reinit the tree, so we can have metadata

10 files changed, 535 insertions, 0 deletions

diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest
new file mode 100644
index 000000000000..2f8a991763a5
--- /dev/null
+++ b/sci-libs/cifparse-obj/Manifest
@@ -0,0 +1,13 @@
+AUX cifparse-obj-7.025-gcc4.3.patch 3926 SHA256 784a0f0a08fae029152c4f995740f94ec13cbc37d193d89d137f539dd4d6e789 SHA512 4ae441c3b576817e0302f69cceb1dd04f17bfff5226c888557732c49f4dac336d12014dc699e2703a248597eb04a118c2037a3defc18e0e3aed1fa73dd5ba892 WHIRLPOOL 5bc3f60946914863f3c6316cd58434e3ca7210e051c6b7c96fda3e0a38cf8506a4f686425c5b3b417b3c58e1c4a675132898b2f856cf6fb85624b54e36de2f5a
+AUX cifparse-obj-7.025-gcc4.7.patch 2339 SHA256 41f442585c48e85fd08a41a13817f4223ec24044cbb32386e9f6db83e9676c6a SHA512 f4ca881116a0bfb5688d441f0a29abd81fc173bb496b6640128054fc2307b88a5a02d4ebcc6c9203af091302a104474b0767f9373c334955a691a865853efd03 WHIRLPOOL bc78efcf3287e5e919fce68230dc17c7cc5d79ebea3363476b882db4e0baed950c9eda35058fc39d4c6a68941f8e0eec54b56a1d11f240faa3d2394d9df939fa
+AUX cifparse-obj-7.025-gcc5_6.patch 524 SHA256 3ec0853db06d6bb9dd6c3a246a220b6805109874a88f1fb79130d00c5ac11fa3 SHA512 f2469b15eb74192b61b78c165249e8b953c58d0f7478d38f1bebf8c2c884e95ad42ba18af23b1ea7e4915979b5d4f70c2637e083a14a2c40e20f83a09acf616e WHIRLPOOL 6e89983c303f10aaed998845f3f0ba56df75eadd104e57444bb945f8a2c9c50ad1e18e7f496cf97aa3b48f8bd436c51e4001bfff995dfc2e930be5dbc8eea14a
+AUX cifparse-obj-7.025-makefile.patch 4405 SHA256 1b70620f492e027f01273f316e6bf543b22c1586555d9df5a589edaa7cdc3a79 SHA512 8e74758f8ff8993a6e304a0cf80e59f60d0d162aee8f3a798552534f51055406d35c2bc1c6b91b6d9e41ff2d2666ea1d5580c71a66f1c3485c7e86deee169c69 WHIRLPOOL 446589a8914e507f0dd98c3a3470d072755a13deb96d1a83fdbaec5034478c92414a5e634bc16473ef7ea38fb8d1df3741b32f63d612aaa079a236b08fdf4384
+AUX cifparse-obj-7.025-strncasecmp-declaration.patch 477 SHA256 f2b5bfcf74b651d3820cd6855b1a3d8d237015f70599b7f0a301a05fe07c1d7f SHA512 536e1f22c82cc88a0f3e24e5785b393ac7b602eb60f05da581afe7f79a7921e3f9e60463f9fec0190d3b85bc222ccc9782380f3c12dbd85172da7d2ccef5e5d0 WHIRLPOOL 98b681497b6d4f6c1818a3caca3d76bcbcff66dec55345c620bbff2d877b6787a245c99ca9e1c6aac8438cef0d7a2f50a1e2cf62b0cbb1afcf2ed3d2ad8b0066
+AUX cifparse-obj-7.105-makefile.patch 3790 SHA256 5e975bfb55d6cd265a02590b7464ba6ca772e708571c5334c909d92daf499406 SHA512 310f13e88f7dfb19ac2bdc003a2ab2f095583a90694d27232c1ab15a298bc88313e89590e062274da10d5eaba53f6bfcb3341d1d4f7d1c388520c75643364d61 WHIRLPOOL bd65c4efc9401bd0c784e2c684c5ac10518f25860fea40ea42f7318de0fd1b4cc812715e5cb035085951772374d3abf1542270bbfe6b4d6092fd4aefb7e7e45d
+DIST cifparse-obj-v7.025-prod-src.tar.gz 928484 SHA256 f2fd71fc2af0995839d9ee7825403e383209bb45a1bad68c270e5756476a8ef8 SHA512 bf5d6b55592aca8678396eb9819f5bd7bff4d912410590dfb750c9ad85bdcdbd251425c45b67e2db027a8ce8d028b77c91edcc5333279ed1190f6049c01f5cc9 WHIRLPOOL 0bd0376f3ea1d562c9650186dd1b48eef454f8acd0f4c0e074a1fccbbccf6edbef2d3e2dcd92799c1e15f0e0a4f1d32a50aaee0120c06ef846f6c971cede4924
+DIST cifparse-obj-v7.105-prod-src.tar.gz 931151 SHA256 3a0d48d6101fbe5fca4b65c53e5669726979db1a57bccf11ee769a3e40f2a856 SHA512 d626aa055bdd6762eda4b5b04121f37fff3bc09460b12cd6cb80566545d23e5c08a8ad54fa184076932d2cff38aa9d91fa659fbe9a70d4a07b8b1677c28549f4 WHIRLPOOL e1cb2e89916b40ad3094b2c53050869dfee0dbb4f8a4219153bef51a5c90729bda0922103a1d423bba1c6768c1b65c975f43c9f542ba1c333a85207f6fa09e9a
+EBUILD cifparse-obj-7.025-r1.ebuild 1206 SHA256 a32b5453c1536de261bead14f88fba628459eeff94508f0f305782b8d390b4fa SHA512 bd4faf64ea58641708ad9d05c9d2cda01ddbf93759ab1579d6afadbbfc52ffab4daab6699ecc7e163b359d848c599f49dacf75de2e1d2cfaa952b4658a5bee18 WHIRLPOOL b8ac0435fc3989540304396513b5c3b2aa7dea6ba63fbd8d294982d0c211cca79d238f332c890add428c73762ac4af0217e39d199d2acaa5230a8d4676801732
