11 files changed, 0 insertions, 444 deletions
diff --git a/sci-chemistry/hollow/Manifest b/sci-chemistry/hollow/Manifest
deleted file mode 100644
index 9c9dec2ce5a3..000000000000
--- a/sci-chemistry/hollow/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST hollow-1.2.zip 62554 BLAKE2B 825ebbd5b9085d47be3487331ecabf80a6af73eda4525e1d073eea05b5fb0c1892b115f669c8ce3227bfb573f266d1a0225c7aaeee844338496bceb55d88edd6 SHA512 e253680cc0fae286ec697b2dac822b9e165d509cc7eefb27bbcafae6ab2617c3edc8cd9c8beefcc9ef2eb920c9d839fd0bc25f79d22160d857b1705cefbc05ca
diff --git a/sci-chemistry/hollow/hollow-1.2-r1.ebuild b/sci-chemistry/hollow/hollow-1.2-r1.ebuild
deleted file mode 100644
index d1db2c19db3f..000000000000
--- a/sci-chemistry/hollow/hollow-1.2-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1 vcs-clean
-
-DESCRIPTION="Production of surface images of proteins"
-HOMEPAGE="http://hollow.sourceforge.net/"
-#SRC_URI="mirror://sourceforge/${P}.zip"
-SRC_URI="http://hollow.sourceforge.net/${P}.zip"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-3"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND="${PYTHON_DEPS}
-	app-arch/unzip"
-
-src_install() {
-	python_setup
-	esvn_clean
-	python_foreach_impl python_domodule pdbstruct
-	python_moduleinto ${PN}
-	python_foreach_impl python_domodule *.py hollow.txt
-
-	python_foreach_impl python_newscript ${PN}.py ${PN}
-
-	dodoc README
-	python_optimize
-}
diff --git a/sci-chemistry/hollow/metadata.xml b/sci-chemistry/hollow/metadata.xml
deleted file mode 100644
index 266ef9d56913..000000000000
--- a/sci-chemistry/hollow/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
-  <upstream>
-    <remote-id type="sourceforge">hollow</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
deleted file mode 100644
index 69e1780c97f5..000000000000
--- a/sci-chemistry/modeller/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST modeller-9.20.tar.gz 34909796 BLAKE2B d89c81823c4d7784a7b3d64fdb01158a973edc7d8b316c773e038ba8645797c543d5bc58c1bff5462ae5975a6c2796f4b2d500641d226c3b2281cf794cfeba8d SHA512 667edeeda0a9038258f6932b3cef22a1e9d0fe47f47bd2ac612e7bac7f23a863f5a65cfd93abfa405310e7fb7b305d53e71d6c6e930613b0dbd43b24dcd5919a
-DIST modeller-9.22.tar.gz 34953371 BLAKE2B 3bf8828b38f22955dea973cfe54cbd2f77bf021900bd5aa3c75f083b12e2a7199c3173de526acfeab005c0606816bac347b9bdfb6b62d5e3db9c9e18fed99ac4 SHA512 0056f09a07d6e2b565c8f4accca48ad176c9d32634b75bc4db60a187d56f22ef1710296dfd31bf27f496c5ed100146420be7cfdb135ca8b2b0fac7d7f5fa877f
diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
deleted file mode 100644
index da36ecbfcd6a..000000000000
--- a/sci-chemistry/modeller/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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>
-</pkgmetadata>
diff --git a/sci-chemistry/modeller/modeller-9.20.ebuild b/sci-chemistry/modeller/modeller-9.20.ebuild
deleted file mode 100644
index 641395067b0d..000000000000
--- a/sci-chemistry/modeller/modeller-9.20.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib versionator
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="https://salilab.org/modeller/"
-SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all() {
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all() {
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/modeller/modeller-9.22.ebuild b/sci-chemistry/modeller/modeller-9.22.ebuild
deleted file mode 100644
index 2bc08bd43d4e..000000000000
--- a/sci-chemistry/modeller/modeller-9.22.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="https://salilab.org/modeller/"
-SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all() {
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all() {
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest
deleted file mode 100644
index 3e5c1d3ef747..000000000000
--- a/sci-chemistry/pymol-plugins-msms/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-plugins-msms-100415.py 62320 BLAKE2B 2778221bd0138764b9f0b75202de8bc46d71005b26d0e23faba582d5f49fc0c3edca04d0ffcddf8f3be541a2142b739afe8a2904912a29d2443d9e6974f453a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489
diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
deleted file mode 100644
index 0d26fb31c5f1..000000000000
--- a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch
+++ /dev/null
@@ -1,33 +0,0 @@
- 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
deleted file mode 100644
index 214696c4a1f7..000000000000
--- a/sci-chemistry/pymol-plugins-msms/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?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
deleted file mode 100644
index 33c7dbf9be7d..000000000000
--- a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# 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
-}