diff options
author | Drobot Viktor | 2019-04-05 21:52:48 +0300 |
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committer | Drobot Viktor | 2019-04-05 21:52:48 +0300 |
commit | e561704da581f8bd8a0e41fe883b930a9fe5455d (patch) | |
tree | 5059fdcacb4ddaa73fb10d9b9c6196a79d67638b | |
download | aur-e561704da581f8bd8a0e41fe883b930a9fe5455d.tar.gz |
First release
-rw-r--r-- | .SRCINFO | 30 | ||||
-rw-r--r-- | PKGBUILD | 56 | ||||
-rw-r--r-- | apbstools_tcltk8.6.patch | 106 |
3 files changed, 192 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..936ce638aaa0 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,30 @@ +pkgbase = pymol-python2 + pkgdesc = Molecular visualization system on an Open Source foundation + pkgver = 2.3.0 + pkgrel = 1 + url = https://pymol.org/ + arch = x86_64 + license = custom + makedepends = desktop-file-utils + makedepends = gendesk + makedepends = libmmtf + makedepends = msgpack-c + depends = freetype2 + depends = glew + depends = glm + depends = glut + depends = python2-numpy + depends = tcsh + optdepends = python2-pmw: pmw based UI + optdepends = python2-pyqt5: Qt5 based UI + provides = pymol + conflicts = pymol + source = https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz + source = pymol.png::https://c.fsdn.com/allura/p/pymol/icon + source = apbstools_tcltk8.6.patch + sha512sums = e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133 + sha512sums = 39917c1dc80cd6a59e8f6b3ea49a59491eaf23d14e32ac264f6d71f33007f686deb6a66e50e7f20ef9df5337038e3572b018633c361460d5ee0c1d8f0a8259d1 + sha512sums = 90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c + +pkgname = pymol-python2 + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..6dd82bf9ed56 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com +# Contributor: Evgeniy Alekseev <arcanis at archlinux dot org> +# Contributor: graysky +# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com> + +pkgname=pymol-python2 +_pkgname=pymol +pkgver=2.3.0 +pkgrel=1 +pkgdesc="Molecular visualization system on an Open Source foundation (Python 2 version)" +arch=('x86_64') +url="https://pymol.org/" +license=('custom') +depends=('freetype2' 'glew' 'glm' 'glut' 'python2-numpy' 'tcsh') +makedepends=('desktop-file-utils' 'gendesk' 'libmmtf' 'msgpack-c') +optdepends=('python2-pmw: pmw based UI' + 'python2-pyqt5: Qt5 based UI') +conflicts=('pymol') +provides=('pymol') +source=("https://github.com/schrodinger/pymol-open-source/archive/v${pkgver}.tar.gz" + ${_pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon" + "apbstools_tcltk8.6.patch") +sha512sums=('e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133' + '39917c1dc80cd6a59e8f6b3ea49a59491eaf23d14e32ac264f6d71f33007f686deb6a66e50e7f20ef9df5337038e3572b018633c361460d5ee0c1d8f0a8259d1' + '90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c') + +prepare() { + # create desktop file + gendesk -f -n --pkgname "${_pkgname}" --pkgdesc "${pkgdesc}" \ + --name="PyMOL Molecular Graphics System" \ + --categories="Science;Chemistry" + + # suppress non-zero exit code that breaks makepkg + sed -i '/sys.exit/ s,2,0,' "${srcdir}/${_pkgname}-open-source-${pkgver}/setup.py" + # change python to python2 + find "${_pkgname}-open-source-${pkgver}" -name '*.py' -type f -exec \ + sed -i 's|env python|env python2|g' {} \; + find "${_pkgname}-open-source-${pkgver}/test" -type f -exec \ + sed -i 's|bin/python|bin/python2|g' {} \; + # fix FS#39526 + cd "${srcdir}/${_pkgname}-open-source-${pkgver}" + patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch" +} + +build() { + cd "${srcdir}/${_pkgname}-open-source-${pkgver}" + python2 setup.py build +} + +package() { + cd "${srcdir}/${_pkgname}-open-source-${pkgver}" + python2 setup.py install --prefix=/usr --root="${pkgdir}" + install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${_pkgname}/LICENSE" + install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop" + install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png" +} diff --git a/apbstools_tcltk8.6.patch b/apbstools_tcltk8.6.patch new file mode 100644 index 000000000000..f60b5c78a69a --- /dev/null +++ b/apbstools_tcltk8.6.patch @@ -0,0 +1,106 @@ +--- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400 ++++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400 +@@ -612,7 +612,8 @@ + # Set up the Main page + page = self.notebook.add('Main') + group = Pmw.Group(page,tag_text='Main options') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + self.selection = Pmw.EntryField(group.interior(), + labelpos='w', + label_text='Selection to use: ', +@@ -856,7 +864,8 @@ + page.grid_columnconfigure(5,weight=1) + page = self.notebook.add('Program Locations') + group = Pmw.Group(page,tag_text='Locations') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + def quickFileValidation(s): + if s == '': return Pmw.PARTIAL + elif os.path.isfile(s): return Pmw.OK +@@ -955,7 +964,8 @@ + + page = self.notebook.add('Temp File Locations') + group = Pmw.Group(page,tag_text='Locations') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(), + labelpos = 'w', + label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename), +@@ -1003,17 +1013,20 @@ + page = self.notebook.add('Visualization (1)') + group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1) + self.visualization_group_1 = group +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + + page = self.notebook.add('Visualization (2)') + group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2) + self.visualization_group_2 = group +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + + # Create a couple of other empty pages + page = self.notebook.add('About') + group = Pmw.Group(page, tag_text='About PyMOL APBS Tools') +- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) ++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) + text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/). + + Documentation may be found at +@@ -2271,7 +2284,8 @@ + self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0) + self.update_buttonbox.pack(side=LEFT) + self.update_buttonbox.add('Update',command=self.refresh) +- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface') + self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0) +@@ -2322,7 +2336,8 @@ + bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high) + Pmw.alignlabels(bars) + for bar in bars: bar.pack(side=LEFT) +- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines') + self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0) +@@ -2337,7 +2352,8 @@ + text = """Follows same coloring as surface.""", + ) + label.pack() +- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) ++ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface') + self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0) +@@ -2356,7 +2372,8 @@ + entryfield_validate = {'validator' : 'real', 'min':0} + ) + self.pos_surf_val.pack(side=LEFT) +- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface') + self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0) +@@ -2375,7 +2392,8 @@ + entryfield_validate = {'validator' : 'real', 'max':0} + ) + self.neg_surf_val.pack(side=LEFT) +- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) ++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) + + + |