From 5930b3956951b216ca14eda8be4e575f8c2d330a Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 15 Jun 2010 08:16:52 +0000 Subject: [PATCH] New addition, unbundled from sci-chemistry/refmac Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- sci-chemistry/ccp4/Manifest | 11 +++-- sci-chemistry/makecif/ChangeLog | 11 +++++ sci-chemistry/makecif/Manifest | 15 ++++++ .../makecif/files/5.6.6-makefile.patch | 49 +++++++++++++++++++ sci-chemistry/makecif/makecif-5.6.6.ebuild | 42 ++++++++++++++++ sci-chemistry/makecif/metadata.xml | 17 +++++++ 6 files changed, 140 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/makecif/ChangeLog create mode 100644 sci-chemistry/makecif/Manifest create mode 100644 sci-chemistry/makecif/files/5.6.6-makefile.patch create mode 100644 sci-chemistry/makecif/makecif-5.6.6.ebuild create mode 100644 sci-chemistry/makecif/metadata.xml diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest index c9c3361cfd05..fb2a5c11c021 100644 --- a/sci-chemistry/ccp4/Manifest +++ b/sci-chemistry/ccp4/Manifest @@ -43,13 +43,14 @@ DIST util_windows.tcl-r1.27-r1.27.2.1.diff 1486 RMD160 06b5598bcff7da11e19ec62c7 EBUILD ccp4-6.0.1-r1.ebuild 13681 RMD160 881038127962bb7aea4f9f77b4cc5b8c170dd688 SHA1 34d43786b53b4adfeec8740036cd2a9081823452 SHA256 bfda422f6d798d29c22faf86b789e4ac5db9799508d027e3428a8f264d286fc7 EBUILD ccp4-6.0.2-r1.ebuild 14094 RMD160 e273884aea608217207b0c8751fce978c67a53e7 SHA1 7d9569120787984943be86b9e0e838a43cbb5b29 SHA256 dbd1c61f294ce3ed091809dc9952f6d027dd01c6b7fd9cb71f3046264ebcb02a EBUILD ccp4-6.0.2.ebuild 13248 RMD160 747c3e19277ef49aeda2d42cd8a93597a545775f SHA1 ef54e5d59b6a29ac6d0b06f23e47e274f2c6925b SHA256 f46b1fc972615e04d4f643f33b8b3f5a1df4c19217e221afa621cce6918cb17f +EBUILD ccp4-6.1.3-r1.ebuild 898 RMD160 b855c8823b28c8153909a0762f906c561742b974 SHA1 a7e0fc85eaaf1e07b62c952cc5ae99416cb10216 SHA256 41f74fb4480d94bf395498214ccca5147217d91ce359d9ec944d1dbf83e68fb6 EBUILD ccp4-6.1.3.ebuild 858 RMD160 2d7b43dce48ae070e7f297f4dd93e063e69fbaa3 SHA1 069271a426ae6a755a075c46f295cab938eded0c SHA256 8a50241824d62ee37ec3aa3938b8a984289e3c795cd55b9fac13d3ee4bb7ff26 -MISC ChangeLog 4431 RMD160 fd57504cc529f827b8bc406169ba57fe167a10c3 SHA1 0d5a6111c39d676663614edc174bcb090396afcf SHA256 75f5e64fbc8be8e01acc6f1f40dbc3f12726bc033498c70c65d172874f04b9d1 +MISC ChangeLog 4556 RMD160 bcb86cfe72180dc06cdb34ea3c596291c06c0735 SHA1 124bdea8bbac92e27e8e2b7afaae53f567cf665f SHA256 42059be84daf8678225f4375989a21f025b4e48ddfaaf04ce8c2e1e5b8b29710 MISC metadata.xml 311 RMD160 7773ed578c7688537f2cf40b5417f9712fe84d8c SHA1 cd3e212d34f7c968d06bab6a2bc64e223b232b3e SHA256 1c5a8d16813aba13725a331bb6d0ed0d2a3bc4d0942775ceced4dc0a7fe4b653 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.14 (GNU/Linux) +Version: GnuPG v2.0.15 (GNU/Linux) -iEYEARECAAYFAkuvXKUACgkQgAnW8HDreRbvGACgtmWVwogfGpUuNaA1mropdfXW -gOgAoKVN1Vp1Mm0C1dfYB7WoSEywEyj3 -=i0d+ +iEYEARECAAYFAkwXN50ACgkQgAnW8HDreRa9jQCbBb1uTqlgK2mbQTDpGr8kf3+P +zKcAnizKP3BYkCHBquhYe+rehSpjvfgc +=qcTP -----END PGP SIGNATURE----- diff --git a/sci-chemistry/makecif/ChangeLog b/sci-chemistry/makecif/ChangeLog new file mode 100644 index 000000000000..665055a12388 --- /dev/null +++ b/sci-chemistry/makecif/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-chemistry/makecif +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/makecif/ChangeLog,v 1.1 2010/06/15 08:16:52 jlec Exp $ + +*makecif-5.6.6 (15 Jun 2010) + + 15 Jun 2010; Justin Lecher +files/5.6.6-makefile.patch, + +makecif-5.6.6.ebuild, +metadata.xml: + New addition, unbundled from sci-chemistry/refmac + + diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest new file mode 100644 index 