sci-chemistry/pdb2pqr: Version Bump

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

6 files changed, 260 insertions, 16 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 5bbf9582a6ba..c90d76e18459 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pdb2pqr
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.37 2012/10/19 10:10:18 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.38 2014/10/24 10:54:05 jlec Exp $
+
+*pdb2pqr-1.8.0 (24 Oct 2014)
+
+  24 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.8.0.ebuild,
+  +files/pdb2pqr-1.8.0-automagic.patch, +files/pdb2pqr-1.8.0-ldflags.patch,
+  metadata.xml:
+  Version Bump
 
   19 Oct 2012; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.5.0-r2.ebuild,
   pdb2pqr-1.7.0.ebuild, pdb2pqr-1.7.0-r2.ebuild:
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 9be28519f990..5f72adbef837 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,22 +1,37 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 1.7.0-install.patch 5165 SHA256 965c0bf8077eebc733c60d4e80d05167ce31d7188b01ca43c0fb5c0b27ede22b SHA512 72f290d8df7051f0fc2d42543f0d09fef4350656194f5013f132abb7edbe4dc11f18a3329bbd41b86f9a582b170fea53d472be320f5e08a2f0d84d42b4f4639c WHIRLPOOL ea71e6271c0dd491a7778cf3c0f54ebce79f35680abb49eadfbb6208379b1d5c69b18eacde92183bd005ffad26db115b05f69b7cbcf5256fa72d94caab9509c4
 AUX pdb2pqr-1.4.0-automagic.patch 3526 SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a SHA512 dfb5a219fabe4b57da82098c80eb6556e6826cd91d3db2da2e858964180cfe3268314562320159b82dc811a08714ca3a0e78881244949ff7ffeef2f797397237 WHIRLPOOL 03061ecbab813a572f18a794609655aa9ad9a16d6ed10c421437dddac589de750adacdfe2f89b17e022cccf0ffe0018a40bbe2e7f37c692d025f6998088364af
 AUX pdb2pqr-1.4.0-install.patch 5372 SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643 SHA512 615e984335d67668689423d4ab37be996cb178450a2ae0782432d47d7be2cfa8aaeb18776e604c706df743d2a30b93bc1febc28722ef7b5b2480545ca3ccd510 WHIRLPOOL c054c12d1c9ed4ad093326736fd74c6af54d7124ef6455120e5bf37a1a683cf1a5d1a9faec7ff323c7512c4bdbd53c703ee305daf6c76847e87aa2b9a58f7b59
 AUX pdb2pqr-1.4.0-ldflags.patch 1293 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726 SHA512 4edf74ae59b5ca99e2c492103d16769f300293df07f833d78d8e7d24d85c10531ac7907c5444b65507952f4622608459952ae57835f52af8b0f7e09637f1fcf5 WHIRLPOOL 359a84ecaa55cadfa7cf1bb3c116105c486f1fa737d74b6f2ba2f399147dfcd15d088682c75efee7a69394a3f7adf7dc0c978c060ad64c105b3e96a0b75f49d5
+AUX pdb2pqr-1.8.0-automagic.patch 2544 SHA256 135cfe03fc38a7bef028452010dedab3cc90c1f554cef1139b1d9836824520e9 SHA512 65dc03368909a9378ecda6c8357e9119bd76311b5fd6dc0ce00ff7d5b948190ad9f07ac3626dad04915928558f911f4deea5f44725e6cf029ca26dcb2e54b76c WHIRLPOOL 8462f3288722bcaca651845242b3354f365a9686a6400d3fae9c8ca69e3fa55d9282a62bdc2a3374eb468fbfae2611f8fa700ddecc404943c2a08080fad34b06
