biology/dsr-pdb: Add c++11 flags because boost isn't found without it

Also add patches for missing includes that only gcc complains about.

PR:		235519
Reported by:	Piotr Kubaj <pkubaj@anongoth.pl>

biology/dsr-pdb/Makefile

@@ -2,6 +2,7 @@
 
 PORTNAME=	dsr-pdb
 DISTVERSION=	1.0.3
+DISTVERSIONSUFFIX=	1
 CATEGORIES=	biology
 MASTER_SITES=	https://graphics.stanford.edu/~drussel/
 DISTNAME=	${PORTNAME}
@@ -13,12 +14,14 @@ COMMENT=	Simple C++ PDB reader (reads the protein description format)
 LICENSE=	LGPL21
 LICENSE_FILE=	${WRKSRC}/COPYING.txt
 
-USES=		gmake libtool tar:tgz
+LIB_DEPENDS=	libboost_program_options.so:devel/boost-libs
+
+USES=		compiler:c++11-lang gmake libtool localbase:ldflags tar:tgz
 GNU_CONFIGURE=	yes
 USE_LDCONFIG=	yes
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
-CXXFLAGS+=	-fPIC
+CXXFLAGS+=	-fPIC --std=c++11 # libboost_program_options.so isn't found without --std=c++11
 
 post-patch:
 .for dir in lib tools test

biology/dsr-pdb/files/patch-include_dsrpdb_Point.h

@@ -0,0 +1,10 @@
+--- include/dsrpdb/Point.h.orig	2019-02-05 18:18:53 UTC
++++ include/dsrpdb/Point.h
+@@ -22,6 +22,7 @@ MA 02111-1307, USA. */
+ #define DSR_PDB_POINT_H
+ #include <iostream>
+ #include <dsrpdb/config.h>
++#include <assert.h>
+ 
+ #ifdef PDB_USE_CGAL 
+ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>

biology/dsr-pdb/files/patch-lib_Protein__pdb.cc

@@ -0,0 +1,10 @@
+--- lib/Protein_pdb.cc.orig	2019-02-05 18:17:52 UTC
++++ lib/Protein_pdb.cc
+@@ -23,6 +23,7 @@ MA 02111-1307, USA. */
+ #include "pdb_utils.h"
+ #include <dsrpdb_internal/Error_logger.h>
+ #include <sstream>
++#include <string.h>
+ 
+ namespace dsrpdb {
+