New package to add hydrogens to a Protein Data Bank (PDB) molecule structure file.

(Portage version: 2.1_rc3-r1)

6 files changed, 207 insertions, 0 deletions

diff --git a/sci-chemistry/reduce/ChangeLog b/sci-chemistry/reduce/ChangeLog
new file mode 100644
index 000000000000..c8c894d1aeaa
--- /dev/null
+++ b/sci-chemistry/reduce/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/reduce
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.1 2006/06/04 09:05:46 spyderous Exp $
+
+*reduce-2.21.030604 (04 Jun 2006)
+
+  04 Jun 2006; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/2.21.030604-gcc4.patch, +metadata.xml, +reduce-2.21.030604.ebuild:
+  New package to add hydrogens to a Protein Data Bank (PDB) molecule structure
+  file.
+
diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
new file mode 100644
index 000000000000..74a72e5ae993
--- /dev/null
+++ b/sci-chemistry/reduce/Manifest
@@ -0,0 +1,21 @@
+AUX 2.21.030604-gcc4.patch 3946 RMD160 f9c8d7f884bc942e31bd0273fe4f43d8f0e2ecc6 SHA1 c596c6ac2741567bc179e50871cc3d607327cec1 SHA256 9c6372e7d44ff83b42ab0ad7f08b7173c8cbfabe204b991ec828c5428d048ff8
+MD5 8a698c351b0f63bb4df171fd994e956f files/2.21.030604-gcc4.patch 3946
+RMD160 f9c8d7f884bc942e31bd0273fe4f43d8f0e2ecc6 files/2.21.030604-gcc4.patch 3946
+SHA256 9c6372e7d44ff83b42ab0ad7f08b7173c8cbfabe204b991ec828c5428d048ff8 files/2.21.030604-gcc4.patch 3946
+DIST reduce.2.21.030604.src.tgz 132262 RMD160 db5ff4ea12e50c7ea9d8215011f80966ce5397b6 SHA1 c69944bb28beb50013e8c8b6ea67d2581e924777 SHA256 0889c1bed10680090a1fd62cce1a46a13768b4ea77cbf036245b15e2e542337d
+DIST reduce_het_dict.txt.zip 983850 RMD160 5d1aa16adc4c9e3355b58937dbe8033afa4e8a17 SHA1 13a73d98315deef4abc76afa3cb5b7dc775c3882 SHA256 382802ebb89332dd0a0f208ef5ca6b9cd0ddca5b7a5d6bf8226d5aa1f506a384
+EBUILD reduce-2.21.030604.ebuild 1578 RMD160 176a176207692681657b715c70a4c994f5ac7f12 SHA1 979c0d47a72b23f927615ea55f82d37d50b5c91b SHA256 d0346b830e2168182b0134d9a814f000b24780ede9d9bfdbd8e578e08638c9dd
+MD5 f4cbccd8f7680256a954544c12fd3761 reduce-2.21.030604.ebuild 1578
+RMD160 176a176207692681657b715c70a4c994f5ac7f12 reduce-2.21.030604.ebuild 1578
+SHA256 d0346b830e2168182b0134d9a814f000b24780ede9d9bfdbd8e578e08638c9dd reduce-2.21.030604.ebuild 1578
+MISC ChangeLog 375 RMD160 6ade7010b650915f78da926bad81c541b161eef9 SHA1 4b26f0753d129bd94a9bc9799f53776a10e73843 SHA256 546af60cab87f9862c504f0974aa805683a9a5dc6f59154e1b6197151a5174f4
+MD5 0135970e7e6ce6930767af4af0de74dd ChangeLog 375
+RMD160 6ade7010b650915f78da926bad81c541b161eef9 ChangeLog 375
+SHA256 546af60cab87f9862c504f0974aa805683a9a5dc6f59154e1b6197151a5174f4 ChangeLog 375
+MISC metadata.xml 248 RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 SHA1 75a648fddef9922cdfe21fb0298a1c746190fd82 SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
+MD5 c11171b0a99e888d7e44388991357d64 files/digest-reduce-2.21.030604 509
+RMD160 1d2f43617d6b6b136e2ab041298b74aa23d0fd29 files/digest-reduce-2.21.030604 509
+SHA256 f543714aaf050596c1f088716c350a5d6e15c160a6022b9289911a1d14fb4a78 files/digest-reduce-2.21.030604 509
diff --git a/sci-chemistry/reduce/files/2.21.030604-gcc4.patch b/sci-chemistry/reduce/files/2.21.030604-gcc4.patch
new file mode 100644
index 000000000000..67b36ab476a7
--- /dev/null
