[cctbxbb] input_atom_labels_list() not available in Python?

Thanks Nathaniel.. I too was using the approach of looking at the phenix scripts to figure things out. But I was hoping that there was a "google hidden" source of documentation for the python interfaces that I was not aware of. For the present moment the c++ documentation is much more useful .After I sent the email out , I did notice the section in the manual which says.. "Most documented C++ interfaces are also available at the Python layer. Unfortunately the documentation tools available are not capable of merging the documentations. Therefore Python users need to also consult the C++ documention." On an unrelated note The Nov 2006 newsletter and the c++ and python documentation lists a function in the class iotbx.pdb.input called input_atom_labels_list() This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses this function However I dont see that in the python interface with the current version? Is that true or am I using a different build that does not make this available in python Just curious Hari On Tue, Aug 26, 2008 at 12:50 PM, Nathaniel Echols < [email protected]> wrote:

Having spent the last few months trying to learn the python side of cctbx for my own work, I recommend looking at some of the actual programs that call these functions (e.g. the various phenix scripts, or testing scripts) for clues on how to use them. In particular, iotbx/pdb/tst_atom_selection.py has examples of selection caches. (I'm not sure how exactly the "cache" class fits in, since it isn't invoked directly in that script, but hopefully the test script has some approximation of what you're trying to do.) I haven't found it necessary to look at the C++ code - boost.python obscures many details anyway, and it's usually pretty obvious to me what's going on in the python sources based on the variable/class/function names. The various CCP4 newsletter articles may have some useful suggestions, but I haven't looked at these in much detail yet.

On Tue, Aug 26, 2008 at 9:18 AM, hari jayaram wrote:

...

Hi , I am a few days into learning to use the cctbx libraries. My interests are mostly to be able to write scripts that plot various statistics from mtz files and use things like iotbx.pdb to manipulate coordinate files. While I have managed to write a few scripts and have read the very descriptive examples in the newsletters and the few routines inside of phenix. I have a problem with getting much out of the python interface documentation at the sourceforge site.

Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html , the documentation gives me a "cache" class __init__ method that says

__init__(self, root, wildcard_escape_char=r'\')

How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments.

In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html return an error page.

I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Thanks in advance hari

_______________________________________________ cctbxbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/cctbxbb