Date: Tue, 29 Jan 2019 07:56:30 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r491546 - in head/biology: . dsr-pdb dsr-pdb/files Message-ID: <201901290756.x0T7uUT3099774@repo.freebsd.org>
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Author: yuri Date: Tue Jan 29 07:56:30 2019 New Revision: 491546 URL: https://svnweb.freebsd.org/changeset/ports/491546 Log: New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description format) Added: head/biology/dsr-pdb/ head/biology/dsr-pdb/Makefile (contents, props changed) head/biology/dsr-pdb/distinfo (contents, props changed) head/biology/dsr-pdb/files/ head/biology/dsr-pdb/files/patch-Makefile.in (contents, props changed) head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h (contents, props changed) head/biology/dsr-pdb/files/patch-lib_PDB.cc (contents, props changed) head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc (contents, props changed) head/biology/dsr-pdb/pkg-descr (contents, props changed) head/biology/dsr-pdb/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Jan 29 07:56:29 2019 (r491545) +++ head/biology/Makefile Tue Jan 29 07:56:30 2019 (r491546) @@ -25,6 +25,7 @@ SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond + SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta Added: head/biology/dsr-pdb/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/Makefile Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= dsr-pdb +DISTVERSION= 1.0.3 +CATEGORIES= biology +MASTER_SITES= https://graphics.stanford.edu/~drussel/ +DISTNAME= ${PORTNAME} +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Simple C++ PDB reader (reads the protein description format) + +LICENSE= LGPL21 +LICENSE_FILE= ${WRKSRC}/COPYING.txt + +USES= gmake libtool tar:tgz +GNU_CONFIGURE= yes +USE_LDCONFIG= yes + +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} +CXXFLAGS+= -fPIC + +post-patch: +.for dir in lib tools test + @cd ${WRKSRC}/${dir} && ${LN} -s ../ dsrpdb +.endfor + +post-build: # the project itself doesn't support shared libraries in a regular way + @cd ${WRKSRC}/lib && ${CXX} ${LDFLAGS} --shared -Wl,-soname,libdsrpdb.so -o libdsrpdb.so *.o + +post-install: + ${INSTALL_DATA} ${WRKSRC}/config.h ${STAGEDIR}${PREFIX}/include/dsrpdb + ${INSTALL_LIB} ${WRKSRC}/lib/libdsrpdb.so ${STAGEDIR}${PREFIX}/lib + +.include <bsd.port.mk> Added: head/biology/dsr-pdb/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/distinfo Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,3 @@ +TIMESTAMP = 1548747311 +SHA256 (dsr-pdb-1.0.3/dsr-pdb.tgz) = e9fea9c4b8fc0255ee0e2bca11ab267d10cc9687cf5ba515c704875bcee21837 +SIZE (dsr-pdb-1.0.3/dsr-pdb.tgz) = 958360 Added: head/biology/dsr-pdb/files/patch-Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/files/patch-Makefile.in Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,11 @@ +--- Makefile.in.orig 2019-01-29 07:52:25 UTC ++++ Makefile.in +@@ -173,7 +173,7 @@ sbindir = @sbindir@ + sharedstatedir = @sharedstatedir@ + sysconfdir = @sysconfdir@ + target_alias = @target_alias@ +-SUBDIRS = lib tools test include doc ++SUBDIRS = lib tools test include + dist_noinst_DATA = COPYING.txt + all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive Added: head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,11 @@ +--- include/dsrpdb/geometry_internal.h.orig 2019-01-29 07:04:14 UTC ++++ include/dsrpdb/geometry_internal.h +@@ -59,7 +59,7 @@ namespace dsrpdb { + unsigned int b= it->second; + assert(a < map.size() && b < map.size()); + if (map[a] !=-1 && map[b]!=-1) { +- *bout = std::pair<int,int>(map[a], map[b]); ++ *bout = std::pair<dsrpdb::PDB_index<dsrpdb::Atom>,dsrpdb::PDB_index<dsrpdb::Atom>>(map[a], map[b]); + ++bout; + } + } Added: head/biology/dsr-pdb/files/patch-lib_PDB.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/files/patch-lib_PDB.cc Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,11 @@ +--- lib/PDB.cc.orig 2019-01-29 06:57:50 UTC ++++ lib/PDB.cc +@@ -82,7 +82,7 @@ namespace dsrpdb { + assert(i < models_.size()); + return models_[i]; + }; +- unsigned int PDB::number_of_models() const { ++ size_t PDB::number_of_models() const { + return models_.size(); + } + Added: head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,10 @@ +--- tools/pdb_align_points.cc.orig 2019-01-29 07:00:56 UTC ++++ tools/pdb_align_points.cc +@@ -23,6 +23,7 @@ + #include <vector> + #include <iterator> + #include <fstream> ++#include <sstream> + #include <dsrpdb/align.h> + #include <dsrpdb/distance.h> + Added: head/biology/dsr-pdb/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/pkg-descr Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,12 @@ +dsr-pdb is a simple C++ PDB reader along with a couple of programs which use it +to manipulate pdb files (applying a rigid transform or splitting/merging). The +are aimed at people interested in proteins from a geometric viewpoint as they +allow easy access to the geometry and bond structure in addition of the +biological information. The reader has two modes for reading/writing a pdb file. +The simplest one, through the Protein class just reads and writes a single +protein from/to a pdb file (which must have only one chain, but can have +multiple models). The second, through the PDB class can handle pdb files with +multiple models and herogens (although these are just passed through and not +currently interpreted). + +WWW: https://graphics.stanford.edu/~drussel/pdb/ Added: head/biology/dsr-pdb/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/dsr-pdb/pkg-plist Tue Jan 29 07:56:30 2019 (r491546) @@ -0,0 +1,28 @@ +bin/pdb_align +bin/pdb_align_points +bin/pdb_cat +bin/pdb_distance +bin/pdb_distance_matrix +bin/pdb_split +bin/pdb_stats +bin/pdb_transform +include/dsrpdb/Atom.h +include/dsrpdb/Matrix.h +include/dsrpdb/Model.h +include/dsrpdb/PDB.h +include/dsrpdb/PDB_index.h +include/dsrpdb/Point.h +include/dsrpdb/Protein.h +include/dsrpdb/Residue.h +include/dsrpdb/Transform.h +include/dsrpdb/align.h +include/dsrpdb/config.h +include/dsrpdb/distance.h +include/dsrpdb/geometry.h +include/dsrpdb/geometry_internal.h +include/dsrpdb/iterator.h +include/dsrpdb/label.h +include/dsrpdb/labeled_index.h +include/dsrpdb/small_map.h +lib/libdsrpdb.a +lib/libdsrpdb.so
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