+AUX pdb2pqr-1.8.0-ldflags.patch 1098 SHA256 b9ab2740e062b130c4b61d385b762d4ce54ec3d6a040f37b8b501b4f107890b8 SHA512 0bd250efd74c70096011ed6f9f6fd2f22a987bbe0355f5ba33ad4675141d1d7b02e9eaa90bc1c7328454da2225183a56dae6acbaae97a929b2455430ca55ab4e WHIRLPOOL 75b4110d4259454551256c3a647b1981aa4ee040f73baf8f3e5ce1f0a4b01b54cdf2879030265dde4c7dbc0a5c60bd400a0d498f00446c88125d147c291ef107
 DIST pdb2pqr-1.5.tar.gz 5747178 SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
-DIST pdb2pqr-1.7.tar.gz 6906538 SHA256 8d27f2df430c40b99cde7952d0e96e72e433871a289d39c970b5eefe34345757
+DIST pdb2pqr-1.7.tar.gz 6906538 SHA256 8d27f2df430c40b99cde7952d0e96e72e433871a289d39c970b5eefe34345757 SHA512 64938ad08f2e86e0e1a121a2401aa599ffeecd313e5e69dd832e6b5afd698995aba3e96aec5e7c27c433d1429cbaa41d4bae1200e380fd2b954c08fbcd6a1484 WHIRLPOOL 5e937daa3a18c08988bc58167227c8143e7176ccb98cc041f7ec0138a0f991c94e38500bba5f196f4c1486085cb782017cdaa344ac5e8503a18087697ff2269d
+DIST pdb2pqr-1.8.tar.gz 6781507 SHA256 78470c21e5dc7afa12d782559b11d2cb04b755d93086bb80a43bd09fa0c3521f SHA512 3f640979d21511c4b08ab20c49f4662d959dddf67d9fedfb5e528d0869d897cd5770e77059b78a16c9778760593f410caf39eaaae2b664113af6875052873316 WHIRLPOOL bd582efba5544ec6450cf94e06f9449ba9d6a2861d64d0f88616302e3f93bf16332f210eecb01e268e2b1022bf6c5cbce3667b006b8e9345c9d18cebca373e74
 EBUILD pdb2pqr-1.5.0-r2.ebuild 3668 SHA256 09b59ed6461c60ca7fdcdca1604306579f054db992b1833226cce00566f05a7a SHA512 2d1ce04378e15d814dfc73d407149465e61b04d646710b918708e4f8eb1a6f1973c85cfca0d63dfa8f85aa6cf1e61b3a950c82833ff7853e2d6d3bc223890f6d WHIRLPOOL 3e4da41f599befa813ec693c8fd2b42ffda163047a43ecbe8f83a3fd63e1066a61e05e56993b2fa3fcc507e652ad60ad3aeca7c6fbb1e967edcc1ead362b943d
 EBUILD pdb2pqr-1.7.0-r2.ebuild 3859 SHA256 3c0213ade23aa4a13f9091ca96d69dc1c4f2eb2b80195759b1b4eb7b3ac5072e SHA512 61f4c29714a428fb956c7cb47c47c8a7d50d4796ef5dd406f88a9336494732d732cef13608fabfd055a78407eaf091fdc548e3c91a0e4547e55c7775e33e83ea WHIRLPOOL 34f203002dded65e8723b9220a310f183fdff28df8069aab1f6f464f6cc3a3a3c44f07fe6e51e043c9d2dcfc2cc98da2bed95eaf73ffc0645746f2640f56b8b7
 EBUILD pdb2pqr-1.7.0.ebuild 3661 SHA256 83a908824110516331cb4e7a8acce26c3992971af13d2514ca0345ab14d3b44f SHA512 f6a942958f120eeee05b9e70751cca487ba06c29a39127f65075936b41521575e089b8c764f53e06a2c286899d4fdf16be9eefc46c0e9942c03ac1c74803c093 WHIRLPOOL dc3c3292217517bb3503fd53313e055ccf008f556eea319b738f88fb82cbc18be1c76099a6dcde4cc32861b8ecf9362554a0039fae896aeacf802e0ae2b05eb4
-MISC ChangeLog 6095 SHA256 e998f25b6bb91374bf45431d917f99149d2bb38212c78613236fe8d8e37b1484 SHA512 9afe45616a6b86de1587ec308604dd85e3dec4c218fa005bf66e449264e9171a7811b0c5265fd745d54dc16a1011fff5d7efcf3df15145f161fa3d5e24375fad WHIRLPOOL f78a826c684f453361c907a9de9a977897128b3f00be6d420d57bcdd05fd0a09c1c7e1f7f4771b62da858dcc96897f51400d40cc4fe5252ca1e552701c59281d
