gentoo auto-resync : 20:07:2024 - 12:29:37

19 files changed, 0 insertions, 869 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index dbbd5c59e90e..fa838783aca7 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
deleted file mode 100644
index de2fa35a0b3d..000000000000
--- a/sci-chemistry/aqua/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX aqua-3.2-flags.patch 4211 BLAKE2B 032048ea0f08aa798758489beda88aa0f07635e7ee965d25791b73a2995224920392c7eaf52b0da97d4e0df70df9901d5dd915c2a0adc499e6e17160e2fac467 SHA512 059cea5403fb4cb01b0fcd4d2a2fe4b4aea725e9362a6188ccd3756ced35e324cda5efb21d3ad2a95a842e9d83f8e728a16b36e4b6a479ae32da8816d7eafdfc
-DIST aqua-3.2-nmr_manual.tar.gz 632031 BLAKE2B 1f595a111af4b5e91fc059b5af590a6c37a44654fcae42e6003b40cf7fdf542cb772d3ef25bf2475455ce8638cd0aebcbbc8c66bb57688ce919af2eac9b535cb SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f
-DIST aqua3.2.tar.gz 688408 BLAKE2B 898e0e3bbc4ff7b6ce8a8128ce6ffef45db607c74e2d78a70cefc26818d39049e4d18159b65250a3651112f64318ccce838037e563d3a985be7ef369d89b594e SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a
-EBUILD aqua-3.2-r3.ebuild 2087 BLAKE2B 053412cfb8802a1fd07e2ab53e19d8cca8f422063bd0d64723e2152b4d2fce4fc4597db2fd906b08b899937fac27c390abf73e1638f0a77f356e3bf86dea7d7f SHA512 1d5e6cdefb415613ade4170837b0092772a2c76bbb29b4c10e6ef75044f380c724371509fc5ec50144828bc6dcbd04b282135a0147561b424267331ad79b802a
-MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049
diff --git a/sci-chemistry/aqua/aqua-3.2-r3.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
deleted file mode 100644
index 78d987ec1460..000000000000
--- a/sci-chemistry/aqua/aqua-3.2-r3.ebuild
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2 toolchain-funcs
-
-DESCRIPTION="Program suite in this distribution calculates restraint violations"
-HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
-SRC_URI="
-	${PN}${PV}.tar.gz
-	doc? ( ${P}-nmr_manual.tar.gz )"
-
-SLOT="0"
-LICENSE="procheck"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-
-RDEPEND="sci-chemistry/procheck"
-DEPEND="app-shells/tcsh"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"/${PN}${PV}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-flags.patch
-)
-
-pkg_nofetch() {
-	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
-	elog "And follow the instructions for downloading the following into your DISTDIR"
-	elog "directory:"
-	elog "  ${PN}${PV}.tar.gz"
-	if use doc; then
-		elog "  nmr_manual.tar.gz  ->  ${P}-nmr_manual.tar.gz"
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e 's:nawk:gawk:g' \
-		-e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \
-		-e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \
-		-i $(find . -type f) || die
-	default
-}
-
-src_compile() {
-	cd src || die
-	emake \
-		MYROOT="${WORKDIR}" \
-		CC="$(tc-getCC)" \
-		FC="$(tc-getFC)" \
-		CFLAGS="${CFLAGS} -I../sub/lib" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		exth
-	emake \
-		MYROOT="${WORKDIR}" \
-		CC="$(tc-getCC)" \
-		FC="$(tc-getFC)" \
-		CFLAGS="${CFLAGS} -I../sub/lib" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	rm -f scripts/conv* || die
-	dobin bin/* scripts/*
-	dosym AquaWhat /usr/bin/qwhat
-	dosym AquaHow /usr/bin/qhow
-	dosym AquaPseudo /usr/bin/qpseudo
-	dosym AquaDist /usr/bin/qdist
-	dosym AquaCalc /usr/bin/qcalc
-	dosym AquaAssign /usr/bin/qassign
-	dosym AquaRedun /usr/bin/qredun
-	dosym AquaCompl /usr/bin/qcompl
-
-	dodoc HISTORY HOW_TO_USE NEW README doc/*
-	dohtml html/*
-
-	insinto /usr/share/${PN}
-	doins data/*
-	if use examples; then
-		doins -r exmpls
-	fi
-
-	if use doc; then
-		dohtml -r manual
-	fi
-
-	cat >> "${T}"/34aqua <<- EOF
-	AQUADATADIR="${EPREFIX}/usr/share/${PN}"
-	EOF
-	doenvd "${T}"/34aqua
-}
diff --git a/sci-chemistry/aqua/files/aqua-3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch
deleted file mode 100644
index a60841b8ce08..000000000000
--- a/sci-chemistry/aqua/files/aqua-3.2-flags.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 3113471..dd7a320 100644
---- a/src/makefile
-+++ b/src/makefile
-@@ -176,47 +176,46 @@ nrutil.h:
- # Executable files
- 
- $(BIN)/AquaWhat:    AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
--	$(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
- 
- $(BIN)/AquaHow:	    AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
--	$(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
- 
- $(BIN)/AquaPseudo:  AquaPseudo.o $(OBJECTS) $(R_OBJECTS) 
--	$(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
