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Re: [OpenBabel-scripting] Open Babel-Ruby - Success!
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From: richard a. <ric...@ya...> - 2006-10-28 06:08:53
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Open Babel conversions work in Ruby!
After studying the Python examples, I found that the
Open Babel-Ruby interface handles SMILES and Molfile
formats quite well (and presumably the others):
$ irb
irb(main):001:0> require 'openbabel_wrap'
=> true
irb(main):002:0> obc=Openbabel_wrap::OBConversion.new
=> #<Openbabel_wrap::OBConversion:0x2b5d3ca6bf98>
irb(main):003:0> mol=Openbabel_wrap::OBMol.new
=> #<Openbabel_wrap::OBMol:0x2b5d3ca670d8>
irb(main):004:0> obc.SetInAndOutFormats("smi", "mdl")
=> true
irb(main):005:0> obc.ReadString(mol, 'c1ccccc1')
=> true
irb(main):006:0> mol.NumAtoms
=> 6
irb(main):007:0> mol.AddHydrogens
=> true
irb(main):008:0> mol.NumAtoms
=> 12
irb(main):009:0> molfile=obc.WriteString mol
=> "\n OpenBabel10270622492D\n\n 12 12 0 0 0 0 0
0 0 0999 V2000\n 0.0000 0.0000 0.0000 C 0
0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0
0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0
0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0\n
0.0000 0.0000 0.0000 C 0 0 0 0 0\n
0.0000 0.0000 0.0000 C 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n
0.0000 0.0000 0.0000 H 0 0 0 0 0\n 1 6
2 0 0 0\n 1 2 1 0 0 0\n 1 7 1 0 0 0\n
2 3 2 0 0 0\n 2 8 1 0 0 0\n 3 4 1 0 0
0\n 3 9 1 0 0 0\n 4 5 2 0 0 0\n 4 10 1
0 0 0\n 5 6 1 0 0 0\n 5 11 1 0 0 0\n 6
12 1 0 0 0\nM END\n"
irb(main):010:0>
I'm wondering about the best names for the library and
its modules. For example, this looks ideal to me:
require 'openbabel' # the name of the wrapper lib
# is openbabel - assuming no
# name clash w/ OB itself - I'll
# check this out.
mol = OpenBabel::OBMol.new
obc = OpenBabel::OBConversion.new
# etc.
This is easy to set up by editing the wrapper
generated by SWIG.
With some simple Ruby metaprogramming techniques, it's
even possible to give method names that follow Ruby
convention:
require 'openbabel'
mol = OpenBabel::OBMol.new
atom_count = mol.num_atoms
mw = mol.mol_wt
# ... etc.
And then it might be worth offering a RubyGem.
RMagick, which is the Ruby interface for ImageMagick
followed this route.
cheers,
Rich
--- richard apodaca <ric...@ya...> wrote:
> Success!
>
> Geoff, I think this works now. I checked out OB-SVN.
> With a couple of minor modifications (for example,
> changing openbabel_ruby.cpp to openbabel_wrap.cpp,
> adding #include <math.h>) - I'll detail them
> shortly),
> I got the scripts/ruby wrapper compiled.
>
> Behold:
>
> $ irb
> irb(main):001:0> require 'openbabel_wrap'
> => true
> irb(main):002:0> m=Openbabel_wrap::OBMol.new
> => #<Openbabel_wrap::OBMol:0x2ba75b5563c8>
> irb(main):003:0> h=m.NewAtom
> => #<Openbabel_wrap::OBAtom:0x2ba75b552778>
> irb(main):004:0> h.SetAtomicNum(1)
> => nil
> irb(main):005:0> m.GetMolWt
> => 1.00794
>
> It looks like all of the format interconversion
> utilities (smiles, mdl, etc) are missing, but we
> should be able to fix that. The important thing is
> now
> we've got a good place to start from.
>
> It must have been the older version of OB that I was
> using (2.0.2) that was the source of the problems.
>
> Could you verify that the above Ruby code works for
> you too?
>
> BTW, I'll respond in more detail to you're
> suggestions
> below shortly.
>
> cheers,
> Rich
>
> --- Geoffrey Hutchison <ge...@ge...>
> wrote:
>
> >
> > On Oct 14, 2006, at 4:47 PM, richard apodaca
> wrote:
> >
> > > (3) edit openbabel.i: comment out line 27 (Swig
> > can't
> > > find std_list.i for Ruby - it works for Python,
> > > though). Change line 5 to %module openbabel_wrap
> > > (don't want to risk a collision w/ installed
> > openbabel
> > > library)
> >
> > Seems like it might soon be a good idea to have
> > different openbabel.i
> > files for the different scripting modules. The SVN
> > version (for
> > 2.1.0bX) has the std_list.i #ifdef'ed out
> > automatically.
> >
> > > This generates lots of warnings that don't
> appear
> > when
> > > the argument is -python instead of -ruby (maybe
> > this
> > > is the problem):
> >
> > Nah. I get these for Perl and Python too. The
> > problem is that C++ has
> > different naming restrictions than scripting
> > languages. So some
> > functions may not be available until remapped. Not
> a
> > problem for core
> > functionality, as far as I've seen.
> >
> > > (8) save the following as "extconf.rb":
> > > require 'mkmf'
> > >
> > > dir_config('openbabel')
> > > dir_config('openbabel-2.0')
> > > have_library('openbabel')
> > >
> > > create_makefile('openbabel_wrap')
> >
> > One bit which might be good is to have a path to
> the
> > libopenbabel
> > too. On my system it was looking in the normal
> > search path, which may
> > or may not work for everyone (e.g., with a custom
> > --prefix call to
> > the Open Babel configure script.)
> >
> > > (9) create the makefile:
> > >
> > > ruby extconf.rb
> > >
> >
>
--with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
> > >
> >
>
--with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'
> >
> > Ideally could this be something that could go into
> > the scripts/
> > Makefile.am as a shell script? The Makefiles
> should
> > have the correct
> > paths already.
> >
> > > (13) require 'openbabel_wrap'
> > > irb(main):001:0> require 'openbabel_wrap'
> >
> > Here (on OS X, Ruby 1.8.4), I get:
> >
> > irb(main):001:0> require 'openbabel_wrap'
> > => true
> >
> > Not quite sure of enough ruby (or the binding) to
> > try anything else
> > yet... Maybe you should try this on the SVN
> version?
> > I'd obviously
> > like to get a ruby module into 2.1.0 anyway.
> >
> > Cheers,
> > -Geoff
> >
>
>
>
>
>
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