Drop old, fixes bug #478592

Signed-off-by: Justin Lecher <jlec@gentoo.org>
Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!

9 files changed, 25 insertions, 692 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index a1a3589acb8a..2231d93962da 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.50 2015/08/07 10:36:03 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.51 2015/08/07 11:03:57 jlec Exp $
+
+  07 Aug 2015; Justin Lecher <jlec@gentoo.org> -files/1.7.0-install.patch,
+  -files/pdb2pqr-1.4.0-automagic.patch, -files/pdb2pqr-1.4.0-install.patch,
+  -files/pdb2pqr-1.4.0-ldflags.patch, -files/pdb2pqr-1.8.0-automagic.patch,
+  -files/pdb2pqr-1.8.0-ldflags.patch, -pdb2pqr-1.5.0-r2.ebuild:
+  Drop old, fixes bug #478592
 
   07 Aug 2015; Agostino Sarubbo <ago@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
   Stable for x86, wrt bug #534696
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 4cf1dfb86726..f60b680dc530 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,36 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
-AUX 1.7.0-install.patch 5165 SHA256 965c0bf8077eebc733c60d4e80d05167ce31d7188b01ca43c0fb5c0b27ede22b SHA512 72f290d8df7051f0fc2d42543f0d09fef4350656194f5013f132abb7edbe4dc11f18a3329bbd41b86f9a582b170fea53d472be320f5e08a2f0d84d42b4f4639c WHIRLPOOL ea71e6271c0dd491a7778cf3c0f54ebce79f35680abb49eadfbb6208379b1d5c69b18eacde92183bd005ffad26db115b05f69b7cbcf5256fa72d94caab9509c4
 AUX pdb2pka 270 SHA256 ae1112d6b793b10399a4ae14dc5cfd0518c463121d98e00ab08b2827db061303 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b WHIRLPOOL ef5d1fac1bacd6403219e36955701b2a2d33a2aa9936b2334ed7ea48346b1cae74481bb634ba67f9250e7bac73723ce2e4da6c759b87c57111fad166624f0b82
 AUX pdb2pqr 263 SHA256 f07b197ec4903125e9566b394ed6a620f56511413bf14ba5fdd3484302d166e2 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d WHIRLPOOL 8e4889677ec874a88f3d485b133d3e92a3618d0ed90f4199d05add55f1819df94be762d3950ef9bd21db1112fa75adf26f909d04fdc57c4686cccb3244687fd2
-AUX pdb2pqr-1.4.0-automagic.patch 3526 SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a SHA512 dfb5a219fabe4b57da82098c80eb6556e6826cd91d3db2da2e858964180cfe3268314562320159b82dc811a08714ca3a0e78881244949ff7ffeef2f797397237 WHIRLPOOL 03061ecbab813a572f18a794609655aa9ad9a16d6ed10c421437dddac589de750adacdfe2f89b17e022cccf0ffe0018a40bbe2e7f37c692d025f6998088364af
-AUX pdb2pqr-1.4.0-install.patch 5372 SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643 SHA512 615e984335d67668689423d4ab37be996cb178450a2ae0782432d47d7be2cfa8aaeb18776e604c706df743d2a30b93bc1febc28722ef7b5b2480545ca3ccd510 WHIRLPOOL c054c12d1c9ed4ad093326736fd74c6af54d7124ef6455120e5bf37a1a683cf1a5d1a9faec7ff323c7512c4bdbd53c703ee305daf6c76847e87aa2b9a58f7b59
-AUX pdb2pqr-1.4.0-ldflags.patch 1293 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726 SHA512 4edf74ae59b5ca99e2c492103d16769f300293df07f833d78d8e7d24d85c10531ac7907c5444b65507952f4622608459952ae57835f52af8b0f7e09637f1fcf5 WHIRLPOOL 359a84ecaa55cadfa7cf1bb3c116105c486f1fa737d74b6f2ba2f399147dfcd15d088682c75efee7a69394a3f7adf7dc0c978c060ad64c105b3e96a0b75f49d5