+EBUILD cifparse-obj-7.105.ebuild 1140 SHA256 9efa3db3a98f33506c2d3c68586dd400690f0a1bde3bc2797573354e826dee10 SHA512 72fc0b191f9603e8cd7e42ca2e475d0bdb0120d1841784f7bad9b6a455da655b04129632dbb174b871d9ac5c31449bcefb9d328d723dea5a28629d6cf798b169 WHIRLPOOL d287b8b921f4583264a918e693d0b13d0a374dda9a42ffb4a9688c137ea4ba8b3aa20f0f62890d50ef8438d0615a8498549e2c747932aaeb7a0c341deaed5681
+MISC ChangeLog 3210 SHA256 6003731766f75d153b3aa3bb860b549e29e805d5b48219ecd5f913ff9b2eed63 SHA512 fa3b365b0fe07c0830f1e5b66529e8cbc8b4c98c1e45c974875a268adfecf0b031945a788067437fa45b6d856a5cfa53220d9ff8c5176d57d0376d685efe5e9f WHIRLPOOL d8e965ef898c1f0470fce0408102b9bf6d074155c1742a03ddce60cd7489dd280c2f6f804c620162083d108f43955b8f03bc836ed235172948cf498c616b913f
+MISC ChangeLog-2015 3020 SHA256 79f9372c4d2d8e8c5787908a38f5a48db4471fc29af585d121bb9615a82dea45 SHA512 986ba5398f70051a8a3e50c15e01f7589adf8237d629c53dbcbd97985cf45b199ce7579107d0d6109a2f0645877cd58c0d562c9556b0265c1ceb8fd22a1e917c WHIRLPOOL 18c507a690fe2cdd326f78c714703604256e968fb99a6c278c073d32ca0661b3a9afa551dbee9db1de306b66ffcdbde2cdfb24feaab09aa1c7d25a56a3b9a517
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild
new file mode 100644
index 000000000000..647673dcd240
--- /dev/null
+++ b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}-v${PV}-prod-src"
+
+DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format"
+HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz"
+
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE=""
+
+RDEPEND=""
+DEPEND="
+	sys-devel/bison
+	sys-devel/flex"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-makefile.patch \
+		"${FILESDIR}"/${P}-gcc4.3.patch \
+		"${FILESDIR}"/${P}-gcc4.7.patch \
+		"${FILESDIR}"/${P}-gcc5_6.patch \
+		"${FILESDIR}"/${PN}-7.025-strncasecmp-declaration.patch
+
+	sed \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(F77=\).*:\1${FORTRANC}:g" \
+		-e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \
+		-e "s:-static::g" \
+		-i "${S}"/etc/make.* || die "Failed to fix makefile"
+}
+
+src_compile() {
+	# parallel make fails
+	emake -j1
+}
+
+src_install() {
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+}
diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild
new file mode 100644
index 000000000000..622af4794346
--- /dev/null
+++ b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}-v${PV}-prod-src"
+
+DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format"
+HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz"
+
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE=""
+
+RDEPEND=""
+DEPEND="
+	sys-devel/bison
+	sys-devel/flex"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${PN}-7.025-gcc5_6.patch
+)
+
+src_prepare() {
+	default
+
+	sed \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(F77=\).*:\1${FORTRANC}:g" \
+		-e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \
+		-e "s:-static::g" \
+		-i "${S}"/etc/make.* || die "Failed to fix makefile"
+}
+
+src_compile() {
+	# parallel make fails
+	emake -j1 \
+		C_OPT="${CFLAGS}" \
+		CXX_OPT="${CXXFLAGS}"
+}
+
+src_install() {
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+}
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch
new file mode 100644
index 000000000000..1715f493a6e0
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch
@@ -0,0 +1,87 @@
+diff -Naur cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C
+--- cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C	2008-09-03 09:36:41.000000000 -0400
+@@ -153,6 +153,7 @@
+ // VLAD - Carefully examine all methods that accept with, for cases where
+ // with is 0. This may happen if the value is empty !!
