[63877] trunk/dports/science

[ryandesign at macports.org]

Revision: 63877
          http://trac.macports.org/changeset/63877
Author:   ryandesign at macports.org
Date:     2010-02-17 10:29:25 -0800 (Wed, 17 Feb 2010)
Log Message:
-----------
pynmr: new port, version 0.37f; see #21642

Added Paths:
-----------
    trunk/dports/science/pynmr/
    trunk/dports/science/pynmr/Portfile
    trunk/dports/science/pynmr/files/
    trunk/dports/science/pynmr/files/pynmr.diff

Added: trunk/dports/science/pynmr/Portfile
===================================================================
--- trunk/dports/science/pynmr/Portfile	                        (rev 0)
+++ trunk/dports/science/pynmr/Portfile	2010-02-17 18:29:25 UTC (rev 63877)
@@ -0,0 +1,51 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+
+name                pynmr
+version             0.37f
+categories          science
+maintainers         bromo.med.uc.edu:howarth
+
+description         NMR plugin for pymol
+
+long_description    PyNMR features loading multiple pdb files, dihedral restraints checks, \
+                    NOE restraints checks, and superimposition. PyNMR was written by Leigh Willard.
+
+homepage            http://pelican.rsvs.ulaval.ca/mediawiki/index.php/PyNMR
+platforms           darwin
+master_sites        http://diablo.ucsc.edu/~wgscott/pymol/
+distname            ${name}_${version}_src
+
+checksums           md5  cb4a3906766681ce9230ef5515e1aa1c \
+                    sha1 21aa455421ac4742c62ede878c2e42e22f9eca51 \
+                    rmd160 53f40a547a5ef0a9c0725491c988b3e8bcb8706c
+
+patchfiles          pynmr.diff
+
+depends_build       port:swig-python
+depends_lib         port:meschach port:pymol
+
+use_configure       no
+use_parallel_build  no
+use_bzip2           yes
+
+build.dir           ${worksrcpath}/pmg_tk/startup/pynmr
+build.cmd           ./run.macos
+build.target
+
+post-patch {
+    reinplace  "s|@PREFIX@|${prefix}|g" ${build.dir}/run.macos \
+                                        ${build.dir}/test_data/test.script
+}
+
+destroot {
+    xinstall -d ${destroot}${prefix}/lib/pymol/modules/pmg_tk/startup/pynmr
+    xinstall -m 644 ${worksrcpath}/pmg_tk/startup/plug_nmr.py ${destroot}${prefix}/lib/pymol/modules/pmg_tk/startup
+    xinstall -m 644 -W ${build.dir} Crmsd.so BIOPYTHON_LICENSE LICENSE README ${destroot}${prefix}/lib/pymol/modules/pmg_tk/startup/pynmr
+    foreach d {help images test_data} {
+       copy ${build.dir}/${d} ${destroot}${prefix}/lib/pymol/modules/pmg_tk/startup/pynmr
+    }
+    eval xinstall -m 644 [glob ${build.dir}/*.py] ${destroot}${prefix}/lib/pymol/modules/pmg_tk/startup/pynmr
+}


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

Added: trunk/dports/science/pynmr/files/pynmr.diff
===================================================================
--- trunk/dports/science/pynmr/files/pynmr.diff	                        (rev 0)
+++ trunk/dports/science/pynmr/files/pynmr.diff	2010-02-17 18:29:25 UTC (rev 63877)
@@ -0,0 +1,38 @@
+--- pmg_tk/startup/pynmr/Crmsd.i.org	2009-08-17 22:47:39.000000000 -0400
++++ pmg_tk/startup/pynmr/Crmsd.i	2009-08-17 22:47:48.000000000 -0400
+@@ -4,6 +4,7 @@
+ %array_functions(char *, charArray);
+ %array_functions(int, intArray);
+ %{
++extern char * C_do_best_range(char*, char*, char*, char*, char*, double);
+ %}
+ 
+ extern char * C_do_best_range(char*, char*, char*, char*, char*, double); 
+--- pmg_tk/startup/pynmr/run.macos.org	2006-04-06 10:10:45.000000000 -0400
++++ pmg_tk/startup/pynmr/run.macos	2009-04-03 21:04:39.000000000 -0400
+@@ -1,4 +1,4 @@
+-/Users/leigh/pynmr/swig/swig -python -I/Users/leigh/pynmr/swig/Lib/ -I/Users/leigh/pynmr/swig/Lib/python Crmsd.i
++ at PREFIX@/bin/swig -python Crmsd.i
+ 
+ # now fix the error that swig produces...
+ sed -e '/SWIG_init/s/init_/init/' -e '/SWIG_name/s/_Crmsd/Crmsd/ ' Crmsd_wrap.c > Crmsd_wrap2.c
+@@ -8,8 +8,8 @@
+ #gcc -c Crmsd.c Crmsd_wrap.c -I../../../meschach -I/usr/include/python2.3 -lm 
+ #gcc -shared Crmsd.o Crmsd_wrap.o meschach.a -o Crmsd.so
+ 
+-gcc -fno-common -c Crmsd.c Crmsd_wrap.c -I/Users/leigh/pynmr/meschach -I/usr/include/python2.3  -D_POSIX_C_SOURCE
+-gcc -bundle -flat_namespace -L/usr/include/python2.3 Crmsd.o Crmsd_wrap.o /Users/leigh/pynmr/meschach/meschach.a -lPython -o Crmsd.so
++gcc -O3 -fno-common -c Crmsd.c Crmsd_wrap.c -I at PREFIX@/include/meschach -I at PREFIX@/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6  -D_POSIX_C_SOURCE
++gcc -O3 -bundle -bundle_loader @PREFIX@/bin/python2.6 -flat_namespace -undefined suppress Crmsd.o Crmsd_wrap.o -L at PREFIX@/lib -lmeschach -o Crmsd.so
+ 
+ 
+ 
+--- pmg_tk/startup/pynmr/test_data/test.script.org	2009-04-04 00:49:35.000000000 -0400
++++ pmg_tk/startup/pynmr/test_data/test.script	2009-04-04 00:52:04.000000000 -0400
+@@ -6,5 +6,5 @@
+ 	pairfit=0)
+ nmr_cmd.C_do_best_range('test_1', 'C N CA', \
+ 	"test_1 test_2 test_3", "all", \
+-	"/home2/leigh/Proj/pynmr/pmg_tk/startup/pynmr/test_data/", 1.0)
++	"@PREFIX@/lib/pymol/modules/pmg_tk/startup/pynmr/test_data", 1.0)
+ 
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