-AUX pdb2pqr-1.8.0-automagic.patch 2544 SHA256 135cfe03fc38a7bef028452010dedab3cc90c1f554cef1139b1d9836824520e9 SHA512 65dc03368909a9378ecda6c8357e9119bd76311b5fd6dc0ce00ff7d5b948190ad9f07ac3626dad04915928558f911f4deea5f44725e6cf029ca26dcb2e54b76c WHIRLPOOL 8462f3288722bcaca651845242b3354f365a9686a6400d3fae9c8ca69e3fa55d9282a62bdc2a3374eb468fbfae2611f8fa700ddecc404943c2a08080fad34b06
-AUX pdb2pqr-1.8.0-ldflags.patch 1098 SHA256 b9ab2740e062b130c4b61d385b762d4ce54ec3d6a040f37b8b501b4f107890b8 SHA512 0bd250efd74c70096011ed6f9f6fd2f22a987bbe0355f5ba33ad4675141d1d7b02e9eaa90bc1c7328454da2225183a56dae6acbaae97a929b2455430ca55ab4e WHIRLPOOL 75b4110d4259454551256c3a647b1981aa4ee040f73baf8f3e5ce1f0a4b01b54cdf2879030265dde4c7dbc0a5c60bd400a0d498f00446c88125d147c291ef107
 AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c
 AUX pdb2pqr-1.9.0-install-py.patch 578 SHA256 c82c11eb421a839710d40bfb3de4d99852ef69dc9b35b1ac31f7b51b36ff512d SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 WHIRLPOOL 94348fe88a1910e916ca0d428a78636e5fe8371582a80dbbbda07d433d1fb8a35157a73d525eac88bd9dac6dc1c3a913288fdb7bd06f7584553b0b5c17aa17da
-DIST pdb2pqr-1.5.tar.gz 5747178 SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae
-EBUILD pdb2pqr-1.5.0-r2.ebuild 3668 SHA256 09b59ed6461c60ca7fdcdca1604306579f054db992b1833226cce00566f05a7a SHA512 2d1ce04378e15d814dfc73d407149465e61b04d646710b918708e4f8eb1a6f1973c85cfca0d63dfa8f85aa6cf1e61b3a950c82833ff7853e2d6d3bc223890f6d WHIRLPOOL 3e4da41f599befa813ec693c8fd2b42ffda163047a43ecbe8f83a3fd63e1066a61e05e56993b2fa3fcc507e652ad60ad3aeca7c6fbb1e967edcc1ead362b943d
 EBUILD pdb2pqr-1.9.0-r1.ebuild 3030 SHA256 bebe2059a75043ec8634b6c9130e19f2f1b2ea8a001d83d137e7daca15d8d4f3 SHA512 f0dc8a0464d84e72e595817b17aaa703346666a1f0e07e098eea810cf1b0c039485c0542d7bbe4cf32e06263f5e0bdf4819f0bf951bee70be5945732a3d2f618 WHIRLPOOL 617ac375dacaa0f473adec511ab9d8d02256ac415fee584d3273b37edfd27b52a939c656474d009feea3a538f217f673710c77b7fb8d1e807dc601208a71ef7f
-MISC ChangeLog 7834 SHA256 bed1e46ddeccb2ecdde0e78af7f30e9550ccf68b21851ca8902c93b46e7fbe47 SHA512 f012e61047aacc2b115a9c238dd1fad6489ac6890b3e602cd9d582b0088e144168958d1d2ad15d1accec0b4a19a27d08507c8604c7ff54ffc83505237fe68a27 WHIRLPOOL 8d87d9a8bbf8678a35e248103b3a5f6c245b4b4fd48c56e5c20961d354ae7b88703c9f417406f3c63efd7bd41af5476c8bb32162d63d70065ee74e01d67dfb0a
+MISC ChangeLog 8157 SHA256 c05694b5d9f6956e9beb4ef67234f8f8807c0f707696deafcd58dffbb48ec23c SHA512 515f7a96bd3a1b80b11f46d20d3865c5aab7975ff0c8c77266dbf26b5e54dc0718fc006a6d733bbd4f1946e6975df9dfd98232e6393bf38b7891392f57ffc4aa WHIRLPOOL 660a27a3c807e7a445e54ebba830cb0c84b1ab6d5ae9c20d7a9dafcea45af8f343cd608a4103f560a061cd7081b9b76a50cd0a4cfdd9c4be1b22333c341aaa09
 MISC metadata.xml 408 SHA256 a835ee092251d931dd23459814c2689bfddeb1682c4baffe05ecccc0e5ebe1ff SHA512 16fec7aa9c078b4221412efc4406a78b840f773bd765682a1eb090306db018d68a266d6f2e0a78c1d86bc7b55d7ec61a6d1bb338f385825956750bfe41a693f5 WHIRLPOOL 5bac81102bacccd18fa3b7322e860fb8de8b6e74c9c79502719345bac650da764876e2be3465a50f9bf29d8dda53e1d07de8ba34bbcd3fa23504e27e2e1f162f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.1
 
