sci-chemistry/pdb-extract-3.004.ebuild added for testing

pending bug is 249933

8 files changed, 427 insertions, 0 deletions

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
new file mode 100644
index 000000000..7d6ff02f7
--- /dev/null
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -0,0 +1,53 @@
+# ChangeLog for sci-chemistry/pdb-extract
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  26 Jan 2009; justin Lecher (jlec) <jlec@j-schmitz.net>
+  +sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch,
+  +sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch,
+  +sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch,
+  +sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch,
+  +sci-chemistry/pdb-extract/metadata.xml:
+  bump to 3.004 
+  See bug 249933 Thanks to jlec
+
+  02 Jul 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  pdb-extract-1.700.ebuild:
+  die on failure to install files.
+
+  08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  pdb-extract-1.700.ebuild:
+  Keyword ~amd64, fix quoting.
+
+  15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org>
+  pdb-extract-1.700.ebuild:
+  QA: Removed illegal use of ${ROOT}. Bug #168043
+
+  26 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  pdb-extract-1.700.ebuild:
+  Stable on x86/ppc.
+
+  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  (#148281) Change herd to sci-chemistry from sci.
+
+  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Remove myself as maintainer, anyone feel free to work on this, although I'll
+  continue to do so as well.
+
+  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Update to my new email address.
+
+  26 Apr 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  pdb-extract-1.700.ebuild:
+  Keyword ~ppc.
+
+  24 Apr 2006; Donnie Berkholz <dberkholz@gentoo.org>; ChangeLog:
+  Keyword ~ppc.
+
+*pdb-extract-1.700 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/respect-cflags-and-fix-install.patch, +metadata.xml,
+  +pdb-extract-1.700.ebuild:
+  Extract lots of information from Protein Data Bank files.
+
diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest
new file mode 100644
index 000000000..3b50fb7cd
--- /dev/null
+++ b/sci-chemistry/pdb-extract/Manifest
@@ -0,0 +1,8 @@
+AUX pdb-extract-3.004-Makefile.patch 1506 RMD160 0462c70948aa2f87f519b33e91f4cc14104ccfad SHA1 1f9a951d0d41a368430d39acd0bac8e293fbb554 SHA256 6f7c4d1c60b33a9c1d13e49d30973d67291a2e005012f0379c20ab8e5dea8bb1
+AUX pdb-extract-3.004-env.patch 501 RMD160 6698680915a9e585f7a8c4d266f5c644e3229ce0 SHA1 ccc2371360fb6da39a6370132764ee97952387b1 SHA256 ccba5db2e3e6eb18465c62b795635ea4ecfbd6695f36376bc298132f986dd8ff
+AUX pdb-extract-3.004-gcc-4.3.patch 573 RMD160 a9d563b1834bf6293568793a1895026f5b5b9d39 SHA1 bc726c4461ead9faae1694eff53603726d53d91a SHA256 e92f42fb84198e8b543edc364565804f61fbb440da03103506bcb6e6848750ed
+AUX respect-cflags-and-fix-install.patch 7017 RMD160 f3c679e8de9af6878da91fa494b9ee3e2e79ccf8 SHA1 f0086bdb2c272e905bfb62fc687366a1905ace2d SHA256 e6043ac190f3a0a290983958bbea88cf5bda482bf40da886945a493df581e7b6
+DIST pdb-extract-v3.004-prod-src.tar.gz 942450 RMD160 3d5d46e668a52109678fdf59afbe664dac1643f9 SHA1 7b5d7ce200d33e68fa352cd3658e382bc37e9768 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953
+EBUILD pdb-extract-3.004.ebuild 1878 RMD160 deb341a5755252bf36a8a34bb56c1df1d61bbfdf SHA1 be5112ea8d7fd5b1f1caab03d852dc6607988451 SHA256 fee90e0e7b23dccf1e11d1bec409d70e002bcc31d7116c1040d42529e4e90680
+MISC ChangeLog 1847 RMD160 62cc1539a8ce703b0d72c54349bedaabb59546c5 SHA1 ed9e4ef9c0283410260a85ada79f33a70ad056c1 SHA256 078fb9c69f1dec288f9a623b4c74689e165e06318da8377263763c00b2e0d27a
+MISC metadata.xml 411 RMD160 eb4983e35d99c3ef60ee12c190d2b009c7b1809b SHA1 807b3fe3561c3f7d887cfd42fd941bfe5a0646e4 SHA256 669a67672dba2577f1c0056d08e1070ac50a5564bb5376c7f44b68318ae5e04f
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
new file mode 100644
index 000000000..6e3ed5e14
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
@@ -0,0 +1,46 @@
+--- Makefile	2008-12-05 14:36:44.000000000 +0100
++++ Makefile.new	2008-12-05 14:37:21.000000000 +0100
+@@ -19,13 +19,7 @@
+ CHECKOUT_SCRIPT_MODULE = util
+ CHECKOUT_SCRIPT = checkout.sh
+ 
+-LIBDIRS =  cifobj-common-v4.1 \
+-           tables-v8.0 \
+-           regex-v2.2 \
+-           cif-file-v1.0 \
+-           misclib-v2.2 \
+-           cifparse-obj-v7.0 \
+-           $(EXTRACT)
++LIBDIRS =  $(EXTRACT)
+ 
+ all:	compile
+ 
+--- pdb-extract-v3.0/Makefile	2008-12-05 14:42:58.000000000 +0100
++++ pdb-extract-v3.0/Makefile.new	2008-12-05 14:42:15.510315392 +0100
+@@ -6,6 +6,7 @@
+ 
+ M_INCL_DIR = ../include
+ M_LIB_DIR  = ../lib
++M_LIB_DIR_GENTOO = /usr/GENTOOLIBDIR
+ M_BIN_DIR  = ../bin
+ 
+ PROJ_DIR   = .
