Moved from app-sci/pymol to sci-chemistry/pymol.

9 files changed, 128 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/files/digest-pymol-0.88 b/sci-chemistry/pymol/files/digest-pymol-0.88
new file mode 100644
index 000000000000..bea1a59ed9d6
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.88
@@ -0,0 +1 @@
+MD5 22d56cde503191894cd17a2965981b63 pymol-0_88-src.tgz 2092837
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.90 b/sci-chemistry/pymol/files/digest-pymol-0.90
new file mode 100644
index 000000000000..5d6062d88f16
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.90
@@ -0,0 +1 @@
+MD5 be181d10df622b011725d9541da22070 pymol-0_90-src.tgz 2134293
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.95 b/sci-chemistry/pymol/files/digest-pymol-0.95
new file mode 100644
index 000000000000..99112b99b7c5
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.95
@@ -0,0 +1 @@
+MD5 ca5f7ee698bfec6218f45342bd925e56 pymol-0_95-src.tgz 2676518
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.97 b/sci-chemistry/pymol/files/digest-pymol-0.97
new file mode 100644
index 000000000000..3285748e37b1
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.97
@@ -0,0 +1 @@
+MD5 e1220898cea37483ddd6f410a6fc02d2 pymol-0_97-src.tgz 2753262
diff --git a/sci-chemistry/pymol/files/header_order.patch b/sci-chemistry/pymol/files/header_order.patch
new file mode 100644
index 000000000000..e11f31b24029
--- /dev/null
+++ b/sci-chemistry/pymol/files/header_order.patch
@@ -0,0 +1,36 @@
+--- layer0/MyPNG.c	2004-01-30 00:40:33.000000000 +0100
++++ layer0/MyPNG.c.new	2004-04-20 16:05:35.399498139 +0200
+@@ -14,17 +14,8 @@
+ Z* -------------------------------------------------------------------
+ */
+ 
+-#include"os_predef.h"
+-#include"os_std.h"
+-
+-#include"Base.h"
+-#include "MyPNG.h"
+-#include"MemoryDebug.h"
+-#include "Setting.h"
+-
+ #ifdef _HAVE_LIBPNG
+-#include<png.h>
+-
++#include <png.h>
+  /* The png_jmpbuf() macro, used in error handling, became available in
+   * libpng version 1.0.6.  If you want to be able to run your code with older
+   * versions of libpng, you must define the macro yourself (but only if it
+@@ -37,6 +28,14 @@
+ 
+ #endif
+ 
++#include"os_predef.h"
++#include"os_std.h"
++
++#include"Base.h"
++#include "MyPNG.h"
++#include"MemoryDebug.h"
++#include "Setting.h"
++
+ int MyPNGWrite(char *file_name,unsigned char *p,unsigned int width,unsigned int height)
+ {
+ #ifdef _HAVE_LIBPNG
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
new file mode 100644
index 000000000000..202a7cf88083
--- /dev/null
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -0,0 +1,8 @@
+--- modules/pymol/invocation.py.orig	2003-06-11 13:40:13.000000000 -0400
++++ modules/pymol/invocation.py	2003-06-11 13:40:29.000000000 -0400
+@@ -179,5 +179,3 @@
+ 
+          else:
+             options.deferred.append(a)
+-      if options.show_splash and not options.no_gui:
+-         options.deferred.insert(0,"_do__ cmd.splash(1)")
diff --git a/sci-chemistry/pymol/files/pymol-gentoo.diff b/sci-chemistry/pymol/files/pymol-gentoo.diff
new file mode 100644
index 000000000000..8b4b2baabd4b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-gentoo.diff
@@ -0,0 +1,53 @@
+--- Rules.linux	Sun Mar 31 03:06:22 2002
++++ Rules.make	Tue May 21 15:42:31 2002
+@@ -12,14 +12,13 @@
+ XLIB_DIR = -L/usr/X11R6/lib
+ XINC_DIR = -I/usr/X11R6/include
+ #--- Python
+-PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
++PYTHON_EXE = /usr/bin/python
+ PYTHON_LIB =
+ PYTHON_LIB_DIR = 
+-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \
+-	-I$(PYMOL_PATH)/ext/include/python2.1/Numeric
++PYTHON_INC_DIR = -I/usr/include/python2.2  -I/usr/include/python2.2/Numeric
+ #--- Other external dependencies
+-EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
+-EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
++EXT_INC_DIR = 
++EXT_LIB_DIR = 
+ #---------------------------------------------------------------------
+ #
+ #- Build for LINUX as an importable module ---------------------------
+@@ -48,7 +47,7 @@
+ #
+ #- Choose One --------------------------------------------------------
+ #--- Workaround for XFree86/DRI linux dll problem for module build
+-BUGS = -D_DRI_WORKAROUND
++DEFS += -D_DRI_WORKAROUND
+ #---
+ #BUGS =
+ #---------------------------------------------------------------------
+@@ -58,7 +57,7 @@
+ #PNG = -D_HAVE_LIBPNG 
+ #ZLIB = 
+ #--- Libpng2 available but needs zlib 
+-PNG = -D_HAVE_LIBPNG 
++DEFS += -D_HAVE_LIBPNG 
+ ZLIB = -lz
+ #--- Libpng2 not available
+ #PNG = 
+@@ -77,12 +76,7 @@
+ PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \
+    -I../layer3 -I../layer4 -I../layer5 
+ 
+-C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
+-   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
+-
+-CFLAGS = $(C_FLAGS)
+-
+-
++C_FLAGS := $(CFLAGS) $(PYTHON_INC_DIR) $(XINC_DIR) $(DEFS)
+ 
+ 
+ 
diff --git a/sci-chemistry/pymol/files/setup.py-gentoo.patch b/sci-chemistry/pymol/files/setup.py-gentoo.patch
new file mode 100644
index 000000000000..d67559643594
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup.py-gentoo.patch
@@ -0,0 +1,10 @@
+--- pymol-0.90/setup.py 2003-04-26 21:22:14.000000000 -0400
++++ pymol-0.90.new/setup.py     2003-07-21 09:39:51.000000000 -0400
+@@ -71,6 +71,7 @@
+    "layer0/Map.c",
+    "layer0/Match.c",
+    "layer0/Matrix.c",
++   "layer0/MemoryCache.c",
+    "layer0/MemoryDebug.c",
+    "layer0/MyPNG.c",
+    "layer0/Parse.c",
diff --git a/sci-chemistry/pymol/files/setup2.py-gentoo.patch b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
new file mode 100644
index 000000000000..1d387eaa0f4c
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
@@ -0,0 +1,17 @@
+--- setup2.py.orig	2003-06-10 19:12:35.000000000 -0400
++++ setup2.py	2003-06-10 19:11:46.000000000 -0400
+@@ -12,6 +12,14 @@
+ import sys
+ from distutils import dir_util,file_util
+ 
++import os.path
++pmlibs = os.path.join(os.environ['D'],
++                      sys.prefix[1:],
++                      'lib/python%s' % sys.version[:3],
++                      'site-packages')
++sys.path.insert(0, pmlibs)
++
++
+ if sys.platform=='win32':
+    launch_script = "pymol.bat"
+ elif sys.platform=='cygwin':