blob: 85b3f6e4b19fbe5bfe497144f7233b7efa35125c (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
|
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild,v 1.1 2012/05/11 07:42:54 jlec Exp $
EAPI=4
PYTHON_DEPEND="2:2.5"
SUPPORT_PYTHON_ABIS="1"
PYTHON_EXPORT_PHASE_FUNCTIONS="1"
RESTRICT_PYTHON_ABIS="2.4 3.* 2.7-pypy-*"
inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator
MY_PV=$(get_version_component_range 1-2)
MY_P="${PN}-${MY_PV}"
DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
LICENSE="BSD"
HOMEPAGE="http://pdb2pqr.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
SLOT="0"
IUSE="doc examples opal +pdb2pka"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
virtual/fortran
dev-python/numpy
sci-chemistry/openbabel
opal? ( dev-python/zsi )
pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
DEPEND="${RDEPEND}"
S="${WORKDIR}/${MY_P}"
pkg_setup() {
if [[ -z ${MAXATOMS} ]]; then
einfo "If you like to have support for more then 10000 atoms,"
einfo "export MAXATOMS=\"your value\""
else
einfo "Allow usage of ${MAXATOMS} during calculations"
fi
python_pkg_setup
}
src_prepare() {
epatch \
"${FILESDIR}"/${PN}-1.4.0-ldflags.patch \
"${FILESDIR}"/${PN}-1.4.0-automagic.patch \
"${FILESDIR}"/${PV}-install.patch
sed \
-e '50,200s:CWD:DESTDIR:g' \
-i Makefile.am || die
python_src_prepare
preparation() {
sed \
-e "s:python\$PY_VERSION:$(PYTHON):g" \
-i configure.ac || die
eautoreconf
}
python_execute_function -s preparation
tc-export CC
}
src_configure() {
# we need to compile the *.so as pic
append-flags -fPIC
FFLAGS="${FFLAGS} -fPIC"
configuration() {
# Avoid automagic to numeric
econf \
--enable-propka \
--with-max-atoms=${MAXATOMS:-10000} \
$(use_enable pdb2pka) \
$(use_with opal) \
NUMPY="${EPREFIX}/$(python_get_sitedir)" \
F77="$(tc-getFC)"
}
python_execute_function -s configuration
}
src_compile() {
python_execute_function -d -s
}
src_test() {
testing() {
emake -j1 test
}
python_execute_function -s testing
}
src_install() {
installation() {
dodir $(python_get_sitedir)/${PN}
emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
PREFIX="" install
INPATH="$(python_get_sitedir)/${PN}"
# generate pdb2pqr wrapper
cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
#!/bin/sh
$(PYTHON) ${EPREFIX}${INPATH}/${PN}.py \$*
EOF
cat >> "${T}"/pdb2pka-$(python_get_version) <<-EOF
#!/bin/sh
$(PYTHON) ${EPREFIX}${INPATH}/pdb2pka/pka.py \$*
EOF
dobin "${T}"/{${PN},pdb2pka}-$(python_get_version)
insinto "${INPATH}" && doins __init__.py
exeinto "${INPATH}" && doexe ${PN}.py
insinto "${INPATH}"/dat && doins dat/*
exeinto "${INPATH}"/extensions && doexe extensions/*
insinto "${INPATH}"/src && doins src/*.py
exeinto "${INPATH}"/propka && doexe propka/_propkalib.so
insinto "${INPATH}"/propka && doins propka/propkalib.py propka/__init__.py
insinto "${INPATH}"/pdb2pka && doins pdb2pka/*.{py,so,DAT,h}
dosym ../../apbs/_apbs.so "${INPATH}"/pdb2pka/_apbslib.so
dosym ../../apbs/apbslib.py "${INPATH}"/pdb2pka/apbslib.py
dosym ../../apbs/apbslib.pyc "${INPATH}"/pdb2pka/apbslib.pyc
dosym ../../apbs/apbslib.pyo "${INPATH}"/pdb2pka/apbslib.pyo
}
python_execute_function -s installation
dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
dosym pdb2pka-$(python_get_version -f) /usr/bin/pdb2pka
if use doc; then
pushd doc > /dev/null
sh genpydoc.sh || die "genpydoc failed"
dohtml -r *.html images pydoc
popd > /dev/null
fi
use examples && \
insinto /usr/share/${PN}/ && \
doins -r examples
dodoc ChangeLog NEWS README AUTHORS
}
pkg_postinst() {
python_mod_optimize ${PN}
}
pkg_postrm() {
python_mod_cleanup ${PN}
}
|
GitWeb