+++ b/sci-chemistry/reduce/files/2.21.030604-gcc4.patch
@@ -0,0 +1,100 @@
+Files reduce.2.21.030604.source.orig/libpdb/libpdb++.a and reduce.2.21.030604.source/libpdb/libpdb++.a differ
+diff -urN -x '*Makefile*' reduce.2.21.030604.source.orig/reduce_src/PDBrec.h reduce.2.21.030604.source/reduce_src/PDBrec.h
+--- reduce.2.21.030604.source.orig/reduce_src/PDBrec.h	2003-06-04 16:32:12.000000000 -0700
++++ reduce.2.21.030604.source/reduce_src/PDBrec.h	2006-06-01 15:50:07.000000000 -0700
+@@ -233,7 +233,7 @@
+ 
+    friend ostream& operator << (ostream& s, const PDBrecNAMEout& p);
+ private:
+-   PDBrecNAMEout(const PDBrecNAMEout& p); // can't copy or assign
++//   PDBrecNAMEout(const PDBrecNAMEout& p); // can't copy or assign
+    PDBrecNAMEout& operator=(const PDBrecNAMEout& p);
+ 
+    const PDBrec& _r;
+Files reduce.2.21.030604.source.orig/reduce_src/reduce and reduce.2.21.030604.source/reduce_src/reduce differ
+diff -urN -x '*Makefile*' reduce.2.21.030604.source.orig/toolclasses/Dict.C reduce.2.21.030604.source/toolclasses/Dict.C
+--- reduce.2.21.030604.source.orig/toolclasses/Dict.C	1999-03-15 08:42:34.000000000 -0800
++++ reduce.2.21.030604.source/toolclasses/Dict.C	2006-06-01 15:51:58.000000000 -0700
+@@ -13,6 +13,7 @@
+ // Copyright (C) 1999 J. Michael Word
+ // **************************************************************
+ 
++using std::endl;
+ #include "Dict.h"
+ 
+ // ---------------------------------------------------
+Files reduce.2.21.030604.source.orig/toolclasses/libtoolclasses.a and reduce.2.21.030604.source/toolclasses/libtoolclasses.a differ
+diff -urN -x '*Makefile*' reduce.2.21.030604.source.orig/toolclasses/List.h reduce.2.21.030604.source/toolclasses/List.h
+--- reduce.2.21.030604.source.orig/toolclasses/List.h	2003-06-04 16:48:51.000000000 -0700
++++ reduce.2.21.030604.source/toolclasses/List.h	2006-06-01 16:31:43.000000000 -0700
+@@ -9,6 +9,8 @@
+ #ifndef LIST_H
+ #define LIST_H 1
+ 
++#include "utility.h"
++
+ #ifdef OLD_STD_HDRS
+ #include <iostream.h>
+ #include <limits.h>
+diff -urN -x '*Makefile*' reduce.2.21.030604.source.orig/toolclasses/ListIter.C reduce.2.21.030604.source/toolclasses/ListIter.C
+--- reduce.2.21.030604.source.orig/toolclasses/ListIter.C	1999-01-13 09:58:42.000000000 -0800
++++ reduce.2.21.030604.source/toolclasses/ListIter.C	2006-06-01 15:32:13.000000000 -0700
+@@ -58,29 +58,29 @@
+ 
+ template <class T>
+ bool NonConstListIter<T>::drop() {
+-   bool rc = (_node != NULL);
++   bool rc = (this->_node != NULL);
+    if (rc) {
+-      DblLnkLstNode<T>* prev = _NClist.linkPrev(_node);
+-      _NClist.drop(_node);
+-      _node = prev;
++      DblLnkLstNode<T>* prev = _NClist.linkPrev(this->_node);
++      _NClist.drop(this->_node);
++      this->_node = prev;
+    }
+    return rc;
+ }
+ 
+ template <class T>
+ bool NonConstListIter<T>::insertBefore(const T& e) {
+-   bool rc = (_node != NULL);
++   bool rc = (this->_node != NULL);
+    if (rc) {
+-      _NClist.insertBefore(e, _node);
++      _NClist.insertBefore(e, this->_node);
+    }
+    return rc;
+ }
+ 
+ template <class T>
+ bool NonConstListIter<T>::insertAfter(const T& e) {
+-   bool rc = (_node != NULL);
++   bool rc = (this->_node != NULL);
+    if (rc) {
+-      _NClist.insertAfter(e, _node);
++      _NClist.insertAfter(e, this->_node);