+ 
++#include <algorithm>
+ #include "GenString.h"
+ #include "CifString.h"
+ #include "regex.h"
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C	2008-09-03 09:40:12.000000000 -0400
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdlib>
+ #include "GenString.h"
+ #include "CifFile.h"
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C	2008-09-03 09:40:42.000000000 -0400
+@@ -3,6 +3,7 @@
+ */
+ #include "CifFile.h"
+ #include <iostream>
++#include <cstdlib>
+ 
+ void FillTestTable(ISTable *s);
+ void TwoCifFileObj();
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C	2008-09-03 09:41:06.000000000 -0400
+@@ -1,6 +1,7 @@
+ /* Test for reading binary files of two different versions*/
+ #include "CifFile.h"
+ #include <iostream>
++#include <cstdlib>
+ 
+ 
+ #define FALSE 0
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C	2008-09-03 09:41:50.000000000 -0400
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdlib>
+ #include "CifFile.h"
+ 
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C
+--- cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C	2008-09-03 09:32:17.000000000 -0400
+@@ -138,7 +138,7 @@
+ POSSIBILITY THEREOF. 
+ */
+ 
+-
++#include <cstring>
+ // Needed, since some platforms do not define std:: elsewhere
+ #include <ctype.h>
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C
+--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C	2008-09-03 09:35:57.000000000 -0400
+@@ -150,6 +150,8 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <algorithm>
++#include <climits>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
+diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C
+--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C	2008-09-03 09:35:29.000000000 -0400
+@@ -150,6 +150,8 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <algorithm>
++#include <climits>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch
new file mode 100644
index 000000000000..b828ae618caa
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch
@@ -0,0 +1,64 @@
+ common-v4.5/src/mapped_ptr_vector.C |   14 +++++++-------
+ 1 files changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C
+index 0ffff35..993d0b9 100644
+--- a/common-v4.5/src/mapped_ptr_vector.C
++++ b/common-v4.5/src/mapped_ptr_vector.C
+@@ -256,12 +256,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP,
+     _vector.push_back(inP);
+ 
+     typename tIndex::value_type valuePair(inP->GetName(),
+-      make_pair(_vector.size() - 1, fileIndex));
++      std::make_pair(_vector.size() - 1, fileIndex));
+ 
+     _index.insert(valuePair);
+ 
+     _currentName = inP->GetName();
+-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
++    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
+ 
+ }
+ 
+@@ -274,12 +274,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name,
+     _vector.push_back(NULL);
+ 
+     typename tIndex::value_type valuePair(name,
+-      make_pair(_vector.size() - 1, fileIndex));
++      std::make_pair(_vector.size() - 1, fileIndex));
+ 
+     _index.insert(valuePair);
+ 
+     _currentName = name;
+-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
++    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
+ }
+ 
+ 
+@@ -447,7 +447,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name)
+     if (is_equal(_currentName, name, keyComp))
+     {
+         _currentName.clear();
+-        _currentIndices = make_pair(_vector.size(), (unsigned int)0);
++        _currentIndices = std::make_pair(_vector.size(), (unsigned int)0);
+     }
+ 
+ }
+@@ -532,7 +532,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
+     if (_vector.empty())
+     {
+         // Empty container. Return invalid index.
+-        return(make_pair(_vector.size(), (unsigned int)0));
++        return(std::make_pair(_vector.size(), (unsigned int)0));
+     }
+ 
+     typename tIndex::key_compare keyComp = _index.key_comp();
+@@ -556,7 +556,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
+         else
+         {
+             // Not found. Return invalid index.