- 
- $(BIN)/AquaDist:    AquaDist.o $(OBJECTS) 
--	$(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm
- 
- $(BIN)/AquaCalc:    AquaCalc.o $(OBJECTS) $(RNG_OBJECTS)
--	$(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm
- 
- $(BIN)/AquaAssign:  AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
--	$(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
- 
- $(BIN)/AquaCompl:  AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
--	$(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm  
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm
- 
- $(BIN)/AquaRedun:  AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
--	$(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
- 
- $(BIN)/testnew:	    testnew.o $(OBJECTS)
--	$(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS)
- 
- $(BIN)/getproj:    getproj.c 
--	$(CC) -o $(BIN)/getproj -O getproj.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c
- 
- $(BIN)/AquaPlot:    AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
--	$(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
- 
- $(BIN)/Qext:	   Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
--	$(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
- 
- $(BIN)/StarTest:	StarTest.o
--	$(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
- 
- exth:		exth.f
--	f77 -o exth -O2 exth.f
--	strip exth
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o exth -O2 exth.f
- 
- 
- # Object files
-@@ -269,7 +268,7 @@ AquaCommon.o:	AquaCommon.c AquaCommon.h nrutil.h \
- 	$(CC) -c AquaCommon.c $(CFLAGS)
- 
- nrutil.o:	nrutil.c nrutil.h
--	$(CC) -c nrutil.c -DANSI
-+	$(CC) $(CFLAGS) -c nrutil.c -DANSI
- 
- AquaFuncts.o:	AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\
- 		AquaStrucset.h AquaFiles.h\
-@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o:	$(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\
- 	cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS)
- 
- cv_subs.o:	cv_subs.f
--	f77 -c cv_subs.f $(FFLAGS)
-+	$(FC) -c cv_subs.f $(FFLAGS)
- 
- Qext.o:		Qext.c Qext.h\
- 		$(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS)
diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/aqua/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
deleted file mode 100644
index 4d348875c0d2..000000000000
--- a/sci-chemistry/namd/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX namd-2.10-gentoo.patch 4637 BLAKE2B 0439e424f3d2a73378c68052f9d9dd69dc9590b9f83fa4062d4abc156b3b682f0e8a2cffd8a1e1f751f8dfd71d067c0234ba56946773ca9139e73c57e775c631 SHA512 35afda71ad7567d1b2c4c1f4073792d5977edc997ba7a43cf71c8ed32308062edc5cb4923202d599d59ade2f98602a0fac21138ba205a3bf6b681c86a61411f8
-AUX namd-2.7-iml-dec.patch 520 BLAKE2B c16430d1161b9d7e3faf22257d84ff1090eccf906a296f91d4ec0731fa89d23334d5c39c7988f8ac6d5f5020d403d4491dadbe34b1e9800ada81ad18b2448b7d SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37
-DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92
-EBUILD namd-2.10.ebuild 2644 BLAKE2B 6d91c9f7f90f2b304c18bb176e7fdfcfff98a077bf8d6ed720b24ee186b5dece164fde49cee6db3f3dff217a53bba76d6d1c00b45ca7633ab1d9fb2a0b53ef46 SHA512 816bc445d23cc15fcf7d17bacb11b7ae4566a7bf135a88f80b7587d9630db0650e0f8b54b828bbbe8454008b6967fc276fbfc347cda351ec4b9e370d08671e08
-MISC metadata.xml 377 BLAKE2B 727b1c499d11b56228aab0bb2c47c45f63c48a1406f52b5b3d3fe8d02b69d0113dbad00eca99bcff194fc164605b2b698bdd8581c20fb6401c54169265d73f6b SHA512 4dbe460b1b9a0a8112d7866a11a389a1e2847afa3404c57479bdf39e6b3600d403c5c1f70d76196cd1508770dcd8befcc73687969b6853ff1e5f25cf5d22fea7
diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
deleted file mode 100644
index ffef6dc3ad68..000000000000
--- a/sci-chemistry/namd/files/namd-2.10-gentoo.patch
+++ /dev/null
@@ -1,124 +0,0 @@
-diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw
---- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw	2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/arch/Linux-x86_64.fftw	2015-03-06 17:54:46.641162629 -0700
-@@ -1,7 +1,7 @@
- 
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
- 
-diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl
---- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl	2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/arch/Linux-x86_64.tcl	2015-03-06 17:54:46.641162629 -0700
-@@ -1,9 +1,9 @@
- 
- #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
--TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
- #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
