openbabel-scripting

[OpenBabel-scripting] pybel - obtain unit cell data from cif file

[Pavol J. <ju...@pa...>]

Hello,

I would like to read a structure from cif file and extract the lattice
parameters using the python interface for openbabel.  I went
through the openbabel wiki, also through openbabel API, but
I am still at loss how to perform this task.

Here is my python code:

    import pybel, openbabel
    cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
    uc = cete3.OBMol.GetData(openbabel.UnitCell)

This executes fine, but uc is an instance of openbabel.OBGenericData
class and it does not have GetA() or any other method of the
OBUnitCell() class.  I tried to convert it to OBUnitCell instance
with

    uc1 = openbabel.OBUnitCell(uc)

but that does not work either.

Could anyone advice my how to get to those unit cell parameters
with python openbabel?

Thanks a lot,

Pavol

Re: [OpenBabel-scripting] pybel - obtain unit cell data from cif file

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

On Apr 12, 2007, at 1:00 PM, Pavol Juhas wrote:

>     cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
>     uc = cete3.OBMol.GetData(openbabel.UnitCell)
>
> This executes fine, but uc is an instance of openbabel.OBGenericData
> class and it does not have GetA() or any other method of the
> OBUnitCell() class.

Ugh. In C++ such type conversion is done with casting. I think the  
only solution will be to add conversion functions -- perhaps in the  
SWIG interface file, which allows such conversion. Unfortunately,  
Noel, who contributed Pybel is on vacation right now, or he might  
have some other ideas.

Could you file this as a bug report in the tracker?

Thanks,
-Geoff

P.S. On the plus side, I think we should be able to release a fixed  
Python interface without needing to wait for a 2.1.1 update to Open  
Babel itself.

Re: [OpenBabel-scripting] pybel - obtain unit cell data from cif file

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

This has now been resolved in the development version. The Python code
you describe below works, and 'uc' has the GetA() method, etc.

I am working on adding this to pybel also, where it will be available
as "cete3.unitcell" if present.

Noel

On 12/04/07, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Apr 12, 2007, at 1:00 PM, Pavol Juhas wrote:
>
> >     cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
> >     uc = cete3.OBMol.GetData(openbabel.UnitCell)
> >
> > This executes fine, but uc is an instance of openbabel.OBGenericData
> > class and it does not have GetA() or any other method of the
> > OBUnitCell() class.
>
> Ugh. In C++ such type conversion is done with casting. I think the
> only solution will be to add conversion functions -- perhaps in the
> SWIG interface file, which allows such conversion. Unfortunately,
> Noel, who contributed Pybel is on vacation right now, or he might
> have some other ideas.
>
> Could you file this as a bug report in the tracker?
>
> Thanks,
> -Geoff
>
> P.S. On the plus side, I think we should be able to release a fixed
> Python interface without needing to wait for a 2.1.1 update to Open
> Babel itself.
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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Re: [OpenBabel-scripting] pybel - obtain unit cell data from cif file

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

On 12/04/07, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Apr 12, 2007, at 1:00 PM, Pavol Juhas wrote:
>
> >     cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
> >     uc = cete3.OBMol.GetData(openbabel.UnitCell)
> >
> > This executes fine, but uc is an instance of openbabel.OBGenericData
> > class and it does not have GetA() or any other method of the
> > OBUnitCell() class.
>
> Ugh. In C++ such type conversion is done with casting. I think the
> only solution will be to add conversion functions -- perhaps in the
> SWIG interface file, which allows such conversion. Unfortunately,
> Noel, who contributed Pybel is on vacation right now, or he might
> have some other ideas.

I also really want to be able to access the Data in molecule file
formats. I will discuss some ideas with Geoff. In the meanwhile, you
should check out PyCiFRW, a Python module for reading/writing CIF
files:
(1) http://anbf2.kek.jp/CIF/
(2) http://scripts.iucr.org/cgi-bin/paper?wf5020 (Open Access paper)

> Could you file this as a bug report in the tracker?
>
> Thanks,
> -Geoff
>
> P.S. On the plus side, I think we should be able to release a fixed
> Python interface without needing to wait for a 2.1.1 update to Open
> Babel itself.
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] pybel - obtain unit cell data from cif file

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

If you add:
%inline %{
OpenBabel::OBPairData *GDtoPD(OpenBabel::OBGenericData *data) {
	return (OpenBabel::OBPairData *) data;
}
%}

to openbabel-python.i, you can use it to cast OBGenericData to OBPairData.

