An application for processing and curation of macromolecular structure data.

(Portage version: 2.1_pre1)

8 files changed, 417 insertions, 0 deletions

diff --git a/sci-chemistry/maxit/ChangeLog b/sci-chemistry/maxit/ChangeLog
new file mode 100644
index 000000000000..7f7ce34a810a
--- /dev/null
+++ b/sci-chemistry/maxit/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/maxit
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maxit/ChangeLog,v 1.1 2005/12/20 04:19:43 spyderous Exp $
+
+*maxit-8.2 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +files/README,
+  +files/README-source, +files/respect-cflags-and-fix-install.patch,
+  +metadata.xml, +maxit-8.2.ebuild:
+  An application for processing and curation of macromolecular structure data.
+
diff --git a/sci-chemistry/maxit/Manifest b/sci-chemistry/maxit/Manifest
new file mode 100644
index 000000000000..eb9957d0ac16
--- /dev/null
+++ b/sci-chemistry/maxit/Manifest
@@ -0,0 +1,5 @@
+MD5 68b7fbe58ac131c5de804dfa490cd2ce files/README 1298
+MD5 7acf1939208e2c5ef1541e4c58f5c800 files/README-source 3409
+MD5 f0539a87f3decb3c2a841511143cabb9 files/digest-maxit-8.2 80
+MD5 992d798766fb7d4bed4e02b638fcefe5 files/respect-cflags-and-fix-install.patch 7536
+MD5 3211a966be310e03f1c67d560a04212b maxit-8.2.ebuild 1413
diff --git a/sci-chemistry/maxit/files/README b/sci-chemistry/maxit/files/README
new file mode 100644
index 000000000000..00cac52fc88a
--- /dev/null
+++ b/sci-chemistry/maxit/files/README
@@ -0,0 +1,31 @@
+The MAXIT Program Suite was developed by the PDB (Protein Data Bank) and
+NDB (Nucleic Acid Database) to assist in the processing and curation of
+macromolecular structure data. The functions of the program suite are
+summarized as follows:
+
+(1) Reading and writing PDB and mmCIF format files, and translating between
+file formats.
+
+(2) Performing a variety of consistency checks on coordinates, sequence, and
+crystal data.
+
+(3) Constructing, transforming, and merging information between formats in
+order to minimize the human intervention during file translation and data
+processing operations.
+
+(4) Residue numbering in the coordinate section is aligned with the sequence
+
+(5) Atoms in standard and nonstandard residues and atoms in ligands are
+reordered and renamed in a standard manner. The residue and ligand description
+is held in mmCIF dictionary.
+
+(6) Detection of missing or additional atoms.
+
+
+Note: Binary distribution of this tool contains an additional submodule
+"procheck", which does additional structure checking. This submodule is
+not part of the source distribution. Therefore the users are advised to
+use the binary distribution, if possible.
+
+Refer to README-source or README-binary, depending on the distribution, for
+details on installation, build, demos and application usage.
diff --git a/sci-chemistry/maxit/files/README-source b/sci-chemistry/maxit/files/README-source
new file mode 100644
index 000000000000..45ec67c76454
--- /dev/null
+++ b/sci-chemistry/maxit/files/README-source
@@ -0,0 +1,101 @@
+
+             Installation and Usage Notes for the Maxit Application
+                            (Source Distribution)
+
+Note: It is highly recommended to utilize binary distribution, if possible,
+since it contains an additional submodule, called PROCHECK, which does more
+structure checking. This source distribution does not contain PROCHECK, since
+the PROCHECK module is only available in binary form. 
+
+1.  Installation
+
+a.  Uncompress and unbundle the distribution using the following command:
+
+        zcat maxit-vX.XXX-XXX.tar.gz | tar -xf - 
+
+    The result of this command is a subdirectory maxit-vX.XXX-XXX in the
+    current directory. It contains subdirectories of various source modules
+    and the following items important for the user:
+
+        bin - subdirectory in which the application executable "maxit-v8.01-O"
+          will be placed after the build process.
+        data - subdirectory that contains some data files needed by the
+          application. 
+
+b.  Set up the environment variables.
+
+    - Define RCSBROOT environment variable to point to the installation
+    directory. Assuming that the installation directory is
+    /home/username/maxit-vX.XXX-XXX, execute in the shell:
+
+        For C shell users:
+          setenv RCSBROOT /home/username/maxit-vX.XXX-XXX
+
+        For Bourne shell users:
+          RCSBROOT=/home/username/maxit-vX.XXX-XXX; export RCSBROOT
+
+    - Add "bin" subdirectory to the PATH environment variable.
+    Execute in the shell:
+
+        For C shell users:
+          setenv PATH "$RCSBROOT/bin:"$PATH
+
+        For Bourne shell users:
+          PATH="$RCSBROOT/bin:"$PATH; export PATH
+
+
+2.  Building the Application
+
+a.  Position in the maxit-vX.XXX-XXX directory and run "make" command:
+
+        cd maxit-vX.XXX-XXX 
+        make
+
+    The application executable "maxit-v8.01-O" will be placed in the "bin"
+    subdirectory.
+
+
+    NOTE: The users who are working on Sun platform are strongly advised to
+    check the compiler flags in etc/make.platform.sunos5 file. Depending on
+    the compiler version, users may be required to make modifications to those
+    compiler flags.
+
+b.  Make binary data from ASCII data
+
+    - Position in the maxit-vX.XXX-XXX directory and run "make" command as
+    follows:
+
+        make binary
+
+    This command will create certain binary data files, using the ASCII data
+    files in data/ascii directory. The resulting files are stored in
+    data/binary directory. Note that it may take several minutes for this
