[cctbxbb] input_atom_labels_list() not available in Python?

[hari jayaram]

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 <
nathaniel.echols at gmail.com> 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 <harijay at gmail.com> 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
>>
>>
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>>
>
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