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

[richard a. <ric...@ya...>]

--- 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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