-+#TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
- 
-diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile
---- NAMD_2.10_Source.orig/Makefile	2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/Makefile	2015-03-06 18:01:32.645966590 -0700
-@@ -389,10 +389,10 @@
- 	$(DSTDIR)/stringhash.o
- 
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/gentoo-libdir
- CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast
- #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
- #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
-@@ -418,7 +418,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun
-+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -434,7 +434,7 @@
- 
- namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
- 	$(MAKEBUILDINFO)
--	$(CHARMC) -verbose -ld++-option \
-+	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
- 	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
- 	"$(CHARM_MODULES)" -language charm++ \
- 	$(BUILDINFO).o \
-@@ -484,11 +484,8 @@
- charmd_faceless.exe:
- 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
- 
--charmrun.exe:
--	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
--	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-+	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
- 
- psfgen.exe:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
- 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-@@ -506,7 +503,7 @@
- 	$(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
- 
- flipdcd:	$(SRCDIR)/flipdcd.c
--	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
- 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
- 	chmod +x $@
- 
-@@ -516,7 +513,7 @@
- 	chmod +x $@
- 
- fixdcd:	$(SRCDIR)/fixdcd.c
--	$(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
- 
- dumpdcd:	$(SRCDIR)/dumpdcd.c
- 	$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
-@@ -711,9 +708,7 @@
- 
- DOC_FILES = README.txt announce.txt license.txt notes.txt
- 
--RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
- 
- release: all
- 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -724,17 +719,9 @@
- 	for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
- 	  /bin/rm -rf $$f; \
- 	done
--	if [ -r $(CHARM)/bin/charmd ]; then \
--	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
--	fi
--	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
--	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
--	fi
- 	chmod -R a+rX $(RELEASE_DIR_NAME)
- 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- 	gzip $(RELEASE_DIR_NAME).tar
--	echo $(CHARM)
--	ls -l $(CHARM)/lib
- 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
- 
- winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
deleted file mode 100644
index e5ee3bd6c818..000000000000
--- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
-index 94b71ba..01a2529 100644
---- a/src/flipbinpdb.c
-+++ b/src/flipbinpdb.c
-@@ -9,6 +9,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
- 
- #ifndef MAP_FILE
- #define MAP_FILE 0
-diff --git a/src/flipdcd.c b/src/flipdcd.c
-index 8ec85b7..1c23433 100644
---- a/src/flipdcd.c
-+++ b/src/flipdcd.c
-@@ -13,6 +13,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
- 
- #ifndef MAP_FILE
- #define MAP_FILE 0
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
deleted file mode 100644
index 11bbcb9bf2c8..000000000000
--- a/sci-chemistry/namd/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>nicolasbock@gentoo.org</email>
-		<name>Nicolas Bock</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild
deleted file mode 100644
index 76a34c5a0a19..000000000000
--- a/sci-chemistry/namd/namd-2.10.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MY_PN="NAMD"
-
-inherit multilib toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-SRC_URI="${MY_PN}_${PV}_Source.tar.gz"
-
-LICENSE="namd"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-RDEPEND="
-	>=sys-cluster/charm-6.5.1-r2
-	sci-libs/fftw:3.0
-	dev-lang/tcl:0="
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	app-shells/tcsh"
-
-NAMD_ARCH="Linux-x86_64-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${PV}_Source"
-
-PATCHES=(
-	# apply a few small fixes to make NAMD compile and
-	# link to the proper libraries
-	"${FILESDIR}"/namd-2.10-gentoo.patch
-	"${FILESDIR}"/namd-2.7-iml-dec.patch
-)
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from"
-	einfo "${NAMD_DOWNLOAD}"
-	einfo "after agreeing to the license and then move it to"
-	einfo "your DISTDIR directory."