-iQIcBAEBCAAGBQJVxIoUAAoJELp701BxlEWfOfMQAKawKibqi8y5yVhCFN8IdOEz
-T0xoPUjTaQTIz+ifTzEL0k9Jc3FuEZ+y6IJxDtmzWK+wAoIa8Nukki8rpVxHr0vr
-xZlwQZzdpFD8S92OlLQqE+7Wjbx5d8hFeAsWCb/TItHd1zkXSfyThXn2XZVvYpSj
-RtxJa4b8WEd0uWdv2wGmbPtz5GOqgY1XGOdK5se0udEWRDpyxqz4jUnpbIUjTPzD
-5RezHyY/uUJVeT1KlOmXsc4ItSJAwf+2oTPgPoa3+CwKhOvDZE+T+1oNEi4jb1ZQ
-Xy979hv9zezJ6Fmpkheff50viiQ4G2UiXxXinE1yPRVU6x8cJepBdTEuV3+mGkRw
-rXY48GOWlT0H8OelAvIY//IRkZi497HKH0BFbL4aGkgkgCa5hSm0wxzG0K1cQSNF
-YESRlCbJE0BdukTNviatBfYQLhs4z+nilw5bBsYtzxI7pi9wgvBn7pQN86u02i+X
-xU5CRL1N5nh4OeGO+bMd0Bp9fKjUZe+TTE8QYN2Se9Asuvs9VJZCkeD5cXd9h4MI
-p3AJ/cHyQbsElsQWey7+A6J5KuYp7qb9uqKfbg2dAQ90wZNfiUfN7S1XXGpTgx2c
-kWn7mmYtVJTap+sR3GpnXr3UAJ5wq12ESqepJVTLq1ATa4ARpLRQYK4pJGyYrGo6
-OBYh6aA4lFYpMXBqGGf4
-=HRw3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+=SIa8
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
deleted file mode 100644
index 77ee077937dc..000000000000
--- a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-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-1.4.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
deleted file mode 100644
index addb76b9b4e6..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
---- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
-+++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
-@@ -255,38 +255,6 @@
- 
-   # Test for Numeric install
-   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
--  if (test -n "${NUMERIC}") ; then
--    AC_MSG_RESULT([yes])
--    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
--    if test "$NUMERIC_INC" = ""; then
--      AC_MSG_ERROR([Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}])
--    fi
--    NUMERIC_INC=`dirname ${NUMERIC_INC}`
--    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
--    if test "${NUMERIC_LIB}" = ""; then
--      AC_MSG_ERROR([Please check your NUMERIC path.  Numeric.pth cannot be found in ${NUMERIC}])
--    fi
--    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
--    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
--    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
--    if test "${PACKAGE_PATH}" = ""; then
--      PACKAGE_PATH=${NUMERIC_LIB}
--    else
--      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
--    fi
--    PY_NUMERIC="-I${NUMERIC_INC} "
--    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
--  else
--    AC_MSG_RESULT([no])	
--    AC_MSG_CHECKING([for Numeric include files])
--    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
--      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"   
--      AC_MSG_RESULT([$PY_NUMERIC])
--      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
--    else
--      AC_MSG_RESULT([no])
--    fi
--  fi
- 
-   # If failed, test for numpy
-   AC_MSG_CHECKING([whether you defined numpy])
-@@ -457,29 +425,14 @@
-   HAVE_PDB2PQR_OPAL=1
- fi
- 
--if test "$PDB2PQR_OPAL_URL" != ""; then 
-+if test "$PDB2PQR_OPAL_URL" != "no"; then 
-   HAVE_PDB2PQR_OPAL=1
-   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
-     echo ZSI is installed
-   else
-     #  need to install ZSI
--    echo Installing ZSI.  This might take a while...
