Re: [OpenBabel-scripting] perl use of getSSSR, OBRing

[David R. <tom...@gm...>]

I am having trouble getting this to work.  I used SVN to get the new
version, but am unable to build it successfully; running make yields
the following error messages:

__ZN9OpenBabel8OBFormat14FormatFromMIMEEPKc
__ZN9OpenBabel8OBFormat14RegisterFormatEPKcS2_
__ZN9OpenBabel8OBPlugin12ListAsVectorEPKcS2_RSt6vectorISsSaISsEE
__ZN9OpenBabel12OBDescriptor13AddPropertiesEPNS_6OBBaseERKSs
__ZN9OpenBabel12OBDescriptor13FilterCompareEPNS_6OBBaseERSib
__ZN9OpenBabel12OBDescriptor16DeletePropertiesEPNS_6OBBaseERKSs
__ZN9OpenBabel12OBDescriptor14GetStringValueEPNS_6OBBaseERSs
__ZN9OpenBabel12OBDescriptor7CompareEPNS_6OBBaseERSib
__ZN9OpenBabel8OBPlugin7DisplayERSsPKcS3_
__ZTIN9OpenBabel12OBDescriptorE
__ZTVN9OpenBabel12OBDescriptorE
__ZTVN9OpenBabel8OBPluginE
__ZTIN9OpenBabel8OBPluginE
/usr/bin/libtool: internal link edit command failed
make[3]: *** [libopenbabel.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1


I also tried (perhaps naively) just moving the new openbabel-perl.i
file to my version 2.1.0 source tree and rebuilt that, but it doesn't
seem to have worked either (no errors, but no new functionality
either).

Can anyone offer suggestion?

thanks,
Dave.


On 5/8/07, Noel O'Boyle <bao...@gm...> wrote:
> Your confusion is due to the fact that the Perl wrapper does not yet
> include a vector of  OBRing*, which is what is returned by GetSSSR().
> As a result, you currently can't do anything with the result from
> GetSSSR().
>
> I'm just about to check in the appropriate fix to the development
> code, which is available through subversion (SVN) as described on the
> openbabel install page:
>     http://openbabel.sourceforge.net/wiki/Install
>
> Once you have compiled and installed the latest code, the following
> code will work (it's in Python, but I'm sure you can figure it out):
>
> import pybel
> obmol = pybel.readstring("smi", "c1ccccc1").OBMol    # Benzene
> vector_of_sssr = obmol.GetSSSR()
> print vector_of_sssr.size() # 1
> obring = vector_of_sssr[0]
> print dir(obring)
> # GetParent, IsAromatic, IsInRing, IsMember, etc...
>
> Noel
>
> On 07/05/07, David Rose <tom...@gm...> wrote:
> > Hello:
> >
> >   I am confused about the use, in Perl, of OBMol::getSSSR and OBRing.
> > I am trying to find the size of the largest ring returned by getSSSR.
> > I instantiate an OBMol, and the method getSSSR returns something, but
> > I am unsure what it is or what to do with it.  I assume I can pass it
> > to OBRing->new() to get an OBRing object, and it looks like OBRing has
> > a method called 'size' which is what I want, but I wonder if anyone
> > can offer a snippet of sample code. Thanks for all the help, past and
> > future.
> >
> > David Rose.
> >
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