+@@ -37,12 +38,12 @@
+ include ../etc/Makefile.platform
+ 
+ # Dependent libraries for the pdbml-parser
+-CIF_FILE_LIB      = $(M_LIB_DIR)/cif-file.a
+-CIFPARSE_LIB      = $(M_LIB_DIR)/cifparse-obj.a
+-CIF_TABLE_LIB     = $(M_LIB_DIR)/cif-table-obj.a
+-CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a
+-REGEX_LIB         = $(M_LIB_DIR)/regex.a
+-MISCLIB_LIB       = $(M_LIB_DIR)/misclib.a
++CIF_FILE_LIB      = $(M_LIB_DIR_GENTOO)/cif-file.a
++CIFPARSE_LIB      = $(M_LIB_DIR_GENTOO)/cifparse-obj.a
++CIF_TABLE_LIB     = $(M_LIB_DIR_GENTOO)/tables.a
++CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a
++REGEX_LIB         = $(M_LIB_DIR_GENTOO)/regex.a
++MISCLIB_LIB       = $(M_LIB_DIR_GENTOO)/misclib.a
+ 
+ ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \
+   $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB)
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
new file mode 100644
index 000000000..650671374
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
@@ -0,0 +1,11 @@
+--- pdb-extract-v3.0/src/extract.C	2007-09-11 17:19:48.000000000 +0200
++++ pdb-extract-v3.0/src/extract.C.new	2008-12-05 17:49:59.000000000 +0100
+@@ -1689,7 +1689,7 @@
+         open_file_error(inpfile, "get_mmcif");
+     }
+     
+-    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT");
++    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT");
+     if(temp != NULL) {
+         strcpy(pdb_extract, "");
+         strcpy(pdb_extract_sf, "");
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
new file mode 100644
index 000000000..6907399c2
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
@@ -0,0 +1,20 @@
+--- cifobj-common-v4.1/src/GenString.C	2008-11-13 10:44:01.000000000 +0100
++++ cifobj-common-v4.1/src/GenString.C.new	2008-11-13 10:43:54.000000000 +0100
+@@ -144,6 +144,7 @@
+ #include <string>
+ #include <algorithm>
+ #include <sstream>
++#include <string.h>
+ 
+ #include "GenString.h"
+ 
+--- tables-v8.0/src/ISTable.C	2007-09-11 17:19:47.000000000 +0200
++++ tables-v8.0/src/ISTable.C.new	2008-11-13 10:48:18.000000000 +0100
+@@ -150,6 +150,7 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <limits.h>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
diff --git a/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch b/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch
new file mode 100644
index 000000000..2b0731648
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch
@@ -0,0 +1,199 @@
+diff -uarN pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src/etc/make.platform.darwin3
+--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3	2007-09-11 17:19:46.000000000 +0200
++++ pdb-extract-v3.004-prod-src/etc/make.platform.darwin3	2008-11-13 17:51:34.000000000 +0100
+@@ -91,7 +91,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -159,7 +159,7 @@
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -uarN pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src/etc/make.platform.darwin4
+--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4	2007-09-11 17:19:46.000000000 +0200
++++ pdb-extract-v3.004-prod-src/etc/make.platform.darwin4	2008-11-13 17:51:34.000000000 +0100
+@@ -92,7 +92,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -160,7 +160,7 @@
+ STATIC_LINKING= 
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -uarN pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src/etc/make.platform.gnu3
+--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3	2007-09-11 17:19:46.000000000 +0200
++++ pdb-extract-v3.004-prod-src/etc/make.platform.gnu3	2008-11-13 17:51:34.000000000 +0100
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=/usr/lib
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -89,7 +91,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -107,8 +109,8 @@
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,9 +130,9 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -144,7 +146,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -154,11 +156,11 @@
+ #-----Linkers section----------------------------------------------------#
+ 
+ # Static linking option. If not defined, dynamic linking is used.
