Re: [modeller_usage] code and logic question

[Modeller Caretaker <>]

Christian Meesters wrote:
> If a derived class (see
> http://www.salilab.org/modeller/manual/node27.html for instance) has a
> method defining additional restraints, how, having no conventional
> __init__-method of the base class called, do I know in advance that a
> method is called?

All of these methods are documented in the manual with examples. If you 
want to see where the methods are called from, you'd need to look at the 
actual definition of the base class. But the base class is just Python 
code, so you can just look those Python files directly - there's nothing 
secret about them. You can look at the actual files in the 
modlib/modeller/ directory, use your Python's interpreter's help() 
function on them, or feed them into a documentation engine like epydoc 
if you so desire.

> method is called? I never saw something like
>
> a.special_restraints(aln)
>
> in the examples. (BTW, where does 'aln' come from? special_restraints()
> requires this parameter, but it does not get defined in the code.)

The manual would be far too verbose if we were to put in the full Python 
code of the base classes, and IMHO it would be confusing for most users. 
'aln' is defined in the base class, of course - see the 
modlib/modeller/automodel/automodel.py file in this case. The methods 
themselves are described in the reference section - special_restraints() 
at http://www.salilab.org/modeller/9v2/manual/node66.html for example.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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