xssp: Software for creating DSSP and HSSP files

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: xssp: Software for creating DSSP and HSSP files
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 03 Nov 2018 00:08:20 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 2 19:08:20 2018 -0500
Changeset:	771c771aef8c395de27f2412749594214f89ea2f

Modified Files:
	Makefile
Added Files:
	xssp/DESCR
	xssp/Makefile
	xssp/PLIST
	xssp/distinfo
	xssp/patches/patch-src_hssp-nt.cpp
	xssp/patches/patch-src_mas.h
	xssp/patches/patch-src_progress.h

Log Message:
xssp: Software for creating DSSP and HSSP files

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=771c771aef8c395de27f2412749594214f89ea2f

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                           |  1 +
 xssp/DESCR                         |  9 ++++++
 xssp/Makefile                      | 56 ++++++++++++++++++++++++++++++++++++++
 xssp/PLIST                         |  7 +++++
 xssp/distinfo                      |  9 ++++++
 xssp/patches/patch-src_hssp-nt.cpp | 24 ++++++++++++++++
 xssp/patches/patch-src_mas.h       | 19 +++++++++++++
 xssp/patches/patch-src_progress.h  | 20 ++++++++++++++
 8 files changed, 145 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index f431629258..ff4fa7b8f8 100644
--- a/Makefile
+++ b/Makefile
@@ -4848,6 +4848,7 @@ SUBDIR+=	xrn
 SUBDIR+=	xspd
 SUBDIR+=	xspdapp
 SUBDIR+=	xspread
+SUBDIR+=	xssp
 SUBDIR+=	xtags
 SUBDIR+=	xtraceroute
 SUBDIR+=	xtrackcad
diff --git a/xssp/DESCR b/xssp/DESCR
new file mode 100644
index 0000000000..4a7937e84e
--- /dev/null
+++ b/xssp/DESCR
@@ -0,0 +1,9 @@
+Software for creating DSSP and HSSP files.
+DSSP is a database of secondary structure assignments (and much more) for all
+protein entries in the Protein Data Bank (PDB). DSSP is also the program that
+calculates DSSP entries from PDB entries. DSSP does not predict secondary
+structure.
+HSSP is a database that combines structural and sequence information about
+proteins. This database has the information of the alignment of all available
+homologs of proteins from the PDB database As a result of this, HSSP is also a
+database of homology-based implied protein structures
diff --git a/xssp/Makefile b/xssp/Makefile
new file mode 100644
index 0000000000..dbd7e845a2
--- /dev/null
+++ b/xssp/Makefile
@@ -0,0 +1,56 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri Nov  2 14:05:12 CDT 2018               #
+###########################################################
+
+DISTNAME=	xssp-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=cmbi/}
+GITHUB_PROJECT=	xssp
+GITHUB_TAG=	${PV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/cmbi/xssp
+COMMENT=	Software for creating DSSP and HSSP files
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	autoconf automake autoreconf perl
+GNU_CONFIGURE=	yes
+
+SUBST_CLASSES+=		tuple
+SUBST_STAGE.tuple=	pre-configure
+SUBST_SED.tuple+=	-e 's|tr1/tuple.hpp|tuple/tuple.hpp|g'
+SUBST_FILES.tuple+=	${WRKSRC}/src/mas.cpp
+SUBST_FILES.tuple+=	${WRKSRC}/src/primitives-3d.h
+
+SUBST_CLASSES+=		namespace
+SUBST_STAGE.namespace=	pre-configure
+SUBST_SED.namespace+=	-e 's|std::tr1|std|g'
+SUBST_FILES.namespace+=	${WRKSRC}/src/primitives-3d.cpp
+SUBST_FILES.namespace+=	${WRKSRC}/src/structure.h
+SUBST_FILES.namespace+=	${WRKSRC}/src/primitives-3d.h
+SUBST_FILES.namespace+=	${WRKSRC}/src/structure.cpp
+SUBST_FILES.namespace+=	${WRKSRC}/src/dssp.cpp
+
+SUBST_CLASSES+=		cmath
+SUBST_STAGE.cmath=	pre-configure
+SUBST_SED.cmath+=	-e 's|tr1/cmath.hpp|units/cmath.hpp|g'
+SUBST_FILES.cmath+=	${WRKSRC}/src/hssp-nt.cpp
+
