Initial import

3 files changed, 382 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..d0a364bba3e5
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,26 @@
+pkgbase = mgltools
+	pkgdesc = Visualization and analysis of molecular structures; includes AutoDockTools, Vision and PythonMoleculeViewer
+	pkgver = 1.5.6
+	pkgrel = 1
+	url = http://mgltools.scripps.edu/
+	arch = i686
+	arch = x86_64
+	license = custom
+	depends = swig
+	depends = tk
+	depends = python2-numpy
+	depends = python2-imaging
+	depends = python2-pmw
+	depends = glut
+	depends = zsi
+	depends = python2-simpy
+	depends = libxmu
+	optdepends = autodocksuite
+	options = !emptydirs
+	source = http://mgltools.scripps.edu/downloads/tars/releases/REL1.5.6/mgltools_source_1.5.6.tar.gz
+	source = opengltk.patch
+	md5sums = e37ceac50fd46bd89abb2ba44a812a65
+	md5sums = 357fe047c8edcd89d9cf1b8f7f70d258
+
+pkgname = mgltools
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..0d3b1ba449cb
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,94 @@
+# Maintainer: Michael Schubert <mschu.dev at gmail>
+
+pkgname=mgltools
+pkgver=1.5.6
+pkgrel=1
+pkgdesc="Visualization and analysis of molecular structures; includes AutoDockTools, Vision and PythonMoleculeViewer"
+arch=('i686' 'x86_64')
+url="http://mgltools.scripps.edu/"
+license=('custom')
+depends=('swig' 'tk' 'python2-numpy' 'python2-imaging' 'python2-pmw' 'glut' 'zsi' 'python2-simpy' 'libxmu')
+optdepends=('autodocksuite')
+source=("http://mgltools.scripps.edu/downloads/tars/releases/REL${pkgver}/${pkgname}_source_${pkgver}.tar.gz"
+        opengltk.patch)
+options=('!emptydirs')
+md5sums=('e37ceac50fd46bd89abb2ba44a812a65'
+         '357fe047c8edcd89d9cf1b8f7f70d258')
+
+build() {
+  cd "$srcdir/${pkgname}_source_$pkgver"
+  sed -i "1s:python2.5:python2:" InstTools/install
+
+  # replace path by os.path where needed
+  sed -i "s:path.exists:os.path.exists:; \
+    s:os.os.path.exists:os.path.exists:; \
+    s:path.join:os.path.join:; \
+    s:os.os.path.join:os.path.join:" InstTools/install
+
+  # do not install pmw since it is dependecy already
+  sed -i 's:getYesNo(msg, "Do you wish to install Pmw:False #:' InstTools/install
+  # fix include for strcmp in geomutils
+  sed -i "239i\    if (pkgname == \"geomutils\"): os.popen(\"sed -i '3i#include\
+    <string.h>' src/geomAlgorithms/objfile.cpp\")" InstTools/install
+  # fix opengltk to work with tcl/tk 8.5
+  sed -i "240i\    if (pkgname == \"opengltk\"): \
+    os.popen(\"sed -i 's/stub8.4/stub8.5/g' setup.py\")" InstTools/install
+  
+  # disable license popup - we'll print it to the user later
+  cd "$srcdir/${pkgname}_source_$pkgver/MGLPACKS"
+  tar -xzf mglutil-$pkgver.tar.gz
+  rm -f mglutil-$pkgver.tar.gz
+  echo > mglutil-$pkgver/mglutil/splashregister/license.py
+  tar -czf mglutil-$pkgver.tar.gz mglutil-$pkgver
+
+  # fix opengltk error
+  cd "$srcdir/${pkgname}_source_$pkgver/MGLPACKS"
+  tar -xzf opengltk-$pkgver.tar.gz
+  rm -f opengltk-$pkgver.tar.gz
+  patch -p0 < "$srcdir"/opengltk.patch
+  tar -czf opengltk-$pkgver.tar.gz opengltk-$pkgver
+}
+
+package() {
+  cd "$srcdir/${pkgname}_source_$pkgver"
+
+  # let python know about the new modules
+  pydir=`python2 -c "from distutils.sysconfig import get_python_lib; \
+    print get_python_lib()"`
+  mkdir -p "$pkgdir/$pydir"
+  ./startInstallation --quiet --instDir="$pkgdir/$pydir"
+
+  # link to bin directory
+  install -Dm755 "$pkgdir/$pydir/runAdt" "$pkgdir/usr/bin/adt"
+  install -Dm755 "$pkgdir/$pydir/runPmv" "$pkgdir/usr/bin/pmv"
+  install -Dm755 "$pkgdir/$pydir/runCADD" "$pkgdir/usr/bin/CADD"
+  install -Dm755 "$pkgdir/$pydir/runVision" "$pkgdir/usr/bin/vision"
+
+  echo "MGLToolsPckgs" > "$pkgdir/$pydir/mgltools.pth"
+
+  # fix some python 2.7 issues in the package
+  sed -i "/self.__debug__ = 0/d" \
+    "$pkgdir/$pydir/MGLToolsPckgs/ViewerFramework/VF.py"
+
+  # remove VCS entries
+  rm -rf `find "$pkgdir" -type d -name "CVS"`
+
+  # some other fixes..
