Extract lots of information from Protein Data Bank files.

(Portage version: 2.1_pre1)

6 files changed, 291 insertions, 0 deletions

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
new file mode 100644
index 000000000000..f6b009edffbc
--- /dev/null
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/pdb-extract
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.1 2005/12/20 04:11:02 spyderous Exp $
+
+*pdb-extract-1.700 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <spyderous@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 000000000000..18a6f05555a7
--- /dev/null
+++ b/sci-chemistry/pdb-extract/Manifest
@@ -0,0 +1,4 @@
+MD5 f0539a87f3decb3c2a841511143cabb9 files/digest-pdb-extract-1.700 80
+MD5 2945df7eb475ba3da5fba282404ba5ec files/digest-validation-8.061 79
+MD5 e315289ad58f3b5fb006bbf4d2b482a2 files/respect-cflags-and-fix-install.patch 8415
+MD5 579f9617b4e5f46b5c875eec93df64e5 pdb-extract-1.700.ebuild 1244
diff --git a/sci-chemistry/pdb-extract/files/digest-pdb-extract-1.700 b/sci-chemistry/pdb-extract/files/digest-pdb-extract-1.700
new file mode 100644
index 000000000000..abb82a2a5747
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/digest-pdb-extract-1.700
@@ -0,0 +1 @@
+MD5 8023ecb2deb2b4cd6fcc2e8f32e8b21a pdb-extract-v1.700-prod-src.tar.gz 9081548
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 000000000000..e383615cde48
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/respect-cflags-and-fix-install.patch
@@ -0,0 +1,216 @@
+diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/connect-v2.2/Makefile pdb-extract-v1.700-prod-src/connect-v2.2/Makefile
+--- pdb-extract-v1.700-prod-src.orig/connect-v2.2/Makefile	2005-07-13 06:22:23.000000000 -0700
++++ pdb-extract-v1.700-prod-src/connect-v2.2/Makefile	2005-12-18 23:34:56.000000000 -0800
+@@ -31,22 +31,22 @@
+ #----------------------------------------------------------------------------
+ include ../etc/Makefile.platform
+ 
+-LIBS    = $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libregex.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libndbmisc.a
++LIBS    = $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libregex.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libndbmisc.a
+ 
+ LIBSH   = $(LIBINSTDIR)/libndbhtml.a \
+-          $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libregex.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libndbmisc.a
++          $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libregex.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libndbmisc.a
+ 
+ #----------------------------------------------------------------------------
+ #  Target definitions.
+@@ -261,10 +261,10 @@
+ 	$(CCC) $(C++FLAGS) -o $@  $(OBJ7) $(OBJS4) $(LIBS) $(LDFLAGS) -lm
+ 
+ $(TARGET8): $(OBJ8)
+-	$(CCC) $(C++FLAGS) -o $@  $(OBJ8) $(LIBINSTDIR)/libndbmisc.a $(LDFLAGS) -lm
++	$(CCC) $(C++FLAGS) -o $@  $(OBJ8) $(LIBDIR)/libndbmisc.a $(LDFLAGS) -lm
+ 
+ $(TARGET9): $(OBJ9)
+-	$(CCC) $(C++FLAGS) -o $@  $(OBJ9) $(LIBINSTDIR)/libndbmisc.a $(LDFLAGS) -lm
++	$(CCC) $(C++FLAGS) -o $@  $(OBJ9) $(LIBDIR)/libndbmisc.a $(LDFLAGS) -lm
+ 
+ $(TARGET10): $(LIBSH) $(HFILES) $(NDBLIB) $(OBJ10) $(OBJS6)
+ 	$(CCC) $(C++FLAGS) -o $@  $(OBJ10) $(OBJS6) $(NDBLIB) $(LIBSH) $(LDFLAGS) -lm
+diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3 pdb-extract-v1.700-prod-src/etc/make.platform.gnu3
+--- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3	2005-07-13 06:22:18.000000000 -0700
++++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu3	2005-12-18 23:42:06.000000000 -0800
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR= /usr/lib
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -89,7 +91,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES= -I/usr/include/rcsb
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -107,8 +109,8 @@
+ C_WARNINGS=$(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=
+diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4 pdb-extract-v1.700-prod-src/etc/make.platform.gnu4
+--- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4	2005-07-13 06:22:18.000000000 -0700
++++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu4	2005-12-18 23:33:50.000000000 -0800
+@@ -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) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES= -I/usr/include/rcsb
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -108,8 +110,8 @@
+ C_WARNINGS=$(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=
+diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/Makefile pdb-extract-v1.700-prod-src/Makefile
+--- pdb-extract-v1.700-prod-src.orig/Makefile	2005-07-13 06:22:16.000000000 -0700
++++ pdb-extract-v1.700-prod-src/Makefile	2005-12-18 23:39:23.000000000 -0800
+@@ -22,10 +22,7 @@
+ 
+ DATADIRS = data pdb-extract-data
+ 
+-LIBDIRS =  misclib-v2.1 regex-v2.1 ciflib-common-v3.02 cifobj-common-v4.04 \
+-           btree-obj-v3.1 cif-table-obj-v6.1 cifparse-obj-v6.3 \
+-           htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT) \
+-           validation-v6.2 maxit-v8.2
++LIBDIRS =  htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT)
+ 
+ all:	compile
+ 
+@@ -60,7 +57,7 @@
+ 		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}" install) || exit 1; \
+ 	done
+ 
+ binary:
+diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/pdb-extract-v1.7/Makefile pdb-extract-v1.700-prod-src/pdb-extract-v1.7/Makefile
+--- pdb-extract-v1.700-prod-src.orig/pdb-extract-v1.7/Makefile	2005-07-13 06:22:24.000000000 -0700
++++ pdb-extract-v1.700-prod-src/pdb-extract-v1.7/Makefile	2005-12-18 23:37:16.000000000 -0800
+@@ -27,13 +27,13 @@
+ #----------------------------------------------------------------------------
+ include ../etc/Makefile.platform
+ 
+-CIFLIBS = $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libregex.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libndbmisc.a
++CIFLIBS = $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libregex.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libndbmisc.a
+ 
+ # TARGET1, 2 is only for test
+ TARGET1       = $(BIN)/FOtest1
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/pdb-extract/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild b/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild
new file mode 100644
index 000000000000..8f771eb92c98
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild,v 1.1 2005/12/20 04:11:02 spyderous Exp $
+
+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/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}
+	sci-libs/cifparse-obj"
+PDEPEND="sci-libs/rcsb-data"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/respect-cflags-and-fix-install.patch
+	cd ${S}
+
+	# Get rid of unneeded directories, to make sure we use system files
+	ebegin "Deleting redundant directories"
+	rm -rf btree-obj* ciflib-common* cifobj-common* cif-table-obj* maxit* \
+		misclib* regex* validation*
+	eend
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(GINCLUDE=\).*:\1-I${ROOT}usr/include/rcsb:g" \
+		-e "s:^\(LIBDIR=\).*:\1${ROOT}usr/$(get_libdir):g" \
+		${S}/etc/make.*
+}
+
+src_compile() {
+	emake || die "make failed"
+}
+
+src_install() {
+	exeinto /usr/bin
+	doexe bin/*
+	dolib.a lib/*
+	insinto /usr/include/rcsb
+	doins include/*
+	dodoc README-source README
+}