-	einfo "Be sure to select the ${PV} version!"
-	echo
-}
-
-src_prepare() {
-	CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
-
-	default
-
-	sed \
-		-e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \
-		-i Make.charm || die
-
-	# Remove charm distribution. We don't need it.
-	rm -f charm-*.tar || die
-
-	# proper compiler and cflags
-	sed \
-		-e "s/g++.*/$(tc-getCXX)/" \
-		-e "s/gcc.*/$(tc-getCC)/" \
-		-e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \
-		-e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \
-		-i arch/${NAMD_ARCH}.arch || die
-
-	sed \
-		-e "s/gentoo-libdir/$(get_libdir)/g" \
-		-e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
-		-i Makefile || die "Failed gentooizing Makefile."
-	sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
-}
-
-src_configure() {
-	# configure
-	./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die
-}
-
-src_compile() {
-	# build namd
-	cd "${S}/${NAMD_ARCH}" || die
-	TCLLIB="$($(tc-getPKG_CONFIG) --libs tcl) -ldl -pthread" \
-		emake
-}
-
-src_install() {
-	dodoc announce.txt license.txt notes.txt
-	cd "${S}/${NAMD_ARCH}" || die
-
-	# the binaries
-	dobin ${PN}2 psfgen flipbinpdb flipdcd
-}
-
-pkg_postinst() {
-	echo
-	einfo "For detailed instructions on how to run and configure"
-	einfo "NAMD please consults the extensive documentation at"
-	einfo "http://www.ks.uiuc.edu/Research/namd/"
-	einfo "and the NAMD tutorials available at"
-	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
-	einfo "Have fun :)"
-	echo
-}
diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
deleted file mode 100644
index 176af33f9d5a..000000000000
--- a/sci-chemistry/procheck/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX procheck-3.5.4-close.patch 1073 BLAKE2B 54e9857e3d3ee920becebfc50da34145384046be019a2fcd01d47afc4f9242a5311aac166dcde7dc79de584c2ea08bd8e766ae58310700bff45f6bb1a2829abf SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307
-AUX procheck-3.5.4-ldflags.patch 1649 BLAKE2B 64506db2dbe1eba43dfc07bca233d573646ac553862e8d6eecce7970362047cfd8fdcd18f7c83bb74a0476fde78222ea92e0c2a56b24fba2d71d9c97c563fbb1 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f
-DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a
-DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c
-DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc
-EBUILD procheck-3.5.4-r3.ebuild 1717 BLAKE2B 1919325faefdc9cad032d503166cdedc966f44c949bf1c2c34d3aa7b0132fdbb35a3a7e0f446a967166cbce66596143e114cea7b0c23aa9ca0c99acd9c29ec4a SHA512 04c58e977937275fd413ff217d97f7fa0dfacca2492c57b60d8f2d671565e640852c391e8c408618ed3e9da53f602f96c2863a009d8798011365a9b9f1fa93ec
-MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
deleted file mode 100644
index 16a0658e654d..000000000000
--- a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff --git a/pplot.f b/pplot.f
-index 7e06e68..c86b2b2 100644
---- a/pplot.f
-+++ b/pplot.f
-@@ -4720,6 +4720,7 @@ C---- Initialise variables
-           SCORE(IDIST) = 0.0
-  50   CONTINUE
- 
-+      REWIND(3)
- C---- If the required residue is of a greater number than that required,
- C     read through the file until come to it
-       IF (IRESID.GT.INRES) THEN
-diff --git a/ps.f b/ps.f
-index b652a7d..858b8e5 100644