--    cd contrib/ZSI-2.1-a1 
--    if test `whoami` = "root"; then
--      $py_path setup.py install
--    else
--      zsi_install="true"
--      mkdir -p ${prefix}lib/python$PY_VERSION/site-packages
--      export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages
--      $py_path setup.py install --prefix=${prefix}
--      if test -d ${prefix}ZSI ; then
--        echo ZSI is installed
--      else
--        cp -r ./build/lib/ZSI ${prefix}ZSI
--      fi
--      PYTHONPATH=""
--    fi 
--    cd ../..
-+    echo Missing ZSI
-+    exit 1
-   fi
- fi  
- 
-diff -Naur pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py
---- pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py	2007-10-12 15:52:40.000000000 -0400
-+++ pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py	2009-09-24 19:36:07.000000000 -0400
-@@ -3,10 +3,7 @@
- # PC 2005/09/23
- # Get ligand topologies
- #
--try:
--    import Numeric
--except:
--    import numpy as Numeric
-+import numpy as Numeric
-     
- from sets import Set
- from ligandclean.trial_templates import *
-diff -Naur pdb2pqr-1.4.0/pdb2pka/ligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py
---- pdb2pqr-1.4.0/pdb2pka/ligand_topology.py	2008-06-13 10:15:38.000000000 -0400
-+++ pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py	2009-09-24 19:36:07.000000000 -0400
-@@ -3,10 +3,7 @@
- # PC 2005/09/23
- # Get ligand topologies
- #
--try:
--    import Numeric
--except:
--    import numpy as Numeric
-+import numpy as Numeric
-     
- from sets import Set
- from ligandclean.trial_templates import *
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
deleted file mode 100644
index 4af9eda8e1b3..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
+++ /dev/null
@@ -1,134 +0,0 @@
---- Makefile.am	2008-08-07 04:57:43.000000000 +0200
-+++ Makefile.am.new	2009-04-22 13:45:22.000000000 +0200
-@@ -104,30 +104,11 @@
- 	    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 $$c/jmol.cgi $(CWD)/$$dir/. ; \
--	  echo "Adding jmol.cgi" ; \
--	  cp $$c/visualize.cgi $(CWD)/$$dir/. ; \
--	  echo "Adding visualize.cgi" ; \
--	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
--	  echo "Adding querystatus.cgi" ; \
--	  cp $$c/Jmol.js $(CWD)/$$dir/. ; \
--	  echo "Adding Jmol.js" ; \
--	  cp $$c/JmolApplet.jar $(CWD)/$$dir/. ; \
--	  echo "Adding JmolApplet.jar" ; \
--	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
- 	  if ! test -d $(CWD)/$$dir/dat  ; then \
- 	    mkdir $(CWD)/$$dir/dat ; \
- 	  fi ; \
-@@ -135,44 +115,11 @@
- 	  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/. ; \
--	  if ! test -d $(CWD)/$$dir/extensions ; then \
--	    mkdir $(CWD)/$$dir/extensions ; \
--	  fi ; \
- 	  echo "Adding extensions" ; \
-+	  if ! test -d $(CWD)/$$dir/extensions ; then \
-+	    mkdir $(CWD)/$$dir/extensions ; \
-+	  fi ; \
- 	  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)/$$dir/src ; then \
- 	    mkdir $(CWD)/$$dir/src ; \
- 	  fi ; \
---- Makefile.am	2009-04-22 13:48:23.000000000 +0200
-+++ Makefile.am.new	2009-04-22 13:49:52.000000000 +0200
-@@ -168,49 +168,6 @@
- 	  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-1.4.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch
deleted file mode 100644
index ea5dc85ba07d..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- pdb2pka/Makefile.am	2008-04-24 21:44:28.000000000 +0200
-+++ pdb2pka/Makefile.am.new	2009-04-22 17:26:24.000000000 +0200
-@@ -16,7 +16,7 @@
- 
- noinst_PROGRAMS         = _pMC_mult.so
- _pMC_mult_so_SOURCES     = pMC_mult.cpp pMC_mult_wrap.cpp  
--_pMC_mult_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
