CVS commit: pkgsrc/biology/xmakemol

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/xmakemol
From: "Paolo Vincenzo Olivo" <vins%netbsd.org@localhost>
Date: Fri, 30 Dec 2022 18:17:48 +0000

Module Name:    pkgsrc
Committed By:   vins
Date:           Fri Dec 30 18:17:48 UTC 2022

Added Files:
        pkgsrc/biology/xmakemol: DESCR MESSAGE Makefile PLIST distinfo
        pkgsrc/biology/xmakemol/files: xmakemol.desktop
        pkgsrc/biology/xmakemol/patches: patch-Makefile.in patch-xmakemol.1

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/xmakemol/DESCR \
    pkgsrc/biology/xmakemol/MESSAGE pkgsrc/biology/xmakemol/Makefile \
    pkgsrc/biology/xmakemol/PLIST pkgsrc/biology/xmakemol/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/xmakemol/files/xmakemol.desktop
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/xmakemol/patches/patch-Makefile.in \
    pkgsrc/biology/xmakemol/patches/patch-xmakemol.1

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

Added files:

Index: pkgsrc/biology/xmakemol/DESCR
diff -u /dev/null pkgsrc/biology/xmakemol/DESCR:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/DESCR       Fri Dec 30 18:17:48 2022
@@ -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.
Index: pkgsrc/biology/xmakemol/MESSAGE
diff -u /dev/null pkgsrc/biology/xmakemol/MESSAGE:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/MESSAGE     Fri Dec 30 18:17:48 2022
@@ -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
+
+===========================================================================
Index: pkgsrc/biology/xmakemol/Makefile
diff -u /dev/null pkgsrc/biology/xmakemol/Makefile:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/Makefile    Fri Dec 30 18:17:48 2022
@@ -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"
Index: pkgsrc/biology/xmakemol/PLIST
diff -u /dev/null pkgsrc/biology/xmakemol/PLIST:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/PLIST       Fri Dec 30 18:17:48 2022
@@ -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
Index: pkgsrc/biology/xmakemol/distinfo
diff -u /dev/null pkgsrc/biology/xmakemol/distinfo:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/distinfo    Fri Dec 30 18:17:48 2022
@@ -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

Index: pkgsrc/biology/xmakemol/files/xmakemol.desktop
diff -u /dev/null pkgsrc/biology/xmakemol/files/xmakemol.desktop:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/files/xmakemol.desktop      Fri Dec 30 18:17:48 2022
@@ -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;

Index: pkgsrc/biology/xmakemol/patches/patch-Makefile.in
diff -u /dev/null pkgsrc/biology/xmakemol/patches/patch-Makefile.in:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/patches/patch-Makefile.in   Fri Dec 30 18:17:48 2022
@@ -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@
Index: pkgsrc/biology/xmakemol/patches/patch-xmakemol.1
diff -u /dev/null pkgsrc/biology/xmakemol/patches/patch-xmakemol.1:1.1
--- /dev/null   Fri Dec 30 18:17:48 2022
+++ pkgsrc/biology/xmakemol/patches/patch-xmakemol.1    Fri Dec 30 18:17:48 2022
@@ -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

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