+-STATIC_LINKING=-static
++STATIC_LINKING= 
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+-LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -uarN pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src/etc/make.platform.gnu4
+--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4	2007-09-11 17:19:46.000000000 +0200
++++ pdb-extract-v3.004-prod-src/etc/make.platform.gnu4	2008-11-13 17:51:34.000000000 +0100
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=/usr/lib
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -34,7 +36,7 @@
+ 
+ # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
+ # warnings as errors.
+-WARNINGS_AS_ERRORS=-Werror
++WARNINGS_AS_ERRORS=
+ 
+ # ALL_WARNINGS defines flags to instruct all compilers to report all
+ # warnings.
+@@ -90,7 +92,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -108,8 +110,8 @@
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -129,9 +131,9 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -145,7 +147,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -155,11 +157,11 @@
+ #-----Linkers section----------------------------------------------------#
+ 
+ # Static linking option. If not defined, dynamic linking is used.
+-STATIC_LINKING=-static
++STATIC_LINKING= 
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+-LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -uarN pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src/Makefile
+--- pdb-extract-v3.004-prod-src/Makefile	2007-09-11 17:19:46.000000000 +0200
++++ pdb-extract-v3.004-prod-src/Makefile	2008-11-13 17:51:06.000000000 +0100
+@@ -52,7 +52,7 @@
+ 		echo "------------------------------------------------------------"; \
+ 		echo "**** Making $$libdir ****"; \
+ 		echo "------------------------------------------------------------"; \
+-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
++		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
+ 	done
+ 
+ beta:
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml
new file mode 100644
index 000000000..2d5f72f37
--- /dev/null
+++ b/sci-chemistry/pdb-extract/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>private-overlay</herd>
+	<maintainer>
+		<email>justin@j-schmitz.net</email>
+		<name>Justin Lecher</name>
+	</maintainer>
+	<maintainer>
+		<email>johann@j-schmitz.net</email>
+		<name>Johann Schmitz</name>
+	</maintainer>
+<!--
+	<use>
+		<flag name=''></flag>
+	</use>
+-->
+</pkgmetadata>
+
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild
new file mode 100644
index 000000000..73535767b
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils toolchain-funcs multilib
+
+MY_P="${PN}-v${PV}-prod-src"
+DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
+HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}
+	>=sci-libs/cifparse-obj-7.025"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	local libdir=$(get_libdir)
+	unpack ${A}
+	epatch "${FILESDIR}"/respect-cflags-and-fix-install.patch
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-gcc-4.3.patch
+	epatch "${FILESDIR}"/${P}-Makefile.patch
+	epatch "${FILESDIR}"/${P}-env.patch
+
+	sed -i "s:GENTOOLIBDIR:${libdir}:g" \
+		pdb-extract-v3.0/Makefile || die "fix libdir"
+
+	# Get rid of unneeded directories, to make sure we use system files
+	ebegin "Deleting redundant directories"
+	rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
+		misclib-v2.2 regex-v2.2 tables-v8.0
+	eend
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(GINCLUDES=\).*:\1-I/usr/include/cifparse-obj:g" \
+		-e "s:^\(LIBDIR=\).*:\1/usr/$(get_libdir):g" \
+		"${S}"/etc/make.*
+}
+
+src_compile() {
+	emake || die "make failed"
+}
+
+src_install() {
+	dobin bin/pdb_extract{,_sf} || die
+	newbin bin/extract extract-pdb
+	dolib.a lib/pdb-extract.a || die
+	insinto /usr/include/rcsb
+	doins include/* || die
+	dodoc README-source README
+	insinto /usr/lib/rcsb/pdb-extract-data
+	doins pdb-extract-data/* || die
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="/usr/lib/rcsb/"
+	PDB_EXTRACT_ROOT="/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract
+}
+
+pkg_postinst() {
+	ewarn "We moved extract to extract-pdb due to multiple collision of /usr/bin/extract"
+}