[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/

[Justin Lecher]

commit:     4e20152045ceb0f0a851b14fe5e867c844e97b73
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 21 09:23:14 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Sep 28 09:06:59 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4e201520

sci-chemistry/coot: Adjust pc patch for latest head

Package-Manager: portage-2.2.6

---
 sci-chemistry/coot/ChangeLog           |  3 +++
 sci-chemistry/coot/files/9999-pc.patch | 42 +++++++++++++++-------------------
 2 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 43da818..2d2b7c3 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Sep 2013; Justin Lecher <jlec@g.o> files/9999-pc.patch:
+  Adjust pc patch for latest head
+
   19 Sep 2013; Justin Lecher <jlec@g.o> coot-9999.ebuild:
   Clean for latest HEAD
 

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 16e899f..2f97194 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -313,7 +313,7 @@ index 399f453..3d2ff55 100755
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/configure.in b/configure.in
-index 5928c3c..9e235b5 100644
+index cc549a5..d56f856 100644
 --- a/configure.in
 +++ b/configure.in
 @@ -108,14 +108,18 @@ esac
@@ -357,15 +357,15 @@ index 5928c3c..9e235b5 100644
 +		fi
 +	])
  
- AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
-  coot_enterprise_additions="true",
+ AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ],
+  coot_enhanced_ligand_additions="true",
 diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 009841e..7687d56 100644
+index 05fdf70..1e1c5d2 100644
 --- a/coords/Makefile.am
 +++ b/coords/Makefile.am
 @@ -29,7 +29,7 @@ INCLUDES = \
  	-I$(top_srcdir) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) 		\
 -	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
 +	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -443,7 +443,7 @@ index 3a85b9e..1a11cdf 100644
  pkginclude_HEADERS = db-main.hh db-strands.hh
  pkgincludedir = $(includedir)/coot/db-main
 diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..31d35a0 100644
+index cec561d..c207a43 100644
 --- a/db-main/Makefile.simple
 +++ b/db-main/Makefile.simple
 @@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
@@ -463,7 +463,7 @@ index cec561d..31d35a0 100644
 +CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
  
 -INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
  
  CXXFLAGS = -g $(INCLUDES)
  LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 
@@ -584,7 +584,7 @@ index 3c32c3c..0abd514 100644
  	-I$(top_srcdir)/geometry
  
 diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index 12d4ca6..5367e39 100644
+index df74b90..7f54567 100644
 --- a/lbg/Makefile.am
 +++ b/lbg/Makefile.am
 @@ -6,7 +6,7 @@ INCLUDES = \
@@ -594,7 +594,7 @@ index 12d4ca6..5367e39 100644
 -	$(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
 +	$(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
  	$(COOT_WINDOWS_CFLAGS) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) \
 diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
 index 48d091b..5b148b4 100644
@@ -624,7 +624,7 @@ index 48d091b..5b148b4 100644
  
  lbg:  lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
 diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 2fcb96b..201ceb0 100644
+index 72b28ca..2a184b4 100644
 --- a/lidia-core/Makefile.am
 +++ b/lidia-core/Makefile.am
 @@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
@@ -636,7 +636,7 @@ index 2fcb96b..201ceb0 100644
  #
  INCLUDES = \
  	 -I$(top_srcdir) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) 		\
 -        $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
 +        $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -848,18 +848,15 @@ index 30fdcb9..3e4c0c6 100644
  ifelse([$1], , :, [$1])
  
 diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..fcfde1d 100644
+index 25dc502..21646a5 100644
 --- a/macros/mmdb-ssm.m4
 +++ b/macros/mmdb-ssm.m4
-@@ -31,14 +31,13 @@ AC_ARG_WITH(ssmlib-prefix,
- AC_MSG_CHECKING([for ssm library])
+@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
  
- if test x$with_ssmlib_prefix != x; then
--
     if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
  
 -      MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+   MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
++      MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
        # AFAICS, ssm does not put its libs in $acl_libdirstem
        # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
        MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
@@ -868,15 +865,12 @@ index 25dc502..fcfde1d 100644
  
        # saved_LIBS="$LIBS"
        # saved_CPPFLAGS="$CPPFLAGS"
-@@ -49,12 +48,13 @@ if test x$with_ssmlib_prefix != x; then
- 
+@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
     else 
        AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
--   fi
+    fi
 -   MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+      fi
-+
-+  MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
++   MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
    
  else 
  
@@ -1015,7 +1009,7 @@ index 54872fe..bef7d0e 100644
  AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
  
 diff --git a/src/Makefile.am b/src/Makefile.am
-index fe9656f..384991b 100644
+index af5276b..d0ab482 100644
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
 @@ -195,11 +195,11 @@ INCLUDES = \