+    step to complete. This step must be executed before the tool can be
+    utilized.
+
+
+3.  Application Usage Notes
+
+Maxit application supports many options for all kinds of data processing
+operations. To see all supported options, execute:
+
+    maxit-v8.01-O -
+
+For the purpose of data deposit, only three options are necessary for preparing
+the deposit file.
+
+1. This will translate a PDB format file into mmCIF format file. The output file
+name is file_name.pdb.cif (with extension .cif).
+
+    maxit-v8.01-O -i file_name.pdb -o 1 -exchange_out
+
+2. This will translate a mmCIF format file into PDB format file. The output file
+name is file_name.cif.pdb (with extension .pdb).
+
+    maxit-v8.01-O -i file_name.cif -o 2 -exchange_in
+
+3. This will update a mmCIF format file. The output file name is
+file_name.cif.cif (with extension .cif).
+
+    maxit-v8.01-O -i file_name.cif -o 8 -exchange_in -exchange_out
+
diff --git a/sci-chemistry/maxit/files/digest-maxit-8.2 b/sci-chemistry/maxit/files/digest-maxit-8.2
new file mode 100644
index 000000000000..abb82a2a5747
--- /dev/null
+++ b/sci-chemistry/maxit/files/digest-maxit-8.2
@@ -0,0 +1 @@
+MD5 8023ecb2deb2b4cd6fcc2e8f32e8b21a pdb-extract-v1.700-prod-src.tar.gz 9081548
diff --git a/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch b/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch
new file mode 100644
index 000000000000..7ab999b640eb
--- /dev/null
+++ b/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch
@@ -0,0 +1,207 @@
+diff -ur 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	2005-12-19 00:32:21.000000000 -0800
++++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu3	2005-12-19 00:48:25.000000000 -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 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	2005-12-19 00:32:21.000000000 -0800
++++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu4	2005-12-19 00:48:25.000000000 -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 pdb-extract-v1.700-prod-src.orig/Makefile pdb-extract-v1.700-prod-src/Makefile
+--- pdb-extract-v1.700-prod-src.orig/Makefile	2005-12-19 00:32:21.000000000 -0800
++++ pdb-extract-v1.700-prod-src/Makefile	2005-12-19 00:48:25.000000000 -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 =  maxit-v8.2
+ 
+ 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 pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile
+--- pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile	2005-12-19 00:32:21.000000000 -0800
++++ pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile	2005-12-19 00:51:46.000000000 -0800
+@@ -33,35 +33,35 @@
+ #----------------------------------------------------------------------------
+ include ../etc/Makefile.platform
+ 
+-LIBS    = $(LIBINSTDIR)/libvalidation.a \
+-          $(LIBINSTDIR)/libndbfilter.a \
+-          $(LIBINSTDIR)/libconnect.a \
+-          $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libregex.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libndbmisc.a
+-
+-LIBS1   = $(LIBINSTDIR)/liberfiolib.a \
+-          $(LIBINSTDIR)/liberfutil.a \
+-          $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libndbmisc.a
+-
+-LIBS2   = $(LIBINSTDIR)/liberfiolib.a \
+-          $(LIBINSTDIR)/libconnect.a \
+-          $(LIBINSTDIR)/libciffileobj.a \
+-          $(LIBINSTDIR)/libcifobj.a \
+-          $(LIBINSTDIR)/libistable.a \
+-          $(LIBINSTDIR)/libregex.a \
+-          $(LIBINSTDIR)/libtblindex.a \
+-          $(LIBINSTDIR)/libcifstr.a \
+-          $(LIBINSTDIR)/libndbmisc.a
++LIBS    = $(LIBDIR)/libvalidation.a \
++          $(LIBDIR)/libndbfilter.a \
++          $(LIBDIR)/libconnect.a \
++          $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libregex.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libndbmisc.a
++
++LIBS1   = $(LIBDIR)/liberfiolib.a \
++          $(LIBDIR)/liberfutil.a \
++          $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libndbmisc.a
++
++LIBS2   = $(LIBDIR)/liberfiolib.a \
++          $(LIBDIR)/libconnect.a \
++          $(LIBDIR)/libciffileobj.a \
++          $(LIBDIR)/libcifobj.a \
++          $(LIBDIR)/libistable.a \
++          $(LIBDIR)/libregex.a \
++          $(LIBDIR)/libtblindex.a \
++          $(LIBDIR)/libcifstr.a \
++          $(LIBDIR)/libndbmisc.a
+ #
+ NDBLIB     = $(LIB)/libmaxit.a
+ #
diff --git a/sci-chemistry/maxit/maxit-8.2.ebuild b/sci-chemistry/maxit/maxit-8.2.ebuild
new file mode 100644
index 000000000000..221061d6a360
--- /dev/null
+++ b/sci-chemistry/maxit/maxit-8.2.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maxit/maxit-8.2.ebuild,v 1.1 2005/12/20 04:19:43 spyderous Exp $
+
+inherit eutils toolchain-funcs multilib
+
+# pdb-extract includes a newer 'validation' than 'validation' tarball does,
+# and the filterlib from pdb-extract is incompatible with the validation tarball
+MY_PN="pdb-extract"
+MY_PV="1.700"
+MY_P="${MY_PN}-v${MY_PV}-prod-src"
+DESCRIPTION="An application for processing and curation of macromolecular structure data"
+HOMEPAGE="http://sw-tools.pdb.org/apps/MAXIT/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND="sci-libs/rcsb-data"
+DEPEND="${RDEPEND}
+	sci-chemistry/pdb-extract
+	sci-chemistry/validation"
+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* misclib* \
+		regex* pdb-extract* 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/*
+	dodoc ${FILESDIR}/README*
+}
diff --git a/sci-chemistry/maxit/metadata.xml b/sci-chemistry/maxit/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/maxit/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>