7 files changed, 0 insertions, 216 deletions
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
deleted file mode 100644
index 0663d5136267..000000000000
--- a/sci-chemistry/pdb2pqr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka
deleted file mode 100644
index 2406b0c4773f..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pka
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr
deleted file mode 100644
index 8c0635aea94e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
deleted file mode 100644
index fac32b233e6b..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- pdb2pka/SConscript           | 9 ++++++++-
- pdb2pka/substruct/SConscript | 6 ++++++
- 2 files changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
-index 583cdc5..6c30011 100644
---- a/pdb2pka/SConscript
-+++ b/pdb2pka/SConscript
-@@ -1,4 +1,11 @@
- Import('env')
-+import os
-+
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
- 
- if env['REBUILD_SWIG']:
-     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
-@@ -9,4 +16,4 @@ Default(pyc)
-     
- algorithms_module = SConscript('substruct/SConscript')
- 
--Return('pyc algorithms_module')
-\ No newline at end of file
-+Return('pyc algorithms_module')
-diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
-index 7dbcdb0..56fb577 100644
---- a/pdb2pka/substruct/SConscript
-+++ b/pdb2pka/substruct/SConscript
-@@ -1,7 +1,13 @@
- import distutils
- import numpy
-+import os
- Import('env')
- 
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
- env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
- 
- algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
deleted file mode 100644
index 2695b013c66a..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- SConscript-install.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/SConscript-install.py b/SConscript-install.py
-index e2f9f09..1fdf1a8 100644
---- a/SConscript-install.py
-+++ b/SConscript-install.py
-@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'):
- 		if GetOption("clean"):
- 			env.Default(result)
- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))
-+		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
- 	else:
- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
- 
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
deleted file mode 100644
index 36fd8c04ac52..000000000000
--- a/sci-chemistry/pdb2pqr/metadata.xml
+++ /dev/null
@@ -1,15 +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>
-  <use>
-    <flag name="opal">Add web interface via opal</flag>
-    <flag name="pdb2pka">Install experimental pdb2pka interface</flag>
-  </use>
-  <upstream>
-    <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
deleted file mode 100644
index 179e6448d605..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
+++ /dev/null
@@ -1,114 +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 scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-HOMEPAGE="https://www.poissonboltzmann.org/"
-SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-		sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
-		opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
-	')
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}
-	dev-lang/swig:0"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-flags.patch
-	"${FILESDIR}"/${P}-install-py.patch
-)
-
-pkg_setup() {
-	if [[ -z ${MAXATOMS} ]]; then
-		einfo "If you like to have support for more then 10000 atoms,"
-		einfo "export MAXATOMS=\"your value\""
-		export MAXATOMS=10000
-	else
-		einfo "Allow usage of ${MAXATOMS} during calculations"
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
-
-	export CXXFLAGS="${CXXFLAGS}"
-	export LDFLAGS="${LDFLAGS}"
-
-	epatch "${PATCHES[@]}"
-	tc-export CXX
-	rm -rf scons || die
-}
-
-src_configure() {
-	cat > build_config.py <<- EOF
-		PREFIX="${D}/$(python_get_sitedir)/${PN}"
-		#URL="http://<COMPUTER NAME>/pdb2pqr/"
-		APBS="${EPREFIX}/usr/bin/apbs"
-		#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
-		#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
-		MAX_ATOMS=${MAXATOMS}
-		BUILD_PDB2PKA=$(usex pdb2pka True False)
-		REBUILD_SWIG=True
-	EOF
-}
-
-src_compile() {
-	escons
-}
-
-src_test() {
-	local myesconsargs=( -j1 )
-	escons test
-	escons advtest
-	escons complete-test
-}
-
-src_install() {
-	dodir /usr/share/doc/${PF}/html
-	local lib
-
-	escons install
-
-	find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
-
-	python_doscript "${FILESDIR}"/{${PN},pdb2pka}
-
-	for lib in apbslib.py{,c,o}; do
-		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-	done
-	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-	python_optimize
-
-	if use doc; then
-		pushd doc > /dev/null
-		docinto html
-		dodoc -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodoc *md NEWS
-}