-MISC metadata.xml 305 SHA256 5239d437369038113c15797a9a6074c6ed5e5577154dc8e992ac9634c54ab44b SHA512 5ceb5e50bca1c93dc950f7cdb8f1d5c7bcbe69ae76759f679975aece71c137acbc758559ae301b07f29f909021844ca018b22e598469609c9c7ad87df41d17f2 WHIRLPOOL 879ac374f6da57e20ab483a06219f92e5f670dbd9807dba90ca5103358a70d477c7ee78cab0fd3827b5827523fc5e47aafad25d964846f38a0739b16421421eb
+EBUILD pdb2pqr-1.8.0.ebuild 2608 SHA256 4fbfefc6bcd292e9b37912f6533c471cd9db40c0417c47a9b749c9f003d83a41 SHA512 a2ec007a28d14e4ae0da7eddc088bdfba5e89b1166677be22b7d68f7e3ebfdcec24c82ddc24098012df5dccc610aa79af3abdae681682044656a2e108b5a760a WHIRLPOOL c0638e7d6744851e0630510bb52db88b7c6f74d4c427b473fd86500d9e08146000a2743a92ec7c32a836d1ed4a54f69f618831c1ba30e6b0b0296a71f4f3c500
+MISC ChangeLog 6303 SHA256 f3265e38f7165e029ff5cd0b2ec25bd5d1cdbb551f9f5ec62dd97c94e2ce0bdf SHA512 a6937557c3965cae7c411371c74a947bb0f37fd4ca53aa0ad67f58031a430e5bad466b26da7d9c07d8f12b82afa40a60ecb35b87887cff8c4ffab23c9a810a55 WHIRLPOOL e9f425fc2037dd387b6c7e4c0738fcd2274671ba9b2840b2845ec944fb47723519fbb0b234e25158065842bfc9aab4c7e5e7e53658c4761aef60e0134678b196
+MISC metadata.xml 312 SHA256 8429f63a843f77336614a26f2dea0611353036db4a73026665c69fe09269f109 SHA512 50808ebe11a46f56e2a1fe043274e3dc04e681044dc68762df143cf94df9f2e95c8f5eee201be100479d363dde91ea1f6b7e8138b238f143c4743659b9643e4c WHIRLPOOL 735e2ebaee7b1d623695e6b3b60fe92b16be8264bf6d8a4f2b7b24c43ae49048ded02af0fa8a2e58e8f9ac4374831d708438168835f1908403f5c31f27cb9423
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.19 (GNU/Linux)
-Comment: GPGTools - http://gpgtools.org
+Version: GnuPG v2.0
 
-iEYEAREIAAYFAlCBJwsACgkQgAnW8HDreRaEOwCgt3pM84XAItYI3Q5RIt+nDUg0
-fnEAoMXM2MnaTUgzjXPXP9q0NP/IF8Q8
-=ziCl
+iQJ8BAEBCgBmBQJUSi/OXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w
+ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC
+OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirbCkP/0hbbRvcdZNetJa0GR1/XoWY
+O8aXioleyiZ8jv3oQern/aeUYPkuG9hUZWKBtozwKRUMVYTWcYVorw96Y/khTtbg
+JAfkigjKnFeil237S8BNnj6DtUT/m2n7KT/qpn9bsq2SHJDY7id49N5WEN4UnOd2
+nnSPS8yIg5ds34yfZhmin6jclZHxXfeae7Ibb3SWO0P339W5wlld4lKcN9fzCB84
+IbYhhvmKMfl2iR+xqs6+My94J0UjU7KmMC8x28qMegbGx1VITgn9pRd3CMfiDyAk
+yPJKSVxvZkbuare2EjgqQOt/u02DSD+Ja1ITk/ngOdcVQMPiRrnVN4RyEXAGIPwy
+xqG31kQ7yKw6Psuqm7TggM/NU4Jv4QR8iQzG+5EhQHwUtfENPL0EMJSL+3MYrJ10
+yfoZeg+5BOitqOZEhmJcAB+motP+TiUcLlI/+NS8ICz3peb5XSO8UQkzqITdvFE9
+N2RtNybqJ8uGDcSuGT6jq22eun6zIDXuhxdv8DusHb8DLtmto3iIHGNCZ9YoAXXV
+yCchuDwNOwpmyzGE5+8sRJAnNNaFyBKXRix/N+3wYmt84HjtuA7ILHmJXLkPgrlb
+muLHXCrT8xnSKGPotmIkIYI94wREpUONzoR44j3UbR6B/IXTkoSjBR7yDCVXpZzw
