openbabel-scripting

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

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

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?

Noel

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


 
____________________________________________________________________________________
Any questions? Get answers on any topic at www.Answers.yahoo.com.  Try it now.

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
>
>
>
> ____________________________________________________________________________________
> Any questions? Get answers on any topic at www.Answers.yahoo.com.  Try it now.
>
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Re: [OpenBabel-scripting] Iterators over atoms/bonds/etc.

[Geoffrey H. <ge...@ge...>]

On Dec 13, 2006, at 4:44 AM, Noel O'Boyle wrote:

> 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.

Don't look at me. Those were contributed. :-)

> classes at runtime (or have a Factory method) as there are now about
> 10 iterators of similar structure in obiter.h.

As both Rich and Noel have mentioned, iterating doesn't necessarily  
work the same in C++ as in scripting languages. (Heck, in C++ people  
often have different ways of doing iteration.)

If you think it would be a good idea to have methods to just pass a  
list of atoms or bonds, residues, etc. please let me know. Many of  
these methods already exist, although I haven't checked for  
"completeness" in the API.

SWIG doesn't always make it easy to inject code into the C++  
interface file or the scripting language module that it generates. Of  
course that's why we've put hacks into the Makefiles. So if there are  
bits we'd like to put in either place, let me know and I'll figure  
out an appropriate way to get it done.

Cheers,
-Geoff

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

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

I've just checked in some changes to openbabel-python.i based on the
code in my earlier email on this topic. You can see the file here:
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/scripts/openbabel-python.i?revision=1656&view=markup

Now it's possible to use OBMolAtomIter as if it's a Python iterator:
==================
import openbabel
import pybel
mol = pybel.readstring("smi", "CNC").OBMol
for atom in openbabel.OBMolAtomIter(mol):
    print atom.GetAtomicMass()
=====================

Hopefully, we can get similar methods together for the other language bindings.

Noel


On 13/12/06, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Dec 13, 2006, at 4:44 AM, Noel O'Boyle wrote:
>
> > 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.
>
> Don't look at me. Those were contributed. :-)
>
> > classes at runtime (or have a Factory method) as there are now about
> > 10 iterators of similar structure in obiter.h.
>
> As both Rich and Noel have mentioned, iterating doesn't necessarily
> work the same in C++ as in scripting languages. (Heck, in C++ people
> often have different ways of doing iteration.)
>
> If you think it would be a good idea to have methods to just pass a
> list of atoms or bonds, residues, etc. please let me know. Many of
> these methods already exist, although I haven't checked for
> "completeness" in the API.
>
> SWIG doesn't always make it easy to inject code into the C++
> interface file or the scripting language module that it generates. Of
> course that's why we've put hacks into the Makefiles. So if there are
> bits we'd like to put in either place, let me know and I'll figure
> out an appropriate way to get it done.
>
> Cheers,
> -Geoff
>
>