New port: science/coot: Crystallographic Object-Oriented Toolkit

svn path=/head/; revision=474154

science/Makefile

@@ -46,6 +46,7 @@
     SUBDIR += clhep
     SUBDIR += clipper
     SUBDIR += colt
+    SUBDIR += coot
     SUBDIR += crf++
     SUBDIR += dcl
     SUBDIR += devisor

science/coot/Makefile

@@ -0,0 +1,50 @@
+# $FreeBSD$
+
+PORTNAME=	coot
+DISTVERSION=	0.8.9.1
+CATEGORIES=	science
+MASTER_SITES=	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/${PORTNAME}/source/releases/ \
+		https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/${PORTNAME}/dependencies/:data
+DISTFILES=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX} refmac-monomer-library${EXTRACT_SUFX}:data reference-structures${EXTRACT_SUFX}:data
+DIST_SUBDIR=	${PORTNAME}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Crystallographic Object-Oriented Toolkit
+
+LICENSE=	LGPL3
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+LIB_DEPENDS=	libccp4c.so:science/libccp4 \
+		libclipper-core.so:science/clipper \
+		libcurl.so:ftp/curl \
+		libfontconfig.so:x11-fonts/fontconfig \
+		libfreetype.so:print/freetype2 \
+		libgtkglext-x11-1.0.so:x11-toolkits/gtkglext \
+		libgsl.so:math/gsl \
+		libmmdb2.so:science/mmdb2 \
+		libpng16.so:graphics/png \
+		libsfftw.so:math/fftw-float \
+		libssm.so:science/libssm
+RUN_DEPENDS=	bash:shells/bash
+
+USES=		desktop-file-utils fortran gettext-runtime gmake libtool localbase:ldflags pkgconfig python:2.7 shebangfix sqlite
+SHEBANG_FILES=	src/coot.in
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--with-python
+CONFIGURE_ARGS=	--enable-shared --disable-static
+USE_GNOME=	atk cairo gdkpixbuf2 glib20 gtk20 libartlgpl2 libgnomecanvas pango pangox-compat
+USE_GL=		gl glu glut
+USE_XORG=	ice sm x11 xmu xt
+INSTALL_TARGET=	install-strip
+USE_LDCONFIG=	yes
+INSTALLS_ICONS=	yes
+
+MAKE_ENV=	PYTHON=${PYTHON_CMD}
+CXXFLAGS+=	-I${PYTHON_INCLUDEDIR}
+
+post-install:
+	@${MKDIR} ${STAGEDIR}${DATADIR}/lib/data
+	@cd ${WRKDIR} && ${COPYTREE_SHARE} monomers ${STAGEDIR}${DATADIR}/lib/data/
+	@cd ${WRKDIR} && ${COPYTREE_SHARE} reference-structures ${STAGEDIR}${DATADIR}/
+
+.include <bsd.port.mk>

science/coot/distinfo

@@ -0,0 +1,7 @@
+TIMESTAMP = 1531013796
+SHA256 (coot/coot-0.8.9.1.tar.gz) = 51b6faef11177a8ab682fbe28448f935ae1252ad53b4efa31339ff658a63ff94
+SIZE (coot/coot-0.8.9.1.tar.gz) = 19360553
+SHA256 (coot/refmac-monomer-library.tar.gz) = 03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b
+SIZE (coot/refmac-monomer-library.tar.gz) = 37439851
+SHA256 (coot/reference-structures.tar.gz) = 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
+SIZE (coot/reference-structures.tar.gz) = 6728787

science/coot/files/patch-src_cc-interface-image.hh

@@ -0,0 +1,8 @@
+--- src/cc-interface-image.hh.orig	2018-07-08 02:10:49 UTC
++++ src/cc-interface-image.hh
+@@ -1,4 +1,5 @@
+ 
++#include <Python.h>
+ 
+ // make a png given the info in text_info_dict
+ // fields: text, font, size, colour, slant, weight

science/coot/files/patch-src_rama__plot.cc

@@ -0,0 +1,11 @@
+--- src/rama_plot.cc.orig	2018-07-08 02:28:57 UTC
++++ src/rama_plot.cc
+@@ -39,6 +39,8 @@
+ #include <iostream>
+ #include <algorithm>
+ 
++#include <sys/stat.h>
++
+ #include <gdk/gdkkeysyms.h> // for keyboarding.
+ 
+ #include "utils/coot-utils.hh" // int to string

science/coot/pkg-descr

@@ -0,0 +1,9 @@
+Coot is for macromolecular model building, model completion and validation,
+particularly suitable for protein modelling using X-ray data.
+
+Coot displays maps and models and allows model manipulations such as
+idealization, real space refinement, manual rotation/translation, rigid-body
+fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots,
+skeletonization, non-crystallographic symmetry and more.
+
+WWW: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/