---- a/ps.f
-+++ b/ps.f
-@@ -1705,12 +1705,14 @@ CVAX     -    CARRIAGECONTROL='LIST',
- C---- If this is an existing file, then read through all its records until
- C     get to the end of file
-       IF (.NOT.NEWFIL) THEN
-+          CLOSE(14)
-+          OPEN(14, file=fname, status='old', position='append', err=900)
- 
- C----     Loop through the file until reach the end
-- 100      CONTINUE
--             READ(14,110,END=500) IREC
-- 110         FORMAT(A)
--          GO TO 100
-+C 100      CONTINUE
-+C             READ(14,110,END=500) IREC
-+C 110         FORMAT(A)
-+C          GO TO 100
- 
- C---- If this is a new file, then write the header records to it
-       ELSE
\ No newline at end of file
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
deleted file mode 100644
index 453aebe3211f..000000000000
--- a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-diff --git a/Makefile b/Makefile
-index c5bb58f..0394b0a 100644
---- a/Makefile
-+++ b/Makefile
-@@ -35,31 +35,31 @@ distrib :
- # Individual executables
- # ----------------------
- anglen : anglen.o
--	$(F77) $(FOPTS) -o $@ anglen.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
- clean : clean.o
--	$(F77) $(FOPTS) -o $@ clean.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
- rmsdev : rmsdev.o
--	$(F77) $(FOPTS) -o $@ rmsdev.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
- secstr : secstr.o
--	$(F77) $(FOPTS) -o $@ secstr.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
- gfac2pdb : gfac2pdb.o ps.o
--	$(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
- pplot : pplot.o ps.o
--	$(F77) $(FOPTS) -o $@ pplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
- bplot : bplot.o ps.o
--	$(F77) $(FOPTS) -o $@ bplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
- tplot : tplot.o ps.o
--	$(F77) $(FOPTS) -o $@ tplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
- mplot : mplot.o ps.o
--	$(F77) $(FOPTS) -o $@ mplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
- vplot : vplot.o ps.o
--	$(F77) $(FOPTS) -o $@ vplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
- viol2pdb : viol2pdb.o ps.o
--	$(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
- wirplot : wirplot.o ps.o
--	$(F77) $(FOPTS) -o $@ wirplot.o ps.o
-+	$(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
- nb : nb.c
--	$(CC) $(COPTS) -o nb nb.c $(CLIBS)
-+	$(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
- 
- # Individual rules for FORTRAN files with .inc files
- # --------------------------------------------------
diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/procheck/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
deleted file mode 100644
index 3db0e3f24244..000000000000
--- a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2 multilib toolchain-funcs versionator
-
-DESCRIPTION="Checks the stereochemical quality of a protein structure"
-HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK"
-SRC_URI="
-	${P}.tar.gz ${P}-README
-	doc? ( ${P}-manual.tar.gz )"
-
-LICENSE="procheck"
-SLOT="0"
-KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${PN}"
-
-pkg_nofetch() {
-	elog "Please visit https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
-	elog "and follow the instruction for downloading."
