biology/xmakemol: import package from wip.

XMakemol is a mouse-based program, written using the LessTif widget set,
for viewing and manipulating atomic and other chemical systems. It reads
XYZ input and renders atoms, bonds and hydrogen bonds.

biology/xmakemol/DESCR

@@ -0,0 +1,15 @@
+XMakemol is a mouse-based program, written using the LessTif widget set,
+for viewing and manipulating atomic and other chemical systems. It reads XYZ
+input and renders atoms, bonds and hydrogen bonds.
+
+Features include:
+
+ - Animating multiple frame files
+ - Interactive measurement of bond lengths, bond angles and torsion angles
+ - Control over atom/bond sizes
+ - Exporting to Xpm, Encapsulated PostScript and XYZ formats
+ - Toggling the visibility of groups of atoms
+ - Editing the positions of subsets of atoms
+
+This version incorporates the latest patches from Debian, which provide
+additional tuning of H-bond detection.

biology/xmakemol/MESSAGE

@@ -0,0 +1,8 @@
+===========================================================================
+$NetBSD: MESSAGE,v 1.1 2022/12/30 18:17:48 vins Exp $
+
+To use xmakemol, set the XM_ELEMENTS environmental variable as below:
+
+	export XM_ELEMENTS=${PREFIX}/share/xmakemol/elements
+
+===========================================================================

biology/xmakemol/Makefile

@@ -0,0 +1,61 @@
+# $NetBSD: Makefile,v 1.1 2022/12/30 18:17:48 vins Exp $
+
+DISTNAME=	xmakemol-5.16h
+CATEGORIES=	biology x11
+MASTER_SITES=	ftp://ftp.NetBSD.org/pub/NetBSD/misc/vins/dists/
+EXTRACT_SUFX=	.tar.xz
+
+MAINTAINER=	vins@NetBSD.org
+HOMEPAGE=	https://www.nongnu.org/xmakemol/
+COMMENT=	Program for visualizing atomic and molecular systems
+LICENSE=	gnu-gpl-v2
+
+GNU_CONFIGURE=	yes
+USE_TOOLS+=	gmake perl
+USE_TOOLS+=	autoconf automake autoreconf
+
+REPLACE_PERL=	xmake_anim.pl
+
+ELEM_FILE=	${WRKSRC}/elements
+
+SUBST_CLASSES+=		paths
+SUBST_STAGE.paths=	pre-configure
+SUBST_FILES.paths+=	xmakemol.1
+SUBST_VARS.paths=	PREFIX
+SUBST_MESSAGE.paths=	Replacing PREFIX placeholder.
+
+CONFIGURE_ARGS+=	--with-mesa
+CONFIGURE_ARGS+=	--with-opengl=${BUILDLINK_PREFIX.MesaLib}
+
+BUILDLINK_TRANSFORM+=	l:MesaGL:GL
+BUILDLINK_TRANSFORM+=	l:MesaGLU:GLU
+
+MAKE_FLAGS+=	CC=${CC:Q}
+MAKE_FLAGS+=	CFLAGS='${CFLAGS} -DELEMENTS=\"${ELEM_FILE}\"'
+MAKE_FLAGS+=	CPPLAGS=${CPPLAGS:Q}
+MAKE_FLAGS+=	LDFLAGS=${LDFLAGS:Q}
+
+INSTALLATION_DIRS=	share/applications
+
+WRKSRC=	${WRKDIR}/${DISTNAME:S,h,,}
+
+post-extract:
+	${CP} ${FILESDIR}/xmakemol.desktop ${WRKSRC}
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/xmakemol.desktop \
+		${DESTDIR}${PREFIX}/share/applications/xmakemol.desktop
+
+.include "../../sysutils/desktop-file-utils/desktopdb.mk"
+.include "../../graphics/MesaLib/buildlink3.mk"
+.include "../../graphics/freeglut/buildlink3.mk"
+.include "../../graphics/glw/buildlink3.mk"
+.include "../../graphics/glu/buildlink3.mk"
+.include "../../x11/libX11/buildlink3.mk"
+.include "../../x11/libXt/buildlink3.mk"
+.include "../../x11/libXmu/buildlink3.mk"
+.include "../../x11/libXi/buildlink3.mk"
+.include "../../x11/libXext/buildlink3.mk"
+.include "../../x11/libXpm/buildlink3.mk"
+.include "../../mk/motif.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"

biology/xmakemol/PLIST

@@ -0,0 +1,6 @@
+@comment $NetBSD: PLIST,v 1.1 2022/12/30 18:17:48 vins Exp $
+bin/xmake_anim.pl
+bin/xmakemol
+man/man1/xmakemol.1
+share/applications/xmakemol.desktop
+share/xmakemol/elements

biology/xmakemol/distinfo

@@ -0,0 +1,7 @@
+$NetBSD: distinfo,v 1.1 2022/12/30 18:17:48 vins Exp $
+
+BLAKE2s (xmakemol-5.16h.tar.xz) = 104be5a568d52cceacf8aa0f4c7619d7aa2f0039b4b45ad1ece34aa2c4e895e2
+SHA512 (xmakemol-5.16h.tar.xz) = 63ce47a96aaa61872bd27cb60befe175f72b0a3560ce48056d21fce91e0d268436c73b4ddc9bd9fa539cbabe4934167da92122847e226657178e82a7d0e01280
+Size (xmakemol-5.16h.tar.xz) = 216832 bytes
+SHA1 (patch-Makefile.in) = 57d571687495e824866a9040e43da3ad95ca1904
+SHA1 (patch-xmakemol.1) = ef991119d9e5534d6032b7e94f3ea7d7c1cacbe3

biology/xmakemol/files/xmakemol.desktop

@@ -0,0 +1,8 @@
+[Desktop Entry]
+Version=1.0
+Name=XMakemol
+GenericName=Molecule Viewer
+Comment=View and manipulate atomic and other chemical systems
+Type=Application
+Exec=xmakemol
+Categories=Chemistry;Education;Science;

biology/xmakemol/patches/patch-Makefile.in

@@ -0,0 +1,14 @@
+$NetBSD: patch-Makefile.in,v 1.1 2022/12/30 18:17:48 vins Exp $
+
+datarootdir support.
+
+--- Makefile.in.orig	2022-12-22 06:47:47.695595945 +0000
++++ Makefile.in
+@@ -41,6 +41,7 @@ bindir = @bindir@
+ sbindir = @sbindir@
+ libexecdir = @libexecdir@
+ datadir = @datadir@
++datarootdir = @datarootdir@
+ sysconfdir = @sysconfdir@
+ sharedstatedir = @sharedstatedir@
+ localstatedir = @localstatedir@

biology/xmakemol/patches/patch-xmakemol.1

@@ -0,0 +1,15 @@
+$NetBSD: patch-xmakemol.1,v 1.1 2022/12/30 18:17:48 vins Exp $
+
+Fix hardcoded path.
+
+--- xmakemol.1.orig	2005-03-07 10:49:49.000000000 +0000
++++ xmakemol.1
+@@ -47,7 +47,7 @@ Print version information.
+ 
+ .SH FILES
+ .LP 
+-\fI/usr/share/xmakemol/elements\fP
++\fI@PREFIX@/share/xmakemol/elements\fP
+ List of element properties.
+ 
+ .SH ENVIRONMENT VARIABLES