But how do you find out what data is available?

Noel

On 23/04/07, Noel O'Boyle <bao...@gm...> wrote:
> On 12/04/07, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Apr 12, 2007, at 1:00 PM, Pavol Juhas wrote:
> >
> > >     cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
> > >     uc = cete3.OBMol.GetData(openbabel.UnitCell)
> > >
> > > This executes fine, but uc is an instance of openbabel.OBGenericData
> > > class and it does not have GetA() or any other method of the
> > > OBUnitCell() class.
> >
> > Ugh. In C++ such type conversion is done with casting. I think the
> > only solution will be to add conversion functions -- perhaps in the
> > SWIG interface file, which allows such conversion. Unfortunately,
> > Noel, who contributed Pybel is on vacation right now, or he might
> > have some other ideas.
>
> I also really want to be able to access the Data in molecule file
> formats. I will discuss some ideas with Geoff. In the meanwhile, you
> should check out PyCiFRW, a Python module for reading/writing CIF
> files:
> (1) http://anbf2.kek.jp/CIF/
> (2) http://scripts.iucr.org/cgi-bin/paper?wf5020 (Open Access paper)
>
> > Could you file this as a bug report in the tracker?
> >
> > Thanks,
> > -Geoff
> >
> > P.S. On the plus side, I think we should be able to release a fixed
> > Python interface without needing to wait for a 2.1.1 update to Open
> > Babel itself.
> >
> > -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share your
> > opinions on IT & business topics through brief surveys-and earn cash
> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

Re: [OpenBabel-scripting] pybel - obtain unit cell data from cif file

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

To answer my question, the following code will iterate over all of the data:

for data in mol.BeginData():
    pdata = openbabel.GDtoPD(data)
    print pdata.GetAttribute(), "==", pdata.GetValue()

On 02/05/07, Noel O'Boyle <bao...@gm...> wrote:
> If you add:
> %inline %{
> OpenBabel::OBPairData *GDtoPD(OpenBabel::OBGenericData *data) {
>         return (OpenBabel::OBPairData *) data;
> }
> %}
>
> to openbabel-python.i, you can use it to cast OBGenericData to OBPairData.
>
> But how do you find out what data is available?
>
> Noel
>
> On 23/04/07, Noel O'Boyle <bao...@gm...> wrote:
> > On 12/04/07, Geoffrey Hutchison <ge...@ge...> wrote:
> > >
> > > On Apr 12, 2007, at 1:00 PM, Pavol Juhas wrote:
> > >
> > > >     cete3 = pybel.readfile("cif", "cete3_p1.cif").next()
> > > >     uc = cete3.OBMol.GetData(openbabel.UnitCell)
> > > >
> > > > This executes fine, but uc is an instance of openbabel.OBGenericData
> > > > class and it does not have GetA() or any other method of the
> > > > OBUnitCell() class.
> > >
> > > Ugh. In C++ such type conversion is done with casting. I think the
> > > only solution will be to add conversion functions -- perhaps in the
> > > SWIG interface file, which allows such conversion. Unfortunately,
> > > Noel, who contributed Pybel is on vacation right now, or he might
> > > have some other ideas.
> >
> > I also really want to be able to access the Data in molecule file
> > formats. I will discuss some ideas with Geoff. In the meanwhile, you
> > should check out PyCiFRW, a Python module for reading/writing CIF
> > files:
> > (1) http://anbf2.kek.jp/CIF/
> > (2) http://scripts.iucr.org/cgi-bin/paper?wf5020 (Open Access paper)
> >
> > > Could you file this as a bug report in the tracker?
> > >
> > > Thanks,
> > > -Geoff
> > >
> > > P.S. On the plus side, I think we should be able to release a fixed
> > > Python interface without needing to wait for a 2.1.1 update to Open
> > > Babel itself.
> > >
> > > -------------------------------------------------------------------------
> > > Take Surveys. Earn Cash. Influence the Future of IT
> > > Join SourceForge.net's Techsay panel and you'll get the chance to share your
> > > opinions on IT & business topics through brief surveys-and earn cash
> > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> >
>