+  cd "$pkgdir/$pydir/MGLToolsPckgs"
+  rm -f "mglutil/TestUtil/publishPack.csh"
+
+  # change interpreter from python/2.5 to python2
+  find . -name "*.py" | xargs sed -i "1s/python$/python2/;1s/python2.5$/python2/"
+
+  # install licenses
+  for LICENSE in `find . -name LICENSE`; do
+    install -Dm755 "./$LICENSE" "$pkgdir/usr/share/licenses/mgltools/$LICENSE"
+    rm "$LICENSE"
+  done
+  mv *.egg-info "$pkgdir/usr/share/licenses/mgltools/"
+
+  msg "LICENSE WARNING:"
+  msg "This software is free only for non-commercial usage"
+  msg "see /usr/share/licenses/mgltools/ for more information"
+}
+
diff --git a/opengltk.patch b/opengltk.patch
new file mode 100644
index 000000000000..d2490ae3546e
--- /dev/null
+++ b/opengltk.patch
@@ -0,0 +1,262 @@
+diff -rupNb opengltk-1.5.6-orig/Togl2.0/togl.c opengltk-1.5.6/Togl2.0/togl.c
+--- opengltk-1.5.6-orig/Togl2.0/togl.c	2009-05-14 21:43:34.000000000 +0100
++++ opengltk-1.5.6/Togl2.0/togl.c	2014-02-01 20:50:21.172391074 +0000
+@@ -1,3 +1,5 @@
++#define HAVE_UNISTD_H
++#define STDC_HEADERS
+ /* $Id: togl.c,v 1.2 2009/05/14 20:43:34 vareille Exp $ */
+ 
+ /* vi:set sw=4: */
+diff -rupNb opengltk-1.5.6-orig/include/tcltk84/tk/generic/tkFont.h opengltk-1.5.6/include/tcltk84/tk/generic/tkFont.h
+--- opengltk-1.5.6-orig/include/tcltk84/tk/generic/tkFont.h	1970-01-01 01:00:00.000000000 +0100
++++ opengltk-1.5.6/include/tcltk84/tk/generic/tkFont.h	2014-02-01 20:57:52.138795907 +0000
+@@ -0,0 +1,226 @@
++/*
++ * tkFont.h --
++ *
++ *	Declarations for interfaces between the generic and platform-
++ *	specific parts of the font package.  This information is not
++ *	visible outside of the font package.
++ *
++ * Copyright (c) 1996-1997 Sun Microsystems, Inc.
++ *
++ * See the file "license.terms" for information on usage and redistribution
++ * of this file, and for a DISCLAIMER OF ALL WARRANTIES.
++ *
++ * RCS: @(#) $Id: tkFont.h,v 1.1 2009/06/08 23:29:04 vareille Exp $
++ */
++
++#ifndef _TKFONT
++#define _TKFONT
++
++#ifdef BUILD_tk
++# undef TCL_STORAGE_CLASS
++# define TCL_STORAGE_CLASS DLLEXPORT
++#endif
++
++/*
++ * The following structure keeps track of the attributes of a font.  It can
++ * be used to keep track of either the desired attributes or the actual
++ * attributes gotten when the font was instantiated.
++ */
++
++typedef struct TkFontAttributes {
++    Tk_Uid family;		/* Font family, or NULL to represent
++				 * plaform-specific default system font. */
++    int size;			/* Pointsize of font, 0 for default size, or
++				 * negative number meaning pixel size. */
++    int weight;			/* Weight flag; see below for def'n. */
++    int slant;			/* Slant flag; see below for def'n. */
++    int underline;		/* Non-zero for underline font. */
++    int overstrike;		/* Non-zero for overstrike font. */
++} TkFontAttributes;
++
++/*
++ * Possible values for the "weight" field in a TkFontAttributes structure.