-	elog "Files should be renamed in the following way before being copied to your"
-	elog "DISTDIR directory:"
-	elog "  ${PN}.tar.gz  ->  ${P}.tar.gz"
-	elog "  README  ->  ${P}-README"
-	use doc && elog "  manual.tar.gz  ->  ${P}-manual.tar.gz"
-}
-
-PATCHES=(
-		"${FILESDIR}"/${P}-ldflags.patch
-		"${FILESDIR}"/${P}-close.patch
-)
-
-src_compile() {
-	emake \
-		F77="$(tc-getFC)" \
-		CC="$(tc-getCC)" \
-		COPTS="${CFLAGS}" \
-		FOPTS="${FFLAGS} -std=legacy"
-}
-
-src_install() {
-	for i in *.scr; do
-		newbin ${i} ${i%.scr}
-	done
-
-	exeinto /usr/libexec/${PN}/
-	doexe \
-		anglen \
-		clean \
-		rmsdev \
-		secstr \
-		gfac2pdb \
-		pplot \
-		bplot \
-		tplot \
-		mplot \
-		vplot \
-		viol2pdb \
-		wirplot \
-		nb
-	dodoc "${DISTDIR}"/${P}-README
-
-	insinto /usr/libexec/${PN}/
-	doins *.dat *.prm
-	newins resdefs.dat resdefs.data
-
-	cat >> "${T}"/30${PN} <<- EOF
-	prodir="${EPREFIX}/usr/libexec/${PN}/"
-	EOF
-
-	doenvd "${T}"/30${PN}
-
-	if use doc; then
-		pushd "${WORKDIR}" > /dev/null
-			docinto html
-			dodoc -r manual
-		popd > /dev/null
-	fi
-}
diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest
deleted file mode 100644
index d49a26f26741..000000000000
--- a/sci-chemistry/xyza2pipe/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX xyza2pipe-20121001-gentoo.patch 3974 BLAKE2B cf3f4b58c6348a6295b7874ca20d7d88f6477e1174b54bac7089898ff7509fbf07d8d34aab2d333059c67f7ccc9d1b99e4e40c9bfd8a327f600fc4578a2f1a06 SHA512 7b8be1fd799d65e9a600766afb21e95a4722eff8a657f88d0adaf5aaf11ed369f6d8a27f3e003337570837abc45cfa9e758d1219af275773f79b81d1c1c322c4
-DIST xyza2pipe-20121001.tgz 61002 BLAKE2B 648e65b63cc0b363dd0087b7ef64a1e287654a165baaf7d967821f11cffb70dd7f0da864dfa3b915553546c8cbbc83fda411d9b979551d3d72334db6580e5d64 SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855
-EBUILD xyza2pipe-20121001.ebuild 682 BLAKE2B a1cbd50a946dc37ab1e55f998b2ad6631e53fd6138f886009ef28e4a121721c5a8e6ffcdd0d79c4b387e2016b456c14d9b3db039f95bd6d6c85f774d8fff71b2 SHA512 4253c166e0a2101b3a5b91aed25193107d588cfbc3db07b66f64ab98bb2888a5e3342d093db15c9686be6519d3ad3372cd6b53f52a4091ee35a458d210c428e6
-MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch
deleted file mode 100644
index ec4220dd0695..000000000000
--- a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch
+++ /dev/null
@@ -1,168 +0,0 @@
- Makefile | 106 +++++++++++++++++++++++++++++++++++++--------------------------
- 1 file changed, 63 insertions(+), 43 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 15d4bd3..e738ec2 100644
---- a/Makefile
-+++ b/Makefile
-@@ -4,7 +4,7 @@
- #  Last modified: Feb/22/2012
- #
- 
--CFLAGS		= -O3
-+CFLAGS		?= -O3
- MFLAGS		= -lm
- 
- TARGETS		= xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\
-@@ -62,89 +62,109 @@ clean:
- 	rm -f $(TARGETS) addxyza2pipe
- 
- $(OBJECTS_MATH):
--	$(CC) $*.c -c -o $@ $(CFLAGS) -D__XYZA2PIPE__
-+	$(CC) $(CPPFLAGS) -D__XYZA2PIPE__ $(CFLAGS) $*.c -c -o $@
- 
- .o:
--	$(CC) $< -c -o $@ $(CFLAGS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $< -c -o $@
- 
- xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- nv2pipe: $(OBJECTS_C) $(OBJECTS_NP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2nv: $(OBJECTS_C) $(OBJECTS_PN)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- azara2pipe: $(OBJECTS_C) $(OBJECTS_AP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2azara: $(OBJECTS_C) $(OBJECTS_PA)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- add2pipe: $(OBJECTS_C) $(OBJECTS_DXP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 	rm -f addxyza2pipe
- 	ln -s add2pipe addxyza2pipe
- 
- adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
- 
- addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP)
--	$(CC) $@.c $^ -o $@ \
--	$(CFLAGS) $(MFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+	$(MFLAGS)
-+	mv -v $@ bin/
diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/xyza2pipe/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild
deleted file mode 100644
index e6ba5c19332f..000000000000
--- a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Cross conversion environment of NMR spectra"
-HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src"
-SRC_URI="http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz -> ${P}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="olivia"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
-
-src_prepare() {
-	default
-	tc-export CC
-	mkdir bin || die
-}
-
-src_install() {
-	local i
-	dodoc README FEEDBACK
-	cd bin || die
-	for i in *; do
-		newbin ${i}{,-olivia}
-	done
-}