Hi
Thanks for the suggestion. I may try using STL map. But here is a summary of
what I am trying to do.
I am actually trying to optimize my code where I have N molecules and I am
trying to compare every nth molecule to all N molecules and calculate
Tanimoto (Tc) similarity scores.
So each time I am trying to compare, I have to get/generate the fingerprints
of such pair of molecules every time I loop. So I am thinking my program may
run faster if I first calculate fingerprint in advance and store them as
extra info and just retrieve it whenever I am about to compare (to compute
Tc score). In that way I don't have to regenerate the fingerprints again and
again.
Thanks so much,
Rob
On Thu, Jun 17, 2010 at 10:04 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> On 17 June 2010 14:47, Rob Soe <kym3p...@gmail.com> wrote:
> > Hi
> > Thanks a lot for the suggestions. I can now set and retrieve such data.
> >
> > Currently, I am trying to save the fingerprint information to each
> molecule.
> > I am using GetFingerprint() (from OBFingerprint) and it generates a
> vector
> > of unsigned int (vector<unsigned int>).
> >
> > May I ask which OBGenericData class I should use to store such vector
> info?
>
> Have you considered simply using a STL container such as a std::map
> from OBMol to OBFingerprint? Or simply iterating over a set of
> molecules and push_back the OBFingerprint onto a vector?
>
> > Thanks so much for your help.
> > Rob
> >
> > On Tue, Jun 8, 2010 at 11:15 PM, Tim Vandermeersch
> > <tim.vandermeer...@gmail.com> wrote:
> >>
> >> On Tue, Jun 8, 2010 at 12:06 AM, Rob Soe <kym3p...@gmail.com> wrote:
> >> > Hi,
> >> > Thanks a lot for the suggestions.
> >> >
> >> > I have this plan that I am trying to work out. I am planning to use
> >> > OBSetData() and use SetAttribute() to set a string (converted from a
> >> > float
> >> > number that I want to associate the molecule with).
> >> >
> >> > Here is the code:
> >> >
> >> > //Float to String conversion
> >> > ostringstream buffer;
> >> > double temp=0.987;
> >> > buffer << temp;
> >> > string strTemp = buffer.str();
> >> > //End
> >> >
> >> > //Storing data using OBSetData()
> >> > OBSetData *sim = new OBSetData();
> >> > sim->SetAttribute(strTemp.c_str());
> >> > mol.SetData(sim);
> >> > //End
> >> >
> >> > So now the 'mol' should have the attribute data?
> >>
> >> Yes, but the attribute is the name for your data. SetValue and
> >> GetValue should be used for setting the temperature.
> >>
> >> sim->SettAttribute("temp");
> >> sim->SetValue(strTemp.c_str())
> >> mol.SetData(sim)
> >>
> >> To retrieve:
> >>
> >> OBSetData *data = mol.GetData("temp");
> >>
> >> Tim
> >>
> >> > I am not sure how I can access such attribute data. I tried to use
> >> > mol.getData() but it seems not working.
> >> >
> >> > Thanks!
> >> > Rob
> >> >
> >> > On Mon, Jun 7, 2010 at 2:48 PM, Geoffrey Hutchison
> >> > <ge...@geoffhutchison.net> wrote:
> >> >>
> >> >> > You need create an OBPairData (a subclass of OBGenericData), and
> >> >> > apply
> >> >> > it to the molecule using OBMol.SetData. I usually grep the
> OpenBabel
> >> >> > source for examples of things.
> >> >>
> >> >> There are also working examples in the API documentation, e.g. (see
> the
> >> >> Detailed Description):
> >> >>
> >> >> http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBGenericData.shtml
> >> >>
> >> >> Cheers,
> >> >> -Geoff
> >> >
> >> >
> >> >
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> >> >
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> >
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