sci-chemistry/xcrysden: new package, add 1.6.2

Signed-off-by: Patrick Taylor <patrick.joseph.taylor@gmail.com>

sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch

@@ -0,0 +1,14 @@
+Ensures that Togl is linked properly.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..ba478fa 100644
+--- a/system/Make.sys-shared
++++ b/system/Make.sys-shared
+@@ -48,7 +48,7 @@ X_INCDIR  =
+ 
+ TCL_LIB      = -ltcl$(TCL_VER2)
+ TK_LIB       = -ltk$(TCL_VER2)
+-TOGL_LIB     = -lTogl
++TOGL_LIB     = -Wl,-rpath,"/usr/lib64/Togl2.0" -L/usr/lib64/Togl2.0 -lTogl2.0
+ GLU_LIB      = -lGLU
+ GL_LIB       = -lGL
+ FFTW3_LIB    = -lfftw3

sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch

@@ -0,0 +1,14 @@
+Prevents bwidget from being automatically downloaded when it is already required as a build/run-time dependency.
+diff --git a/Makefile b/Makefile
+index cfdc14a..d0f7e6c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -18,7 +18,7 @@ what:
+ 
+ all: tcl tk mesa togl fftw xcrysden
+ #  meschach 
+-xcrysden: usage bwidget bindir src-C src-F src-Tcl
++xcrysden: usage bindir src-C src-F src-Tcl
+ 
+ usage: $(TOPDIR)/docs/xcrysden.1
+ 	man $(TOPDIR)/docs/xcrysden.1 | awk 'BEGIN {lprint=0; print "## do not edit changes will be lost (file automatically generated)\n"; } /SYNOPSIS/ { lprint=1; } /SEE ALSO/ { lprint=0; } /a*/ { if (lprint) print; }' > usage

sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch

@@ -0,0 +1,14 @@
+Adds -fcommon to CFLAGS to allow compilation on more recent GCC.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..f89f876 100644
+--- a/system/Make.sys-shared
++++ b/system/Make.sys-shared
+@@ -19,7 +19,7 @@ MAKE = make
+ # C-preprocessor flags
+ CPPFLAGS ?=
+ # C-compiler flags
+-CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall
++CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall -fcommon
+ 
+ CC     = gcc 
+ #LDLIB  = -ldl

sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch

@@ -0,0 +1,16 @@
+Ensures that wrapper scripts account for live filesystem merge.
+diff --git a/sys_utils/wrappers.sh b/sys_utils/wrappers.sh
+index 1fa3cc6..e078b22 100755
+--- a/sys_utils/wrappers.sh
++++ b/sys_utils/wrappers.sh
+@@ -5,8 +5,8 @@ do
+ #!/bin/sh -f
+ 
+ # simple wrapper to run $cmd
+-XCRYSDEN_TOPDIR="$prefix/share/$xcrysden"
+-XCRYSDEN_LIB_BINDIR="$prefix/lib/$xcrysden"
++XCRYSDEN_TOPDIR="/usr/share/$xcrysden"
++XCRYSDEN_LIB_BINDIR="/usr/lib/$xcrysden"
+ export XCRYSDEN_TOPDIR
+ export XCRYSDEN_LIB_BINDIR
+ 

sci-chemistry/xcrysden/files/xcrysden.desktop

@@ -0,0 +1,8 @@
+[Desktop Entry]
+Name=XCrySDen
+Type=Application
+Comment=For the visualisation of molecular and crystal structures.
+Exec=xcrysden
+TryExec=xcrysden
+Icon=/usr/share/icons/hicolor/96x96/apps/xcrysden.png
+Categories=Science;