reinit the tree, so we can have metadata

4 files changed, 99 insertions, 0 deletions

diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest
new file mode 100644
index 000000000000..55aa0fb759c1
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/Manifest
@@ -0,0 +1,6 @@
+AUX 100415-msms.patch 1687 SHA256 50509fe85feb3e12d35d0a1aba8fe2edef5dc557d06617bb1fcaaff7dae3938a SHA512 52410d467c314578cd22e777ae45a0012203fd21d2afa6ff329fa67db6d7ee2cb381558ce6aef48a1305a572f9218cf962ab1fc552ebe1873f94a4d6d2db1bcf WHIRLPOOL e3dfc92ea73765e9a236ded4ceaa9d7b7f84b0a554e0b87a328b8f5ad1a703a024d02ed847d7d2ba2eaed38ae3f42bbe562f036b23cd2446d72f02ee5eb20b0d
+DIST pymol-plugins-msms-100415.py 62320 SHA256 1452acdcf8b13f5af22da563d44d51aca9f8fdd108dd7a0548ec41941cb463a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489 WHIRLPOOL c5889b3543ac554083b76c38bb53fad1f001bd46f6686b0cdc36c1a7e576de3dc9a9bba0b459e0d928e30aec21ab09b98a0a8eb128fa64fc5b4228ca9ad7c0e4
+EBUILD pymol-plugins-msms-100415-r1.ebuild 1045 SHA256 eb8cf86edd1fd93d666770c9488123b73b23bc277b0e5f99ffb14920b1564fd5 SHA512 20799591eee520158f5872748c58b5280ec2fa0c0292fc1f069f823b20b6c4134a5b82ac57f884ecd2f8da3add00034ecc961463eada3e503a07246b823c084b WHIRLPOOL f82ddd2befc51b2918edda8f5159f0af95a119682ae9281c5012d9b94f0ae39290625ee4a91913e51b64c17a6d0918dad2a64849fe609e1009f41d12977034dc
+MISC ChangeLog 3077 SHA256 d5d21ab17ea4fb7edc7d0cd473374bca2b2bc0b9828e0e7cb259a36592370fe7 SHA512 ab0d687b9dca24a4a4e32168fa5cea4d3adf15a8cc4d0e6192bbd8053c8a81a034b454bb2fe9ec1369f6f93ea7b5bdb509a68f9607ae57d673bdf3e5cc99de31 WHIRLPOOL 9eac2336e2cc25268b1e52ab42927efb0a28085ee23ad0b6940931109bb0d88c2d48ecf649dc0a9d1e838e09dadea1ad9b9cfa5956929acde3e7fec888c4154a
+MISC ChangeLog-2015 698 SHA256 a71a1b2f16845ce359ccab70e91abdf659fa82338c9340c518e584556ed9cedf SHA512 5bc4cc7d0269560998c3ab1f0e4883075f76b1046ffbf99bba6d5bde26fe36bef4cb49543cb386acc208ff239504e9a59e697cef9e859b7e217e3666b672d65b WHIRLPOOL 72251bb83ccf1d2ec3e899ac4a3b4daf4c21c4623f29f1bb728a23069048b7f2881def5f530da477499ffdac391b2300091844298aad10854fff23d5d4c2ab58
+MISC metadata.xml 705 SHA256 76b53706caf15631163debdc5f1b608ee89d7ac72ad4f6ddd1f8cd6cf55c63eb SHA512 e33e7c380ff1f99f62fc75871dd3f3d0bc98bd3629a5e46c9dcae83ad039f88450d83b46379a6da88636795fb8e7c73c72480c4054a64dedd9c6bb0b501cf210 WHIRLPOOL a0c94989bfc5ac3af677d47e96a9b2a1ec915d9a08160d7c170e359783b51b0519c33410798ad7d97ce60c8ecb82047b34970af6085a8fdf485bf6665ffeb73c
diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
new file mode 100644
index 000000000000..0d26fb31c5f1
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
@@ -0,0 +1,33 @@
+ pymol-plugins-msms-100415.py |   18 ++++++++++--------
+ 1 files changed, 10 insertions(+), 8 deletions(-)
+
+diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py
+index 725934d..7ea00bf 100644
+--- a/pymol-plugins-msms-100415.py
++++ b/pymol-plugins-msms-100415.py
+@@ -99,15 +99,17 @@ class MSMSPlugin:
+         self.cleanup_saved_pymol_sel.set(True) # by default, clean up
+ 
+         self.pdb_fn.set('')
+-        if 'MSMS_BIN' in os.environ:
+-            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
+-            self.msms_bin.set(os.environ['MSMS_BIN'])
+-        else:
+-            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
+-            self.msms_bin.set('')
++        self.msms_bin.set('GENTOOMSMS')
++##        if 'MSMS_BIN' in os.environ:
++##            if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN']
++##            self.msms_bin.set(os.environ['MSMS_BIN'])
++##        else:
++##            if VERBOSE: print 'MSMS_BIN not found in environmental variables.'
++##            self.msms_bin.set('')
+ ##         self.pdb2xyzr_bin.set('')
+-        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
+-        else:                          self.pdb2xyzrn_bin.set('')
++        self.pdb2xyzrn_bin.set('GENTOOXYZRN')
++##        if 'PDB2XYZRN' in os.environ:  self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN'])
++##        else:                          self.pdb2xyzrn_bin.set('')
+         self.tmp_dir.set('/tmp')
+         self.cleanup_msms_output = Tkinter.BooleanVar()
+         self.cleanup_msms_output.set(True) # by default, clean up msms output
diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml
new file mode 100644
index 000000000000..214696c4a1f7
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <longdescription>
+MSMS is an excellent tool for computing protein solvent excluded surface (SES).
+MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and 
+displaying its results in PyMOL. 
+
+1. Citation for this plugin: 
+    Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden.
+2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild
new file mode 100644
index 000000000000..33c7dbf9be7d
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils python-r1
+
+DESCRIPTION="GUI for MSMS and displaying its results in PyMOL"
+HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html"
+SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="BSD pymol"
+IUSE=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	sci-chemistry/msms-bin
+	sci-chemistry/pymol[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	mkdir "${S}" || die
+	cp "${DISTDIR}"/${A} "${S}/" || die
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-msms.patch
+	sed \
+		-e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \
+		-e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \
+		-i ${A} || die
+}
+
+src_install() {
+	python_moduleinto pmg_tk/startup
+	python_foreach_impl python_domodule ${P}.py
+	python_foreach_impl python_optimize
+}