[pkgsrc/trunk]: pkgsrc/biology/xmakemol biology/xmakemol: import package from...

[vins <vins%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/5582c643f235
branches:  trunk
changeset: 390819:5582c643f235
user:      vins <vins%pkgsrc.org@localhost>
date:      Fri Dec 30 18:17:48 2022 +0000

description:
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.

diffstat:

 biology/xmakemol/DESCR                     |  15 +++++++
 biology/xmakemol/MESSAGE                   |   8 +++
 biology/xmakemol/Makefile                  |  61 ++++++++++++++++++++++++++++++
 biology/xmakemol/PLIST                     |   6 ++
 biology/xmakemol/distinfo                  |   7 +++
 biology/xmakemol/files/xmakemol.desktop    |   8 +++
 biology/xmakemol/patches/patch-Makefile.in |  14 ++++++
 biology/xmakemol/patches/patch-xmakemol.1  |  15 +++++++
 8 files changed, 134 insertions(+), 0 deletions(-)

diffs (166 lines):

diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/DESCR    Fri Dec 30 18:17:48 2022 +0000
@@ -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.
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/MESSAGE
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/MESSAGE  Fri Dec 30 18:17:48 2022 +0000
@@ -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
+
+===========================================================================
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/Makefile Fri Dec 30 18:17:48 2022 +0000
@@ -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@localhost
+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"
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/PLIST    Fri Dec 30 18:17:48 2022 +0000
@@ -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
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/distinfo Fri Dec 30 18:17:48 2022 +0000
@@ -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
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/files/xmakemol.desktop
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/files/xmakemol.desktop   Fri Dec 30 18:17:48 2022 +0000
@@ -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;
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/patches/patch-Makefile.in
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/patches/patch-Makefile.in        Fri Dec 30 18:17:48 2022 +0000
@@ -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@
diff -r 84bcfc78db5c -r 5582c643f235 biology/xmakemol/patches/patch-xmakemol.1
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/xmakemol/patches/patch-xmakemol.1 Fri Dec 30 18:17:48 2022 +0000
@@ -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