++Y6oAi9E+aGV870wXPZe
+=zWMN
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
new file mode 100644
index 000000000000..c218fe6a816e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
@@ -0,0 +1,75 @@
+diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
+--- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
++++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
+@@ -255,38 +255,6 @@
+ 
+   # Test for Numeric install
+   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
+-  if (test -n "${NUMERIC}") ; then
+-    AC_MSG_RESULT([yes])
+-    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
+-    if test "$NUMERIC_INC" = ""; then
+-      AC_MSG_ERROR([Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}])
+-    fi
+-    NUMERIC_INC=`dirname ${NUMERIC_INC}`
+-    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
+-    if test "${NUMERIC_LIB}" = ""; then
+-      AC_MSG_ERROR([Please check your NUMERIC path.  Numeric.pth cannot be found in ${NUMERIC}])
+-    fi
+-    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
+-    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
+-    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
+-    if test "${PACKAGE_PATH}" = ""; then
+-      PACKAGE_PATH=${NUMERIC_LIB}
+-    else
+-      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
+-    fi
+-    PY_NUMERIC="-I${NUMERIC_INC} "
+-    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
+-  else
+-    AC_MSG_RESULT([no])	
+-    AC_MSG_CHECKING([for Numeric include files])
+-    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
+-      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"   
+-      AC_MSG_RESULT([$PY_NUMERIC])
+-      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
+-    else
+-      AC_MSG_RESULT([no])
+-    fi
+-  fi
+ 
+   # If failed, test for numpy
+   AC_MSG_CHECKING([whether you defined numpy])
+@@ -457,29 +425,14 @@
+   HAVE_PDB2PQR_OPAL=1
+ fi
+ 
+-if test "$PDB2PQR_OPAL_URL" != ""; then 
++if test "$PDB2PQR_OPAL_URL" != "no"; then 
+   HAVE_PDB2PQR_OPAL=1
+   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
+     echo ZSI is installed
+   else
+     #  need to install ZSI
+-    echo Installing ZSI.  This might take a while...
+-    cd contrib/ZSI-2.1-a1 
+-    if test `whoami` = "root"; then
+-      $py_path setup.py install
+-    else
+-      zsi_install="true"
+-      mkdir -p ${prefix}lib/python$PY_VERSION/site-packages
+-      export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages
+-      $py_path setup.py install --prefix=${prefix}
+-      if test -d ${prefix}ZSI ; then
+-        echo ZSI is installed
+-      else
+-        cp -r ./build/lib/ZSI ${prefix}ZSI
+-      fi
+-      PYTHONPATH=""
+-    fi 
+-    cd ../..