+CXXFLAGS+=	-Wno-unused-const-variable
+CXXFLAGS+=	-Wno-unknown-pragmas
+CXXFLAGS+=	-Wno-error=sign-compare		# Boost header
+# Work around "could not find a version of the library" configure error
+CONFIGURE_ARGS+=	--with-boost-libdir=${PREFIX}/lib
+
+PV=		3.0.1
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+.include "../../wip/libzeep/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/xssp/PLIST b/xssp/PLIST
new file mode 100644
index 0000000000..acae0fa034
--- /dev/null
+++ b/xssp/PLIST
@@ -0,0 +1,7 @@
+@comment $NetBSD$
+bin/hsspconv
+bin/mkdssp
+bin/mkhssp
+bin/test_conv
+bin/test_fasta
+bin/test_readpdb
diff --git a/xssp/distinfo b/xssp/distinfo
new file mode 100644
index 0000000000..4b4e3430d1
--- /dev/null
+++ b/xssp/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+SHA1 (xssp-3.0.1.tar.gz) = dd5070de72f55aaaefb9235c37c1332675fb169b
+RMD160 (xssp-3.0.1.tar.gz) = 36768c5b6c3cc5246e745d26c543df066d73d35f
+SHA512 (xssp-3.0.1.tar.gz) = f7edd906884a104b5692ee0fe0e6ba5a7fbe6e5ae018060c1a2743267e0e002eb36000a4bc6319aa75c25e5119f61d5eced71e9b63709ed2b3efd0cc2a2ee660
+Size (xssp-3.0.1.tar.gz) = 168033 bytes
+SHA1 (patch-src_hssp-nt.cpp) = 021e7e67b59a448f3c78c531ade6a87ae2223bb3
+SHA1 (patch-src_mas.h) = 45fd280429e265e5bd756c45037873bfee5f67fd
+SHA1 (patch-src_progress.h) = ee7c4c71971e7f84b35cbd1c3485f284d084cccf
diff --git a/xssp/patches/patch-src_hssp-nt.cpp b/xssp/patches/patch-src_hssp-nt.cpp
new file mode 100644
index 0000000000..3637d053db
--- /dev/null
+++ b/xssp/patches/patch-src_hssp-nt.cpp
@@ -0,0 +1,24 @@
+$NetBSD$
+
+# Fix unsigned compare
+
+--- src/hssp-nt.cpp.orig	2018-04-06 08:17:20 UTC
++++ src/hssp-nt.cpp
+@@ -23,7 +23,7 @@
+ #include <boost/lexical_cast.hpp>
+ #include <boost/range/adaptor/sliced.hpp>
+ #include <boost/regex.hpp>
+-#include <boost/tr1/cmath.hpp>
++#include <boost/units/cmath.hpp>
+ 
+ #include <algorithm>
+ #include <cmath>
+@@ -474,7 +474,7 @@ void MProfile::AdjustXGapCosts(std::vect
+     {
+       if (ix + d >= m_residues.size() or
+         m_residues[ix + d].m_dist[22] > 0 or
+-        ix - d < 0 or
++        (long)(ix - d) < 0 or
+         m_residues[ix - d].m_dist[22] > 0)
+       {
+         gop[ix] *= (2 + ((8 - d) * 2)) / 8.f;
diff --git a/xssp/patches/patch-src_mas.h b/xssp/patches/patch-src_mas.h
new file mode 100644
index 0000000000..0cefb33dd9
--- /dev/null
+++ b/xssp/patches/patch-src_mas.h
@@ -0,0 +1,19 @@
+$NetBSD$
+
+# Fix collision
+
+--- src/mas.h.orig	2018-07-24 16:34:10 UTC
++++ src/mas.h
+@@ -40,9 +40,9 @@ typedef uint32_t  uint32;
+ typedef int64_t    int64;
+ typedef uint64_t  uint64;
+ 
+-#ifndef nullptr
+-#define nullptr NULL
+-#endif
++//#ifndef nullptr
++//#define nullptr NULL
++//#endif
+ 
+ // we even have globals:
+ extern int VERBOSE;
diff --git a/xssp/patches/patch-src_progress.h b/xssp/patches/patch-src_progress.h
new file mode 100644
index 0000000000..30ce2ff71c
--- /dev/null
+++ b/xssp/patches/patch-src_progress.h
@@ -0,0 +1,20 @@
+$NetBSD$
+
+# Missing header
+
+--- src/progress.h.orig	2018-04-06 08:17:20 UTC
++++ src/progress.h
+@@ -6,7 +6,12 @@
+ 
+ #pragma once
+ 
+-#if defined(__linux__)
++#if defined(__FreeBSD__)
++
++#include <atomic>
++typedef std::atomic<int64>  MCounter;
++
++#elif defined(__linux__)
+ 
+ #if defined(__INTEL_COMPILER_BUILD_DATE) || \
+     (defined(__GNUC__) && (__GNUC__ > 4 || \
Prev by Date: compiler-rt-netbsd: Update to SVN r. 346042
Next by Date: Qemu with NVMM acceleration support.
Previous by Thread: compiler-rt-netbsd: Update to SVN r. 346042
Next by Thread: Qemu with NVMM acceleration support.
Indexes:
Home | Main Index | Thread Index | Old Index