On 17 June 2010 15:23, Rob Soe <kym3p...@gmail.com> wrote:
> 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.
Right. What I would do is store the Fingerprints in a vector, and when
I want to compare molecule 11 with molecule 15, I would simply access
fp_vector[15] and fp_vector.get[11]. I'm not sure but I would expect a
map to be both slower and use more memory.
> 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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