Version Bump; 340867; removed old

Package-Manager: portage-2.2_rc95/cvs/Linux x86_64

4 files changed, 131 insertions, 35 deletions

diff --git a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
new file mode 100644
index 000000000000..77ee077937dc
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
@@ -0,0 +1,131 @@
+diff --git a/Makefile.am b/Makefile.am
+index d5d020d..550d52a 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -113,24 +113,11 @@ install:
+ 	    mkdir $(CWD)/$$dir/tmp ; \
+ 	  fi ; \
+ 	  chmod 777 $(CWD)/$$dir/tmp ; \
+-	  echo "Adding server.html" ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/index.html ; \
+-	  echo "Adding python files" ; \
+-	  cp $$c/*.py* $(CWD)/$$dir/. ; \
++	  cp $$c/main*.py $(CWD)/$$dir/. ; \
+ 	  echo "Adding __init__.py" ; \
+ 	  cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \
+ 	  echo "Adding pdb2pqr.py" ; \
+ 	  cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.cgi" ; \
+-	  cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.css" ; \
+-	  cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding apbs_cgi.cgi" ; \
+-	  cp $$c/visualize.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding visualize.cgi" ; \
+-	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding querystatus.cgi" ; \
+-	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
+ 	  if ! test -d $(CWD)/$$dir/dat  ; then \
+ 	    mkdir $(CWD)/$$dir/dat ; \
+ 	  fi ; \
+@@ -138,49 +125,12 @@ install:
+ 	  cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc  ; then \
+-	    mkdir $(CWD)/$$dir/doc ; \
+-	  fi ; \
+-	  echo "Adding doc/" ; \
+-	  cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \
+-	  cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/images  ; then \
+-	    mkdir $(CWD)/$$dir/doc/images ; \
+-	  fi ; \
+-	  cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/pydoc ; then \
+-	    mkdir $(CWD)/$$dir/doc/pydoc ; \
+-	  fi ; \
+-	  cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples ; then \
+-	    mkdir $(CWD)/$$dir/examples ; \
+-	  fi ; \
+-	  echo "Adding examples/" ; \
+-	  cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/1a1p ; then \
+-	    mkdir $(CWD)/$$dir/examples/1a1p ; \
+-	  fi ; \
+-	  cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \
+-	  cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/ligands ; then \
+-	    mkdir $(CWD)/$$dir/examples/ligands ; \
+-	  fi ; \
+-	  cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \
++	  echo "Adding extensions" ; \
+ 	  if ! test -d $(CWD)/$$dir/extensions ; then \
+ 	    mkdir $(CWD)/$$dir/extensions ; \
+ 	  fi ; \
+ 	  echo "Adding extensions" ; \
+ 	  cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \
+-	  if ! test -d $(CWD)/$$dir/html  ; then \
+-	    mkdir $(CWD)/$$dir/html ; \
+-	  fi ; \
+-	  cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \
+-	  if ! test -d $(CWD)/$$dir/jmol ; then \
+-	    mkdir $(CWD)/$$dir/jmol ; \
+-	  fi ; \
+-	  echo "Adding jmol/" ; \
+-	  cp -rf $$c/jmol/*.* $(CWD)/$$dir/jmol/. ; \
+ 	  if ! test -d $(CWD)/$$dir/src ; then \
+ 	    mkdir $(CWD)/$$dir/src ; \
+ 	  fi ; \
+@@ -229,49 +179,6 @@ install:
+ 	  echo PDB2PQR has been installed in $(CWD)/$$dir ; \
+ 	  echo ; \
+ 	  cd $(CWD)/$$dir ; \
+-	  cd $$c; \
+-	  rm lastfieldfile prefixfile dir1file fieldfile ; \
+-	  echo $(URL) > url_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \
+-	  last_url=`cat url_file_2` ; \
+-	  echo $(PREFIX) > p_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \
+-	  last_p=`cat p_file_2` ; \
+-	  rm -f url_file* p_file* ; \
+-	  if test `whoami` = "root" ; then \
+-            webviewable="true" ; \
+-	    echo ${prefix} > prefix_file_tmp ; \
+-            first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \
+-	    second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \
+-	    third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \
+-	    rm -f prefix_file_tmp ; \
+-	    if test $$first != var || test $$second != www || test $$third != html ; then  \
+-	      webviewable=false ; \
+-	    fi ; \
+-	    if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \
+-	      echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \
+-	      if test -d "/var/www/html/$$last_url" ; then \
+-	        echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \
+-		echo Do you want to overwrite this? \(Y/N\); \
+-		read choice ; \
+-	        while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n")  \
+-	          do  \
+-	          echo You have entered $$choice. Please enter Y or N: ; \
+-	          read choice ; \
+-	        done ; \
+-	        if test $$choice = "N" || test $$choice = "n" ; then  \
+-	          echo Please run configure again and specify a different --prefix ; \
+-	          exit 0 ; \
+-	        fi ; \
+-	  	rm -rf /var/www/html/"$$last_url" ; \
+-	      fi ; \
+-	      ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	      echo "Symbolic link created." ; \
+-	    fi ; \
+-	  else  \
+-	    echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \
+-	    echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	  fi ; \
+ 	fi
+ 
+ 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
deleted file mode 100644
index 2ccd01785213..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp
---- pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp	2006-12-05 20:35:43.000000000 -0500
-+++ pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp	2008-06-19 08:53:22.000000000 -0400
-@@ -8,6 +8,8 @@
- //
- //
- 
-+#include <cstdlib>
-+
- void MC::reformat_arrays() {
-   //
-   // Reformat the matrix
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch
deleted file mode 100644
index 57f02f264ba8..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-ldflags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.3.0/propka/Makefile.in pdb2pqr-1.3.0.new/propka/Makefile.in
---- pdb2pqr-1.3.0/propka/Makefile.in	2007-10-11 18:26:48.000000000 -0400
-+++ pdb2pqr-1.3.0.new/propka/Makefile.in	2008-10-11 07:10:51.000000000 -0400
-@@ -169,7 +169,7 @@
- 	-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
- _propkalib.so$(EXEEXT): $(_propkalib_so_OBJECTS) $(_propkalib_so_DEPENDENCIES) 
- 	@rm -f _propkalib.so$(EXEEXT)
--	$(_propkalib_so_LINK) $(_propkalib_so_LDFLAGS) $(_propkalib_so_OBJECTS) $(_propkalib_so_LDADD) $(LIBS)
-+	$(_propkalib_so_LINK) $(_propkalib_so_LDFLAGS) $(LDFLAGS) $(_propkalib_so_OBJECTS) $(_propkalib_so_LDADD) $(LIBS)
- propka$(EXEEXT): $(propka_OBJECTS) $(propka_DEPENDENCIES) 
- 	@rm -f propka$(EXEEXT)
- 	$(F77LINK) $(propka_LDFLAGS) $(propka_OBJECTS) $(propka_LDADD) $(LIBS)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
deleted file mode 100644
index 09405ec7c3f3..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pdb2pka/pMC_mult.cpp.orig	2009-05-19 23:35:45.000000000 +0400
-+++ pdb2pka/pMC_mult.cpp	2009-05-19 23:36:27.000000000 +0400
-@@ -7,7 +7,7 @@
- //
- //
- //
--
-+#include <stdio.h>
- #include <cstdlib>
- 
- void MC::reformat_arrays() {