+    }
+    return rc;
+ }
+diff -urN -x '*Makefile*' reduce.2.21.030604.source.orig/toolclasses/ListIter.h reduce.2.21.030604.source/toolclasses/ListIter.h
+--- reduce.2.21.030604.source.orig/toolclasses/ListIter.h	1999-01-13 09:58:42.000000000 -0800
++++ reduce.2.21.030604.source/toolclasses/ListIter.h	2006-06-01 15:07:29.000000000 -0700
+@@ -63,13 +63,13 @@
+ 			      : ListIter<T>(li), _NClist(li._NClist) {}
+ 
+    T& data() const {
+-      assert(_node);
+-      return _NClist.linkData(_node);
++      assert(this->_node);
++      return _NClist.linkData(this->_node);
+    }
+ 
+    void update(const T& e) const {
+-      assert(_node);
+-      _NClist.linkData(_node) = e;
++      assert(this->_node);
++      _NClist.linkData(this->_node) = e;
+    }
+ 
+    bool drop(); // remove the current element
diff --git a/sci-chemistry/reduce/files/digest-reduce-2.21.030604 b/sci-chemistry/reduce/files/digest-reduce-2.21.030604
new file mode 100644
index 000000000000..48b5fb10b15c
--- /dev/null
+++ b/sci-chemistry/reduce/files/digest-reduce-2.21.030604
@@ -0,0 +1,6 @@
+MD5 87030e9c734c7098aff3a2ac94791c00 reduce.2.21.030604.src.tgz 132262
+RMD160 db5ff4ea12e50c7ea9d8215011f80966ce5397b6 reduce.2.21.030604.src.tgz 132262
+SHA256 0889c1bed10680090a1fd62cce1a46a13768b4ea77cbf036245b15e2e542337d reduce.2.21.030604.src.tgz 132262
+MD5 1ec7b357d652fb46c9db3a14cabefcd1 reduce_het_dict.txt.zip 983850
+RMD160 5d1aa16adc4c9e3355b58937dbe8033afa4e8a17 reduce_het_dict.txt.zip 983850
+SHA256 382802ebb89332dd0a0f208ef5ca6b9cd0ddca5b7a5d6bf8226d5aa1f506a384 reduce_het_dict.txt.zip 983850
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/reduce/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/reduce/reduce-2.21.030604.ebuild b/sci-chemistry/reduce/reduce-2.21.030604.ebuild
new file mode 100644
index 000000000000..cb464ae5c1f5
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-2.21.030604.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-2.21.030604.ebuild,v 1.1 2006/06/04 09:05:46 spyderous Exp $
+
+# If you want to fix the warnings about friend declaration 'foo' declared as
+# a non-template function, see http://gcc.gnu.org/faq.html#friend.
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}"
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/ftpsite/pub/software/reduce/${MY_P}.src.tgz
+	http://kinemage.biochem.duke.edu/ftpsite/pub/software/reduce/reduce_het_dict.txt.zip"
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}.source"
+
+src_unpack() {
+	DICT_DIR="/usr/$(get_libdir)/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+	DICT_LOC="${DICT_DIR}/${DICT_FILE}"
+
+	unpack ${A}
+	epatch ${FILESDIR}/${PV}-gcc4.patch
+
+	# Get Makefiles that are at least somewhere close to right
+	einfo "Updating Makefiles"
+	for dir in libpdb reduce_src toolclasses; do
+		pushd "${S}"/${dir} > /dev/null
+		mv Makefile Makefile.old
+		mv Makefile.g++ Makefile
+		popd > /dev/null
+	done
+
+	# Do after replacing Makefiles
+	einfo "Fixing CFLAGS and locations"
+	sed -i \
+		-e "s:^\(DICT_HOME\).*:\1 = ${DICT_LOC}:g" \
+		-e "s:-DBRACKETOPERPARMS::g" \
+		"${S}"/*/Makefile
+}
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin ${S}/reduce_src/reduce
+	dodoc ${S}/README*
+	insinto ${DICT_DIR}
+	doins ${WORKDIR}/${DICT_FILE}
+}