++    echo Missing ZSI
++    exit 1
+   fi
+ fi  
+ 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
new file mode 100644
index 000000000000..5a7e04419ce6
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
@@ -0,0 +1,30 @@
+ pdb2pka/Makefile.am           | 2 +-
+ pdb2pka/substruct/Makefile.am | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am
+index 75f6ffd..e40a2f6 100644
+--- a/pdb2pka/Makefile.am
++++ b/pdb2pka/Makefile.am
+@@ -16,7 +16,7 @@ SUBDIRS          = substruct
+ 
+ noinst_PROGRAMS         = _pMC_mult.so
+ _pMC_mult_so_SOURCES     = pMC_mult.cpp pMC_mult_wrap.cpp  
+-_pMC_mult_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
++_pMC_mult_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
+ _pMC_mult_so_LDADD       = $(PY_LDFLAGS)
+ 
+ #all:
+diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am
+index b1638a0..ae95e94 100644
+--- a/pdb2pka/substruct/Makefile.am
++++ b/pdb2pka/substruct/Makefile.am
+@@ -15,7 +15,7 @@ CLEANFILES       = Algorithms.so
+ 
+ noinst_PROGRAMS          = Algorithms.so
+ Algorithms_so_SOURCES     = Algorithms.cpp  
+-Algorithms_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
++Algorithms_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
+ Algorithms_so_LDADD       = $(PY_LDFLAGS)
+ 
+ distclean-local: clean-local
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
index 678d75f1cf5a..efc939161a8f 100644
--- a/sci-chemistry/pdb2pqr/metadata.xml
+++ b/sci-chemistry/pdb2pqr/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<use>
-		<flag name="opal">Add web interface via opal</flag>
-		<flag name="pdb2pka">Install experimental pdb2pka interface</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <use>
+    <flag name="opal">Add web interface via opal</flag>
+    <flag name="pdb2pka">Install experimental pdb2pka interface</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild
new file mode 100644
index 000000000000..39f2cbef012f
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild,v 1.1 2014/10/24 10:54:05 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools eutils fortran-2 flag-o-matic python-r1 toolchain-funcs versionator
+
+MY_PV=$(get_version_component_range 1-2)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+LICENSE="BSD"
+HOMEPAGE="http://www.poissonboltzmann.org/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal +pdb2pka"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	dev-python/numpy
+	sci-chemistry/openbabel
+	opal? ( dev-python/zsi )
+	pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
+DEPEND="${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 ${MAXATOMS} during calculations"
+	fi
+	fortran-2_pkg_setup
+	python_export_best
+}
+
+src_prepare() {
+	rm -rf contrib/* || die
+	epatch \
+		"${FILESDIR}"/${P}-ldflags.patch \
+		"${FILESDIR}"/${PN}-1.4.0-automagic.patch \
+		"${FILESDIR}"/1.7.0-install.patch
+	sed \
+		-e '50,200s:CWD:DESTDIR:g' \
+		-i Makefile.am || die
+
+	eautoreconf
+
+	tc-export CC
+}
+
+src_configure() {
+	# we need to compile the *.so as pic
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+	econf \
+		--with-max-atoms=${MAXATOMS:-10000} \
+		$(usex pdb2pka "" --disable-pdb2pka) \
+		$(use_with opal) \
+		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
+		F77="$(tc-getFC)"
+}
+
+src_compile() {
+	default
+	if use doc; then
+		pushd doc > /dev/null
+		sh genpydoc.sh || die "genpydoc failed"
+		popd > /dev/null
+	fi
+}
+
+src_test() {
+	emake -j1 test
+}
+
+src_install() {
+	local lib
+	dodir $(python_get_sitedir)/${PN}
+	emake -j1 \
+		DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
+		PREFIX="" install
+		INPATH="$(python_get_sitedir)/${PN}"
+
+	python_newscript "${ED}"/$(python_get_sitedir)/${PN}/${PN}.py ${PN}
+	python_newscript "${ED}"/$(python_get_sitedir)/${PN}/pdb2pka/pka.py pdb2pka
+
+	for lib in _apbs.so apbslib.py{,c,o}; do
+		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
+	done
+
+	if use doc; then
+		pushd doc > /dev/null
+		dohtml -r *.html images pydoc
+		popd > /dev/null
+	fi
+
+	use examples && \
+		insinto /usr/share/${PN}/ && \
+		doins -r examples
+
+	dodoc ChangeLog NEWS README AUTHORS
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}