+-            return(make_pair(_vector.size(), (unsigned int)0));
++            return(std::make_pair(_vector.size(), (unsigned int)0));
+         } 
+     }
+     
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch
new file mode 100644
index 000000000000..2ac0ec220d9e
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch
@@ -0,0 +1,16 @@
+ etc/platform.sh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/etc/platform.sh b/etc/platform.sh
+index ff0ab51..1b56ab1 100755
+--- a/etc/platform.sh
++++ b/etc/platform.sh
+@@ -60,7 +60,7 @@ case `uname -s` in
+ #   Check if it is a Linux platform
+     Linux)
+ #     Check if it is GCC version 4.x
+-      gcc_ver=`gcc --version | grep -e " 4\."`
++      gcc_ver=`gcc --version | grep -e " [456]\."`
+       if [[ -z $gcc_ver ]]
+       then
+ #       It is not GCC version 4.x. Check if it is GCC version 3.x
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch
new file mode 100644
index 000000000000..9e9a61788ddf
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch
@@ -0,0 +1,115 @@
+diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3
+--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3	2008-09-03 09:18:55.000000000 -0400
+@@ -107,8 +107,8 @@
+ C_WARNINGS=$(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) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,13 +128,13 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
+         $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -144,7 +144,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -157,7 +157,7 @@
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
+diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4
+--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4	2008-09-03 09:20:16.000000000 -0400
+@@ -107,12 +107,12 @@
+ 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) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+-## This part defines C++ compiler information
++
+ 
+ # C++ compiler executable
+ CCC=g++
+@@ -128,13 +128,13 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
+         $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -144,7 +144,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -157,7 +157,7 @@
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
+diff -Naur cifparse-obj-v7.025-prod-src/Makefile cifparse-obj-v7.025-prod-src.new/Makefile
+--- cifparse-obj-v7.025-prod-src/Makefile	2008-02-06 07:17:48.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/Makefile	2008-09-03 09:19:12.000000000 -0400
+@@ -62,7 +62,7 @@
+ 		echo "------------------------------------------------------------"; \
+ 		echo "**** Making $$libdir ****"; \
+ 		echo "------------------------------------------------------------"; \
+-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
++		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CXX_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LD_OPT="${LDFLAGS}" install) || exit 1; \
+ 	done
+ 
+ debug:
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch
new file mode 100644
index 000000000000..9222ff27699e
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch
@@ -0,0 +1,16 @@
+Remove incorrect prototypes of the 'strcasecmp' and 'strncasecmp' functions.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594054
+
+--- a/misclib-v2.2/include/ndb_misclib.h
++++ b/misclib-v2.2/include/ndb_misclib.h
+@@ -167,10 +167,6 @@
+ #define NDB_MSG_BUFFER_LEN    200000
+ 
+ 
+-#if !defined(HAVE_STRCASECMP)
+-int strcasecmp (const char *s1, const char *s2);
+-int strncasecmp (const char *s1, const char *s2, unsigned int n);
+-#endif 
+ /*
+  *   ndb_misclib.c prototypes
+  */
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch
new file mode 100644
index 000000000000..1716cd6390a4
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch
@@ -0,0 +1,110 @@
+ etc/make.platform.gnu3 | 14 +++++++-------
+ etc/make.platform.gnu4 | 16 ++++++++--------
+ 2 files changed, 15 insertions(+), 15 deletions(-)
+
+diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
+index 54b0297..138fa47 100644
+--- a/etc/make.platform.gnu3
++++ b/etc/make.platform.gnu3
+@@ -107,8 +107,8 @@ NON_ANSI_C_FLAG=
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \
++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \
+   $(DEFINES) $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,14 +128,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+   $(DEFINES) $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
+   $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
+ 
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+    $(DEFINES) $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -145,7 +145,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -158,7 +158,7 @@ F77LIBS=
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
+diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
+index 6676f35..51681fa 100644
+--- a/etc/make.platform.gnu4
++++ b/etc/make.platform.gnu4
+@@ -107,11 +107,11 @@ NON_ANSI_C_FLAG=
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
+ 
+ ## C++ compiler
+-## This part defines C++ compiler information
++
+ 
+ # C++ compiler executable
+ CCC=g++
+@@ -127,14 +127,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+   $(DEFINES) $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
+   $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
+ 
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+   $(DEFINES) $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -144,7 +144,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -157,7 +157,7 @@ F77LIBS=
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
diff --git a/sci-libs/cifparse-obj/metadata.xml b/sci-libs/cifparse-obj/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-libs/cifparse-obj/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+</pkgmetadata>