[cctbxbb] using cctbx and sgtbx module

[hari jayaram]

Thanks a lot Ralf,
Running cctbx.python allows the sgtbx and uctbx modules to get imported.
I think I see what needs to be done to use these modules in other
programs , which is what the SuperSym plugin does from within pymol...


Thank you
Hari

On Mon, Nov 2, 2009 at 2:37 PM, Ralf W. Grosse-Kunstleve <rwgk at yahoo.com> wrote:
> Does this work?
>
> cctbx.python
> from cctbx import sgtbx
>
> The setpaths scripts only add one entry to PATH and leave the shell environment unmodified otherwise.
> This is the only way to avoid bad interferrences with other Python-based systems, among other things.
>
> cctbx.python is a small shell script (automatically generated) that updates PYTHONPATH and LD_LIBRARAY_PATH
> "just in time" before calling the actual python executable. You should never have to manually set PYTHONPATH
> for the cctbx modules.
> more cctbx_build/bin/cctbx.python
> to see how it works.
>
> You can set PYTHONPATH to point to other (non-cctbx) packages and it will be preserved when you
> run cctbx.python.
>
> You could also source setpaths_debug.sh to set PYTHONPATH and LD_LIBRARY_PATH for the cctbx packages
> permanently in your environment, but in my experience this can cause a lot of confusion.
>
> Ralf
>
>
>
>
> ----- Original Message ----
> From: hari jayaram <harijay at gmail.com>
> To: cctbxbb at phenix-online.org
> Sent: Mon, November 2, 2009 8:53:45 AM
> Subject: [cctbxbb] using cctbx and sgtbx module
>
> Hi I am trying to use a Python plugin SuperSymExample which has cctbx
> modules sgtbx and uctbx as dependencies.
>
> I wanted to build these modules for my system python 2.5.2  on ubuntu
> hardy heron 8.04 64 bit linux.
>
> I downloaded the selfx file for the cctbx alone ( without Python) and
> then had the build complete fully. I used the setpaths utility and
> then modifies m,y PYTHONPATH.
>
> Now after I add the appropriate directories to my PYTHONPATH , if I
> import sgtbx and uctbx  in a python interactive session I get an error
> ( see below)
>
> My PYTHONPATH has:
>
> export PYTHONPATH="$PYTHONPATH:/rawdata12/cctbx_standalone/cctbx_sources:/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx"
>
> The error I get when I say from cctbx import sgtbx , uctbx:
>
> ImportError: __import__("boost_python_meta_ext"): libboost_python.so:
> undefined symbol: PyUnicodeUCS2_FromEncodedObject
>
> What can I do to avoid the error and use the Plugin correctly.
> Thanks
> Hari
>
>
>
>
>
> Detailed error message:
> hari at charlie:/rawdata12/cctbx_auto/cctbx_build/lib$ python
> Python 2.5.2 (r252:60911, Jul 22 2009, 15:33:10)
> [GCC 4.2.4 (Ubuntu 4.2.4-1ubuntu3)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from cctbx import sgtbx,uctbx
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/sgtbx/__init__.py",
> line 2, in <module>
>    from cctbx import uctbx
>  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/uctbx/__init__.py",
> line 1, in <module>
>    from cctbx.array_family import flex
>  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/array_family/flex.py",
> line 1, in <module>
>    import scitbx.array_family.flex
>  File "/rawdata12/cctbx_standalone/cctbx_sources/scitbx/array_family/flex.py",
> line 1, in <module>
>    import boost.optional
>  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/optional.py",
> line 1, in <module>
>    import boost.python
>  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py",
> line 45, in <module>
>    ext = import_ext("boost_python_meta_ext")
>  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py",
> line 24, in import_ext
>    + ["  "+p for p in sys.path]))
> ImportError: __import__("boost_python_meta_ext"): libboost_python.so:
> undefined symbol: PyUnicodeUCS2_FromEncodedObject
>  sys.path:
>
>    /usr/lib/python2.5/site-packages
>    /rawdata12/wx-widgets-read-only/wxPython
>    /home/hari/ccp4-6.0.99e/share/python
>    /rawdata12/cctbx_auto/cctbx_build/lib
>    /home/hari
>    /rawdata12/cctbx_standalone/cctbx_sources
>    /rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx
>    /usr/lib/python25.zip
>    /usr/lib/python2.5
>    /usr/lib/python2.5/plat-linux2
>    /usr/lib/python2.5/lib-tk
>    /usr/lib/python2.5/lib-dynload
>    /usr/local/lib/python2.5/site-packages
>    /usr/lib/python2.5/site-packages
>    /usr/lib/python2.5/site-packages/Numeric
>    /usr/lib/python2.5/site-packages/PIL
>    /home/hari/djtrunk
>    /usr/lib/python2.5/site-packages/kodos
>    /usr/lib/python2.5/site-packages/gst-0.10
>    /var/lib/python-support/python2.5
>    /usr/lib/python2.5/site-packages/gtk-2.0
>    /var/lib/python-support/python2.5/gtk-2.0
>    /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/cctbxbb
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/cctbxbb
>