Re: [OpenBabel-scripting] Iterators over atoms/bonds/etc.

[Noel O'B. <bao...@gm...>]

I spoke too soon - after playing around with the OBMolAtomIter class
for a while I found that it *is* in working order (from Python's point
of view). It does require some wrapping to make it into a real Python
iterator though. If you look at the interface files (.i), you can see
that Geoff has renamed some methods to good(), deref() and inc().
Using these, it's possible to create a class that behaves as an
iterator.

(Note that .next() and __iter__() are magic methods that Python uses
to create an iterator. Presumably other languages have their own ways
of creating iterators.)

================
import openbabel as ob
import pybel

class Testiter(object):
    def __init__(self, mol):
        self.iter = ob.OBMolAtomIter(mol)
        self.finished = False

    def __iter__(self):
        return self

    def next(self):
        obAtom = self.iter.deref()
        self.iter.inc()
        if not self.finished:
            if not self.iter.good():
                self.finished = True
            return obAtom
        else:
            raise StopIteration

mol = pybel.readstring("smi", "CNC").OBMol

for atom in Testiter(mol):
    print atom.GetAtomicMass()
================

I'll move this into the SWIG interface file somehow; I think it's
possible to replace the existing OBMolAtomIter class with a Python
class of the same name. Hopefully it's also possible to create these
classes at runtime (or have a Factory method) as there are now about
10 iterators of similar structure in obiter.h.

Regards,
   Noel

On 12/12/06, richard apodaca <ric...@ya...> wrote:
>
> --- Noel O'Boyle <bao...@gm...> wrote:
>
> > obiter.h exposes a number of C++ convenience
> > functions for iterating
> > over atoms, bonds, etc. e.g. OBMolAtomIter iterates
> > over the atoms in
> > a molecule.
> >
> > However, these iterator methods don't work very well
> > from scripting
> > languages (I'm not even sure if it's possible to use
> > them as they were
> > designed to be used). It's much easier to use the
> > built-in iterator
> > methods present in the various languages. In Python,
> > the easiest way
> > to do this is to create a list of the atoms of a
> > molecule and then
> > iterate over these:
> >
> > obAtoms = [obMol.GetAtom(i+1) for i in
> > range(obMol.NumAtoms())]
> > for obAtom in obAtoms:
> >       # Do something with obAtom
> >
> > It would be very useful to collect such OpenBabel
> > idioms from
> > different scripting languages and put them on the
> > scripting pages (or
> > even include them in the interface files as
> > convenience functions).
> > Could anyone suggest similar code for
> > Perl/Ruby/Java?
>
> Interesting idea. In Ruby, I'd like to just do
> something like this:
>
> mol.each_atom do |atom|
>   # do something with atom
> end
>
> And similar methods for other iterable collections.
>
> There are a few ways to get there. One would be
> throught the SWIG interface file or C bridge it
> generates. Another would be to just define a Ruby
> class with the iterators built-in.
>
> Another would be through Ruby metaprogramming. This
> has the advantage over the other methods that it can
> be very concise. It comes with a potential decrease in
> speed.
>
> cheers,
> Rich
>
>
>
> ____________________________
> Richard Apodaca
> Blog: http://depth-first.com
>
>
>
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