-+_pMC_mult_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
- _pMC_mult_so_LDADD       = $(PY_LDFLAGS)
- 
- #all:
---- pdb2pka/substruct/Makefile.am	2008-04-24 19:54:39.000000000 +0200
-+++ pdb2pka/substruct/Makefile.am.new	2009-04-22 17:26:57.000000000 +0200
-@@ -15,7 +15,7 @@
- 
- noinst_PROGRAMS          = Algorithms.so
- Algorithms_so_SOURCES     = Algorithms.cpp  
--Algorithms_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
-+Algorithms_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
- Algorithms_so_LDADD       = $(PY_LDFLAGS)
- 
- distclean-local: clean-local
---- propka/Makefile.in	2007-10-12 00:26:48.000000000 +0200
-+++ propka/Makefile.in.new	2009-04-22 17:41:21.000000000 +0200
-@@ -99,7 +99,7 @@
- noinst_PROGRAMS = _propkalib.so propka
- _propkalib_so_SOURCES = propkalib.c propka.f propkac.c
- _propkalib_so_LINK = $(F77)
--_propkalib_so_LDFLAGS = -o $@ $(PY_SHARED)
-+_propkalib_so_LDFLAGS = $(LDFLAGS) -o $@ $(PY_SHARED)
- _propkalib_so_LDADD = $(PY_LDFLAGS)
- propka_SOURCES = propka.f
- 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
deleted file mode 100644
index c218fe6a816e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
---- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
-+++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
-@@ -255,38 +255,6 @@
- 
-   # Test for Numeric install
-   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
--  if (test -n "${NUMERIC}") ; then
--    AC_MSG_RESULT([yes])
--    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
--    if test "$NUMERIC_INC" = ""; then
--      AC_MSG_ERROR([Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}])
--    fi
--    NUMERIC_INC=`dirname ${NUMERIC_INC}`
--    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
--    if test "${NUMERIC_LIB}" = ""; then
--      AC_MSG_ERROR([Please check your NUMERIC path.  Numeric.pth cannot be found in ${NUMERIC}])
--    fi
--    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
--    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
--    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
--    if test "${PACKAGE_PATH}" = ""; then
--      PACKAGE_PATH=${NUMERIC_LIB}
--    else
--      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
--    fi
--    PY_NUMERIC="-I${NUMERIC_INC} "
--    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
--  else
--    AC_MSG_RESULT([no])	
--    AC_MSG_CHECKING([for Numeric include files])
--    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
--      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"   
--      AC_MSG_RESULT([$PY_NUMERIC])
--      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
--    else
--      AC_MSG_RESULT([no])
--    fi
--  fi
- 
-   # If failed, test for numpy
-   AC_MSG_CHECKING([whether you defined numpy])
-@@ -457,29 +425,14 @@
-   HAVE_PDB2PQR_OPAL=1
- fi
- 
--if test "$PDB2PQR_OPAL_URL" != ""; then 
-+if test "$PDB2PQR_OPAL_URL" != "no"; then 
-   HAVE_PDB2PQR_OPAL=1
-   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
-     echo ZSI is installed
-   else
-     #  need to install ZSI
--    echo Installing ZSI.  This might take a while...
--    cd contrib/ZSI-2.1-a1 
--    if test `whoami` = "root"; then
--      $py_path setup.py install
--    else
--      zsi_install="true"
--      mkdir -p ${prefix}lib/python$PY_VERSION/site-packages
--      export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages
--      $py_path setup.py install --prefix=${prefix}
--      if test -d ${prefix}ZSI ; then
--        echo ZSI is installed
--      else
--        cp -r ./build/lib/ZSI ${prefix}ZSI
--      fi
--      PYTHONPATH=""
--    fi 
--    cd ../..
