:2} . %build dos2unix CHANGES.txt COPYRIGHT.txt LICENSE.txt README.txt perl -i -pe 's{\@pkgdatadir\@}{%_datadir/%name}gs' jmol.sh +# man +cp %{S:3} . +sed -i 's/INST_VERSION/%{version}/' jmol.man +sed -i 's/INST_SUMMARY/%{summary}/' jmol.man +gzip jmol.man %install b="%buildroot" # jar mkdir -p "$b/%_datadir/%name" -cp -a Jmol.jar "$b/%_datadir/%name/" +install -D -p -m 644 Jmol.jar "$b/%_datadir/%name/" # script mkdir -p "$b/%_bindir" -cp -a jmol.sh "$b/%_bindir/jmol" +install -D -p -m 755 jmol.sh "$b/%_bindir/jmol" # icon mkdir -p "$b/%_datadir/pixmaps" -cp -a Jmol_icon13.png "$b/%_datadir/pixmaps/%name.png" +install -m 644 Jmol_icon13.png "$b/%_datadir/pixmaps/%name.png" +# manual +mkdir -p %{buildroot}%{_mandir}/man1 +install -m 644 jmol.man.gz "$b/%_mandir/man1/jmol.1.gz" # .desktop -mkdir -p "$b/%_datadir/applications" -cat >"$b/%_datadir/applications/%name.desktop" <<-EOF - [Desktop Entry] - Name=Jmol - Comment=An open-source Java viewer for chemical structures in 3D - GenericName=Jmol - Exec=jmol - Icon=jmol - Terminal=0 - Categories=Education;Science;Chemistry;Physics; - Type=Application -EOF +desktop-file-install --dir %{buildroot}%{_datadir}/applications %{S:4} +%suse_update_desktop_file %{name} %files %defattr(-,root,root) %doc README.txt LICENSE.txt COPYRIGHT.txt CHANGES.txt -%_bindir/jmol +%_bindir/%name %_datadir/%name %_datadir/applications/%name.desktop %_datadir/pixmaps/%name.png +%_mandir/man1/%{name}.1.gz %changelog