000000000000..eeaaa4ab781a --- /dev/null +++ b/sci-chemistry/makecif/Manifest @@ -0,0 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX 5.6.6-makefile.patch 3713 RMD160 9ea6ed99a99132dee094148162ddbf6a66718d69 SHA1 3b7455469a573033646b1cebcaab2b24b7c23659 SHA256 a0ceb0a8e68c58c3bb568f7700a9594956f4dae6f63920d0ce812ef1650abf43 +DIST makecif-5.6.6.tar.gz 3797710 RMD160 f5b914ccf135e8adf2867d6fd19113d7f2808fad SHA1 3ffa1543980cc8babfcf08786a46ef8850cb42d6 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f +EBUILD makecif-5.6.6.ebuild 842 RMD160 1771dfb1a144fc98a4444b6b9ef4d57d7bf776ad SHA1 dfc959e91684e8899060cb817dfb8dd45b09d716 SHA256 7a8e3f5db088f6706a68a0754b992110a3b359766c7eea2e62ae0e371ba476fc +MISC ChangeLog 413 RMD160 f142ae9bc2c20c6e22698c07b6c1a39a0d36409b SHA1 96140f7c187f9ce45e6adf701bce8a576d30687f SHA256 37f8b00ce2356b1b5faaa142db9d0978ec0321edc8eca33c4bd433b0d262d8b9 +MISC metadata.xml 446 RMD160 40e5c82b5b17d257029c66d4a72fbac1aac28aed SHA1 5fd98c72f667351bd74570f3c04515d613b9fcdc SHA256 afd71c5775de3828022164f8fbc6d39f111013fa57f89132528d8f0c21714ae5 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.15 (GNU/Linux) + +iEYEARECAAYFAkwXNwMACgkQgAnW8HDreRYJPwCgyb5XxGtVjdZ/KKFc4j4kZToo +ZPAAn3pLIpE0LqiU5NLzQ5UwMnQ6gd4L +=Evq/ +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch new file mode 100644 index 000000000000..186abb92b7d8 --- /dev/null +++ b/sci-chemistry/makecif/files/5.6.6-makefile.patch @@ -0,0 +1,49 @@ +diff --git a/src/makefile b/src/makefile +index 6c8264a..acdec20 100755 +--- a/src/makefile ++++ b/src/makefile +@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/ + # setenv BLANC_FORT "f77 -O1" + # + ++all: makecif_all libcheck_all modcheck_all emin_all ++ + clean: + rm -f temp_makecif_path.fh + rm -f ../bin/* +@@ -118,7 +120,7 @@ makecif.o: makecif.f lib_com.fh crd_com.fh + $(BLANC_FORT) -c makecif.f + + mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o +- $(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o + # ------------- + libcheck.o: libcheck.f lib_com.fh crd_com.fh + $(BLANC_FORT) -c libcheck.f +@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh + $(BLANC_FORT) -c main_libcheck.f + + lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o +- $(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o + # ------------ + + emin.o: emin.f crd_com.fh atom_com.fh +@@ -143,7 +145,7 @@ main_emin.o: main_emin.f + $(BLANC_FORT) -c main_emin.f + + emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o +- $(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o + + # ------------- + +@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f + $(BLANC_FORT) -c main_modcheck.f + + mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o +- $(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o + + + # ====================================== diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild new file mode 100644 index 000000000000..fe041c47c902 --- /dev/null +++ b/sci-chemistry/makecif/makecif-5.6.6.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/makecif/makecif-5.6.6.ebuild,v 1.1 2010/06/15 08:16:52 jlec Exp $ + +EAPI="3" + +FORTRANC="ifc gfortran" + +inherit eutils fortran + +DESCRIPTION="PDB --> CIF convertor" +HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="ccp4" +IUSE="" + +S="${WORKDIR}"/${PN} + +DEPEND="" +RDEPEND=" + sci-libs/monomer-db + ! + +sci-chemistry + + jlec@gentoo.org + + +PDB --> CIF convertor +check and create correct structure description +create the list of restraints +create dictionary description of new ligands +rebuild missing atoms +create tree like structure +also the part of REFMAC +can use additional user's dictionary + + -- 2.26.2