[62660] trunk/dports/science

[mmoll at macports.org]

Revision: 62660
          http://trac.macports.org/changeset/62660
Author:   mmoll at macports.org
Date:     2010-01-13 07:01:17 -0800 (Wed, 13 Jan 2010)
Log Message:
-----------
new port: science/ce, a tool for 3D protein structure comparison and alignment

Added Paths:
-----------
    trunk/dports/science/ce/
    trunk/dports/science/ce/Portfile
    trunk/dports/science/ce/files/
    trunk/dports/science/ce/files/patch-Makefile.diff
    trunk/dports/science/ce/files/patch-ce.C.diff
    trunk/dports/science/ce/files/patch-pom.h.diff

Added: trunk/dports/science/ce/Portfile
===================================================================
--- trunk/dports/science/ce/Portfile	                        (rev 0)
+++ trunk/dports/science/ce/Portfile	2010-01-13 15:01:17 UTC (rev 62660)
@@ -0,0 +1,22 @@
+# $Id$
+
+PortSystem 1.0
+name                ce
+version             2004-07-06
+categories          science
+maintainers         mmoll
+description         Combinatorial Extension (CE) Method for 3D protein \
+		    structure comparison and alignment
+long_description    $description
+homepage            http://cl.sdsc.edu/ce.html
+platforms           darwin
+master_sites        ftp://ftp.sdsc.edu/pub/sdsc/biology/CE/src
+distname            ${name}
+checksums           md5     ec838ffc2d7c6ac15043e98b094519e1 \
+                    sha1    cb1d7507a931e2635f302cad523c3082ba63596b \
+                    rmd160  5475e00ff66d95fbe61e433d85067f5830259d0d
+worksrcdir          ${name}_distr_${version}
+patchfiles          patch-ce.C.diff patch-Makefile.diff patch-pom.h.diff
+use_configure	    no
+destroot.env-append PREFIX=${prefix}
+universal_variant   no


Property changes on: trunk/dports/science/ce/Portfile
___________________________________________________________________
Added: svn:keywords
   + Id
Added: svn:eol-style
   + native

Added: trunk/dports/science/ce/files/patch-Makefile.diff
===================================================================
--- trunk/dports/science/ce/files/patch-Makefile.diff	                        (rev 0)
+++ trunk/dports/science/ce/files/patch-Makefile.diff	2010-01-13 15:01:17 UTC (rev 62660)
@@ -0,0 +1,16 @@
+--- Makefile.orig	2000-05-25 20:26:03.000000000 -0500
++++ Makefile	2010-01-13 08:49:40.000000000 -0600
+@@ -1,4 +1,4 @@
+-all: make_pom make_ce make_copy
++all: make_pom make_ce
+ 
+ make_ce:
+ 	$(MAKE) -C ce
+@@ -16,3 +16,7 @@
+ use_exe_sgi:
+ 	cp ce/ce_sgi ./CE
+ 	cp pom/mkDB_sgi pom/mkDB
++
++install:
++	cp ce/ce ${DESTDIR}/${PREFIX}/bin/ce
++	cp pom/mkDB ${DESTDIR}/${PREFIX}/bin/mkDB

Added: trunk/dports/science/ce/files/patch-ce.C.diff
===================================================================
--- trunk/dports/science/ce/files/patch-ce.C.diff	                        (rev 0)
+++ trunk/dports/science/ce/files/patch-ce.C.diff	2010-01-13 15:01:17 UTC (rev 62660)
@@ -0,0 +1,20 @@
+--- ce/ce.C.orig	2003-03-13 18:42:38.000000000 -0600
++++ ce/ce.C	2010-01-07 12:12:40.000000000 -0600
+@@ -79,7 +79,7 @@
+   char *user_file1, *entity_id1;
+   setText(&user_file1, pdb_file1);
+ 
+-  setText(&mkdb_command, "pom/mkDB");
++  setText(&mkdb_command, "mkDB");
+   addText(&mkdb_command, " scratch ");
+   addText(&mkdb_command, db_tmp_path);
+   addText(&mkdb_command, " ");
+@@ -96,7 +96,7 @@
+   setText(&user_file2, pdb_file2);
+ 
+ 
+-  setText(&mkdb_command, "pom/mkDB");
++  setText(&mkdb_command, "mkDB");
+   addText(&mkdb_command, " scratch ");
+   addText(&mkdb_command, db_tmp_path);
+   addText(&mkdb_command, " ");

Added: trunk/dports/science/ce/files/patch-pom.h.diff
===================================================================
--- trunk/dports/science/ce/files/patch-pom.h.diff	                        (rev 0)
+++ trunk/dports/science/ce/files/patch-pom.h.diff	2010-01-13 15:01:17 UTC (rev 62660)
@@ -0,0 +1,41 @@
+--- pom/pom.h.orig	2000-05-25 16:38:55.000000000 -0500
++++ pom/pom.h	2010-01-07 12:04:24.000000000 -0600
+@@ -410,11 +410,11 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class Entities {
+-  friend IEntity;
+-  friend ISubentity;
+-  friend IAtom;
+-  friend IMonomer;
+-  friend IBond;
++  friend class IEntity;
++  friend class ISubentity;
++  friend class IAtom;
++  friend class IMonomer;
++  friend class IBond;
+  public:
+   static DB *db_default;
+   DB *db;
+@@ -502,7 +502,7 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class ISubentity {
+-  friend IMonomer;
++  friend class IMonomer;
+   int iE;
+   int iS;
+   int iM;
+@@ -576,9 +576,9 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class IAtom {
+-  friend ISubentity;
+-  friend IMonomer;
+-  friend IBond;
++  friend class ISubentity;
++  friend class IMonomer;
++  friend class IBond;
+   int iE;
+   int iS;
+   int iA;
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