++ * Weight is a subjective term and depends on what the company that created
++ * the font considers bold.
++ */
++
++#define TK_FW_NORMAL	0
++#define TK_FW_BOLD	1
++
++#define TK_FW_UNKNOWN	-1	/* Unknown weight.  This value is used for
++				 * error checking and is never actually stored
++				 * in the weight field. */
++
++/*
++ * Possible values for the "slant" field in a TkFontAttributes structure.
++ */
++
++#define TK_FS_ROMAN	0	
++#define TK_FS_ITALIC	1
++#define TK_FS_OBLIQUE	2	/* This value is only used when parsing X
++				 * font names to determine the closest
++				 * match.  It is only stored in the
++				 * XLFDAttributes structure, never in the
++				 * slant field of the TkFontAttributes. */
++
++#define TK_FS_UNKNOWN	-1	/* Unknown slant.  This value is used for
++				 * error checking and is never actually stored
++				 * in the slant field. */
++
++/*
++ * The following structure keeps track of the metrics for an instantiated
++ * font.  The metrics are the physical properties of the font itself.
++ */
++
++typedef struct TkFontMetrics {
++    int	ascent;			/* From baseline to top of font. */
++    int	descent;		/* From baseline to bottom of font. */
++    int maxWidth;		/* Width of widest character in font. */
++    int fixed;			/* Non-zero if this is a fixed-width font,
++				 * 0 otherwise. */
++} TkFontMetrics;
++
++/*
++ * The following structure is used to keep track of the generic information
++ * about a font.  Each platform-specific font is represented by a structure
++ * with the following structure at its beginning, plus any platform-
++ * specific stuff after that.
++ */
++
++typedef struct TkFont {
++    /*
++     * Fields used and maintained exclusively by generic code.
++     */
++
++    int resourceRefCount;	/* Number of active uses of this font (each
++				 * active use corresponds to a call to
++				 * Tk_AllocFontFromTable or Tk_GetFont).
++				 * If this count is 0, then this TkFont
++				 * structure is no longer valid and it isn't
++				 * present in a hash table: it is being
++				 * kept around only because there are objects
++				 * referring to it.  The structure is freed
++				 * when resourceRefCount and objRefCount
++				 * are both 0. */
++    int objRefCount;		/* The number of Tcl objects that reference
++				 * this structure. */
++    Tcl_HashEntry *cacheHashPtr;/* Entry in font cache for this structure,
++				 * used when deleting it. */
++    Tcl_HashEntry *namedHashPtr;/* Pointer to hash table entry that
++				 * corresponds to the named font that the
++				 * tkfont was based on, or NULL if the tkfont
++				 * was not based on a named font. */
++    Screen *screen;		/* The screen where this font is valid. */
++    int tabWidth;		/* Width of tabs in this font (pixels). */
++    int	underlinePos;		/* Offset from baseline to origin of
++				 * underline bar (used for drawing underlines
++				 * on a non-underlined font). */
++    int underlineHeight;	/* Height of underline bar (used for drawing
++				 * underlines on a non-underlined font). */
++
++    /*
++     * Fields used in the generic code that are filled in by
++     * platform-specific code.
++     */
++
++    Font fid;			/* For backwards compatibility with XGCValues
++				 * structures.  Remove when TkGCValues is
++				 * implemented.  */
++    TkFontAttributes fa;	/* Actual font attributes obtained when the
++				 * the font was created, as opposed to the
++				 * desired attributes passed in to
++				 * TkpGetFontFromAttributes().  The desired
++				 * metrics can be determined from the string
++				 * that was used to create this font. */
++    TkFontMetrics fm;		/* Font metrics determined when font was
++				 * created. */
++    struct TkFont *nextPtr;	/* Points to the next TkFont structure with
++				 * the same name.  All fonts with the
++				 * same name (but different displays) are
++				 * chained together off a single entry in
++				 * a hash table. */
++} TkFont;
++
++/*
++ * The following structure is used to return attributes when parsing an
++ * XLFD.  The extra information is of interest to the Unix-specific code
++ * when attempting to find the closest matching font.
++ */
++
++typedef struct TkXLFDAttributes {
++    Tk_Uid foundry;		/* The foundry of the font. */
++    int slant;			/* The tristate value for the slant, which
++				 * is significant under X. */
++    int setwidth;		/* The proportionate width, see below for
++				 * definition. */
++    Tk_Uid charset;		/* The actual charset string. */
++} TkXLFDAttributes;
++
++/*
++ * Possible values for the "setwidth" field in a TkXLFDAttributes structure.
