Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 491545) +++ head/biology/Makefile (revision 491546) @@ -1,152 +1,153 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond + SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += groopm SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/dsr-pdb/Makefile =================================================================== --- head/biology/dsr-pdb/Makefile (nonexistent) +++ head/biology/dsr-pdb/Makefile (revision 491546) @@ -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 Property changes on: head/biology/dsr-pdb/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/distinfo =================================================================== --- head/biology/dsr-pdb/distinfo (nonexistent) +++ head/biology/dsr-pdb/distinfo (revision 491546) @@ -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 Property changes on: head/biology/dsr-pdb/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/files/patch-Makefile.in =================================================================== --- head/biology/dsr-pdb/files/patch-Makefile.in (nonexistent) +++ head/biology/dsr-pdb/files/patch-Makefile.in (revision 491546) @@ -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 Property changes on: head/biology/dsr-pdb/files/patch-Makefile.in ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h =================================================================== --- head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h (nonexistent) +++ head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h (revision 491546) @@ -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(map[a], map[b]); ++ *bout = std::pair,dsrpdb::PDB_index>(map[a], map[b]); + ++bout; + } + } Property changes on: head/biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/files/patch-lib_PDB.cc =================================================================== --- head/biology/dsr-pdb/files/patch-lib_PDB.cc (nonexistent) +++ head/biology/dsr-pdb/files/patch-lib_PDB.cc (revision 491546) @@ -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(); + } + Property changes on: head/biology/dsr-pdb/files/patch-lib_PDB.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc =================================================================== --- head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc (nonexistent) +++ head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc (revision 491546) @@ -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 + #include + #include ++#include + #include + #include + Property changes on: head/biology/dsr-pdb/files/patch-tools_pdb__align__points.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/pkg-descr =================================================================== --- head/biology/dsr-pdb/pkg-descr (nonexistent) +++ head/biology/dsr-pdb/pkg-descr (revision 491546) @@ -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/ Property changes on: head/biology/dsr-pdb/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/dsr-pdb/pkg-plist =================================================================== --- head/biology/dsr-pdb/pkg-plist (nonexistent) +++ head/biology/dsr-pdb/pkg-plist (revision 491546) @@ -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 Property changes on: head/biology/dsr-pdb/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property