openbabel-scripting

[OpenBabel-scripting] std::vector< OBInternalCoord * >

[<wr...@hu...>]

I was attempting to access the function CartesianToInternal with the
python binding to openbabel. This function has been wrapped, however it
requires a vector of internal coordinate objects. I cannot seem to find a
corresponding vectorInternals object in the bindings. The vector classes
that currently ship with the binding (vers. 1.2) are:
vector3
vectorAngle
vectorBond
vectorData
vectorDouble
vectorInt
vectorMol
vectorResidue
vectorRing
vectorUnsignedInt
Has the proper data structure been wrapped to another name or is it missing?
I appreciate any response, thank you.
     Wilton Wilson

Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:

> Has the proper data structure been wrapped to another name or is it  
> missing?
> I appreciate any response, thank you.

No, at the moment, it's missing. If you have SWIG (1.3.30), you can  
easily regenerate the Python (or other) bindings.

You edit the openbabel-python.i file, look for the %template () lines  
and add something like:

%template (vectorpICoord)   vector<OBBInternalCoord *>

Then take a look at:
http://openbabel.sourceforge.net/wiki/Developer:Building

Cheers,
-Geoff

Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

I'm working on identifying (basically, by grepping the Doxygen XML
docs) any remaining std::vector templates included in OpenBabel that
we need to wrap . This will mean that no more users will have to
complain about this problem...

Noel

On 08/07/07, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:
>
> > Has the proper data structure been wrapped to another name or is it
> > missing?
> > I appreciate any response, thank you.
>
> No, at the moment, it's missing. If you have SWIG (1.3.30), you can
> easily regenerate the Python (or other) bindings.
>
> You edit the openbabel-python.i file, look for the %template () lines
> and add something like:
>
> %template (vectorpICoord)   vector<OBBInternalCoord *>
>
> Then take a look at:
> http://openbabel.sourceforge.net/wiki/Developer:Building
>
> Cheers,
> -Geoff
>
> -------------------------------------------------------------------------
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> Download DB2 Express C - the FREE version of DB2 express and take
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>

Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

For the record, running the following code:

grep -h definition xml/classOpenBabel_1_1*.xml | grep "vector<" |
sed 's/std:://g' | sed 's/<definition>//g' | sed 's/<\/definition>//g'
| sed 's/&gt;/\>/g' | sed 's/\&lt;/\</g' | sed 's/< /</g' | sed 's/
\*/\*/g' | sed 's/ >/>/g' | sed 's/\&amp;/\&/g' | sed 's/ \&/\&/g' |
sed 's/::iterator//g' | awk '{for (i=1; i<NF; i++) {printf("%s ",
$i);}; printf("\n");}' | grep -v "&" | grep -v "_" | sort | uniq

gives:
vector<bool>
vector<double*>
vector<double>
vector<GasteigerState*>
vector<int>
vector<int>*
vector<OBAngle>
vector<OBAtom*>
vector<OBBond*>
vector<OBChemTsfm*>
vector<OBElement*>
vector<OBExternalBond>
vector<OBExternalBond>*
vector<OBGenericData*>
vector<OBInternalCoord*>
vector<OBMol*>
vector<OBMol>
vector<OBResidue*>
vector<OBRing*>
vector<OBRotor*>
vector<OBRotorRule*>
vector<OBSmartsPattern*>
vector<OBTorsion>
vector<pair<int,int>>
vector<pair<OBAtom**,vector<int>>>
vector<pair<OBSmartsPattern*, double>>
vector<pair<OBSmartsPattern*, vector<int>>>
vector<pair<OBSmartsPattern*,int>>
vector<pair<OBSmartsPattern*,pair<int,int>>>
vector<pair<OBSmartsPattern*,string>>
vector<pair<OBSmartsPattern*,vector<double>>>
vector<pair<pair<int,int>,int>>
vector<pair<string,int>>
vector<quad<OBAtom*, OBAtom*, OBAtom*, OBAtom*>>
vector<string>
vector<triple<OBAtom*,OBAtom*,double>>
vector<unsigned char*>
vector<unsigned int>
vector<unsigned short>
vector<vector<double>>
vector<vector<int>>
vector<vector<pair <unsigned int, double>>>
vector<vector<pair<string,int>>>
vector<vector<string>>
vector<vector<unsigned int>>
vector<vector<vector3>>
vector<vector3>

We should probably add the lot.

Noel

On 11/07/07, Noel O'Boyle <bao...@gm...> wrote:
> I'm working on identifying (basically, by grepping the Doxygen XML
> docs) any remaining std::vector templates included in OpenBabel that
> we need to wrap . This will mean that no more users will have to
> complain about this problem...
>
> Noel
>
> On 08/07/07, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:
> >
> > > Has the proper data structure been wrapped to another name or is it
> > > missing?
> > > I appreciate any response, thank you.
> >
> > No, at the moment, it's missing. If you have SWIG (1.3.30), you can
> > easily regenerate the Python (or other) bindings.
> >
> > You edit the openbabel-python.i file, look for the %template () lines
> > and add something like:
> >
> > %template (vectorpICoord)   vector<OBBInternalCoord *>
> >
> > Then take a look at:
> > http://openbabel.sourceforge.net/wiki/Developer:Building
> >
> > Cheers,
> > -Geoff
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>