-+    echo Missing ZSI
-+    exit 1
-   fi
- fi  
- 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
deleted file mode 100644
index 5a7e04419ce6..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- pdb2pka/Makefile.am           | 2 +-
- pdb2pka/substruct/Makefile.am | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am
-index 75f6ffd..e40a2f6 100644
---- a/pdb2pka/Makefile.am
-+++ b/pdb2pka/Makefile.am
-@@ -16,7 +16,7 @@ SUBDIRS          = substruct
- 
- noinst_PROGRAMS         = _pMC_mult.so
- _pMC_mult_so_SOURCES     = pMC_mult.cpp pMC_mult_wrap.cpp  
--_pMC_mult_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
-+_pMC_mult_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
- _pMC_mult_so_LDADD       = $(PY_LDFLAGS)
- 
- #all:
-diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am
-index b1638a0..ae95e94 100644
---- a/pdb2pka/substruct/Makefile.am
-+++ b/pdb2pka/substruct/Makefile.am
-@@ -15,7 +15,7 @@ CLEANFILES       = Algorithms.so
- 
- noinst_PROGRAMS          = Algorithms.so
- Algorithms_so_SOURCES     = Algorithms.cpp  
--Algorithms_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
-+Algorithms_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
- Algorithms_so_LDADD       = $(PY_LDFLAGS)
- 
- distclean-local: clean-local
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild
deleted file mode 100644
index baacac906039..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild,v 1.11 2012/10/19 10:10:18 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/numpy
-	sci-chemistry/openbabel
-	opal? ( dev-python/zsi )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
-	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
-	epatch "${FILESDIR}"/${PN}-1.4.0-install.patch
-	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
-		|| die "Failed to fix Makefile.am"
-	python_src_prepare
-	preparation() {
-		eautoreconf
-	}
-	python_execute_function -s preparation
-}
-
-src_configure() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-
-	configuration() {
-		# Avoid automagic to numeric
-		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
-			F77="$(tc-getFC)" \
-			econf \
-			$(use_with opal)
-	}
-	python_execute_function -s configuration
-}
-
-src_compile() {
-	compilation() {
-		emake || die
-	}
-	python_execute_function -s compilation
-}
-
-src_test() {
-	testing() {
-		emake -j1 test \
-			|| die "tests failed"
-	}
-	python_execute_function -s testing
-}
-
-src_install() {
-	installation() {
-		dodir $(python_get_sitedir)/${PN}
-		emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
-			PREFIX=""  install || die "install failed"
-
-		INPATH="$(python_get_sitedir)/${PN}"
-
-		# generate pdb2pqr wrapper
-		cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
-			#!/bin/sh
-			$(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$*
-		EOF
-
-		dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
-
-		insinto "${INPATH}"
-		doins __init__.py || \
-			die "Setting up the pdb2pqr site-package failed."
-
-		exeinto "${INPATH}"
-		doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-		insinto "${INPATH}"/dat
-		doins dat/* || die "Installing data failed."
-
-		exeinto "${INPATH}"/extensions
-		doexe extensions/* || \
-			die "Failed to install extensions."
-
-		insinto "${INPATH}"/src
-		doins src/*.py || die "Installing of python scripts failed."
-
-		exeinto "${INPATH}"/propka
-		doexe propka/_propkalib.so || \
-			die "Failed to install propka."
-
-		insinto "${INPATH}"/propka
-		doins propka/propkalib.py propka/__init__.py || \
-			die "Failed to install propka."
-
-		insinto "${INPATH}"/pdb2pka
-		doins pdb2pka/*.{py,so,DAT,h} || \
-			die "Failed to install pdb2pka."
-
-		insinto "${INPATH}"/pdb2pka/
-		doins pdb2pka/*.{py,so,DAT,h} || \
-			die "Failed to install pdb2pka."
-	}
-	python_execute_function -s installation
-
-	dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
-
-	if use doc; then
-		cd doc
-		sh genpydoc.sh \
-			|| die "genpydoc failed"
-		dohtml -r *.html images pydoc \
-			|| die "failed to install html docs"
-		cd -
-	fi
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples || die "Failed to install examples."
-	fi
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}