++ * The setwidth is whether characters are considered wider or narrower than
++ * normal.
++ */
++
++#define TK_SW_NORMAL	0
++#define TK_SW_CONDENSE	1
++#define TK_SW_EXPAND	2
++#define TK_SW_UNKNOWN	3	/* Unknown setwidth.  This value may be
++				 * stored in the setwidth field. */
++
++/*
++ * The following defines specify the meaning of the fields in a fully
++ * qualified XLFD.
++ */
++
++#define XLFD_FOUNDRY	    0
++#define XLFD_FAMILY	    1
++#define XLFD_WEIGHT	    2
++#define XLFD_SLANT	    3
++#define XLFD_SETWIDTH	    4
++#define XLFD_ADD_STYLE	    5
++#define XLFD_PIXEL_SIZE	    6
++#define XLFD_POINT_SIZE	    7
++#define XLFD_RESOLUTION_X   8
++#define XLFD_RESOLUTION_Y   9
++#define XLFD_SPACING	    10
++#define XLFD_AVERAGE_WIDTH  11
++#define XLFD_CHARSET	    12
++#define XLFD_NUMFIELDS	    13	/* Number of fields in XLFD. */
++
++/*
++ * Low-level API exported by generic code to platform-specific code.
++ */
++
++#define TkInitFontAttributes(fa)   memset((fa), 0, sizeof(TkFontAttributes));
++#define TkInitXLFDAttributes(xa)   memset((xa), 0, sizeof(TkXLFDAttributes));
++
++EXTERN int		TkFontParseXLFD _ANSI_ARGS_((CONST char *string,
++			    TkFontAttributes *faPtr, TkXLFDAttributes *xaPtr));
++EXTERN char **		TkFontGetAliasList _ANSI_ARGS_((CONST char *faceName));
++EXTERN char ***		TkFontGetFallbacks _ANSI_ARGS_((void));
++EXTERN int		TkFontGetPixels _ANSI_ARGS_((Tk_Window tkwin, 
++			    int size));
++EXTERN int		TkFontGetPoints _ANSI_ARGS_((Tk_Window tkwin, 
++			    int size));
++EXTERN char **		TkFontGetGlobalClass _ANSI_ARGS_((void));
++EXTERN char **		TkFontGetSymbolClass _ANSI_ARGS_((void));
++
++/*
++ * Low-level API exported by platform-specific code to generic code. 
++ */
++
++EXTERN void		TkpDeleteFont _ANSI_ARGS_((TkFont *tkFontPtr));
++EXTERN void		TkpFontPkgInit _ANSI_ARGS_((TkMainInfo *mainPtr));
++EXTERN TkFont *		TkpGetFontFromAttributes _ANSI_ARGS_((
++			    TkFont *tkFontPtr, Tk_Window tkwin,
++			    CONST TkFontAttributes *faPtr));
++EXTERN void		TkpGetFontFamilies _ANSI_ARGS_((Tcl_Interp *interp,
++			    Tk_Window tkwin));
++EXTERN TkFont *		TkpGetNativeFont _ANSI_ARGS_((Tk_Window tkwin,
++			    CONST char *name));
++
++# undef TCL_STORAGE_CLASS
++# define TCL_STORAGE_CLASS DLLIMPORT
++
++#endif	/* _TKFONT */
+diff -rupNb opengltk-1.5.6-orig/setup.py opengltk-1.5.6/setup.py
+--- opengltk-1.5.6-orig/setup.py	2012-11-08 22:55:20.000000000 +0000
++++ opengltk-1.5.6/setup.py	2014-02-01 20:59:59.720304555 +0000
+@@ -142,7 +142,7 @@ elif os.name == 'nt': #for Windows
+ ###################################################################
+ 
+ if tcltk_ver == '8.4':
+-    tcl_libs = {'posix':[ "tclstub8.4", "tkstub8.4"],
++    tcl_libs = {'posix':[],
+             'nt':[ "tclstub84", "tkstub84"]}.get(os.name,[])
+ else:
+     tcl_libs = {'posix':[ "tclstub8.5", "tkstub8.5"],
+@@ -295,8 +295,8 @@ if os.name == 'nt':
+     Togl ='Togl'
+     toglversion = '1.7'
+ else:
+-    Togl = "Togl2.1"
+-    toglversion = '2.1'
++    Togl = "Togl2.0"
++    toglversion = '2.0'
+ #elif sys.platform == 'darwin':
+ #    Togl ='Togl2.0'
+ #else: