openbabel-scripting

[OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@mo...>]

OK.  I'm probably missing something really simple here, but I am 
converting a dataset from a bunch of grody old hyperchem files into an 
SD file. Along the way, I am using:

mol.title=name

to supposedly set the molecule's title to the value of name (just a 
hacked-up variant of the filename it came from).

The problem is that the title doesn't get exported as I write the file 
to the new sd file.  I get a molblock header that looks like:

  OpenBabel09030819443D

  78 81  0  0  0  0  0  0  0  0999 V2000

and then the molecular coordinates.  I didn't see anything obvious 
online about this behavior.  Am I doing something really stupid, or is 
this a known will-fix that I am jumping the gun on?

Thanks,
	Andy

[OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@po...>]

OK.  I'm probably missing something really simple here, but I am 
converting a dataset from a bunch of grody old hyperchem files into an 
SD file. Along the way, I am using:

mol.title=name

to supposedly set the molecule's title to the value of name (just a 
hacked-up variant of the filename it came from).

The problem is that the title doesn't get exported as I write the file 
to the new sd file.  I get a molblock header that looks like:

  OpenBabel09030819443D

  78 81  0  0  0  0  0  0  0  0999 V2000

and then the molecular coordinates.  I didn't see anything obvious 
online about this behavior.  Am I doing something really stupid, or is 
this a known will-fix that I am jumping the gun on?

Thanks,
     Andy

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

I can't easily check at the moment (I'm on holidays), but earlier
versions of Pybel didn't allow the user to set the title, just read
the title. If it's not available in the latest Pybel (just look at the
source code of pybel.py in the Molecule class), for sure it's in the
pybel.py that's bundled with cinfony.

Noel

2008/9/4 Andrew Fant <fa...@po...>:
> OK.  I'm probably missing something really simple here, but I am
> converting a dataset from a bunch of grody old hyperchem files into an
> SD file. Along the way, I am using:
>
> mol.title=name
>
> to supposedly set the molecule's title to the value of name (just a
> hacked-up variant of the filename it came from).
>
> The problem is that the title doesn't get exported as I write the file
> to the new sd file.  I get a molblock header that looks like:
>
>  OpenBabel09030819443D
>
>  78 81  0  0  0  0  0  0  0  0999 V2000
>
> and then the molecular coordinates.  I didn't see anything obvious
> online about this behavior.  Am I doing something really stupid, or is
> this a known will-fix that I am jumping the gun on?
>
> Thanks,
>     Andy
>
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Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@po...>]

Fair enough.  I'll dig into the code and see.  If the title is 
immutable, shouldn't an attempt to change it raise some sort of 
exception though, rather than just silently dropping it on the floor?

Andy

Noel O'Boyle wrote:
> I can't easily check at the moment (I'm on holidays), but earlier
> versions of Pybel didn't allow the user to set the title, just read
> the title. If it's not available in the latest Pybel (just look at the
> source code of pybel.py in the Molecule class), for sure it's in the
> pybel.py that's bundled with cinfony.
> 
> Noel
> 
> 2008/9/4 Andrew Fant <fa...@po...>:
>> OK.  I'm probably missing something really simple here, but I am
>> converting a dataset from a bunch of grody old hyperchem files into an
>> SD file. Along the way, I am using:
>>
>> mol.title=name
>>
>> to supposedly set the molecule's title to the value of name (just a
>> hacked-up variant of the filename it came from).
>>
>> The problem is that the title doesn't get exported as I write the file
>> to the new sd file.  I get a molblock header that looks like:
>>
>>  OpenBabel09030819443D
>>
>>  78 81  0  0  0  0  0  0  0  0999 V2000
>>
>> and then the molecular coordinates.  I didn't see anything obvious
>> online about this behavior.  Am I doing something really stupid, or is
>> this a known will-fix that I am jumping the gun on?
>>
>> Thanks,
>>     Andy
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

In the 'new' version, an exception is raised (thanks to Andrew Dalke
for the patch).

On 05/09/2008, Andrew Fant <fa...@po...> wrote:
> Fair enough.  I'll dig into the code and see.  If the title is immutable,
> shouldn't an attempt to change it raise some sort of exception though,
> rather than just silently dropping it on the floor?
>
>  Andy
>
>
>  Noel O'Boyle wrote:
>
> > I can't easily check at the moment (I'm on holidays), but earlier
> > versions of Pybel didn't allow the user to set the title, just read
> > the title. If it's not available in the latest Pybel (just look at the
> > source code of pybel.py in the Molecule class), for sure it's in the
> > pybel.py that's bundled with cinfony.
> >
> > Noel
> >
> > 2008/9/4 Andrew Fant <fa...@po...>:
> >
> > > OK.  I'm probably missing something really simple here, but I am
> > > converting a dataset from a bunch of grody old hyperchem files into an
> > > SD file. Along the way, I am using:
> > >
> > > mol.title=name
> > >
> > > to supposedly set the molecule's title to the value of name (just a
> > > hacked-up variant of the filename it came from).
> > >
> > > The problem is that the title doesn't get exported as I write the file
> > > to the new sd file.  I get a molblock header that looks like:
> > >
> > >  OpenBabel09030819443D
> > >
> > >  78 81  0  0  0  0  0  0  0  0999 V2000
> > >
> > > and then the molecular coordinates.  I didn't see anything obvious
> > > online about this behavior.  Am I doing something really stupid, or is
> > > this a known will-fix that I am jumping the gun on?
> > >
> > > Thanks,
> > >    Andy
> > >
> > >
> -------------------------------------------------------------------------
> > > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > > Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> > > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > >
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> > >
> >
>
>

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

On Sep 5, 2008, at 7:50 AM, Noel O'Boyle wrote:

> I can't easily check at the moment (I'm on holidays), but earlier
> versions of Pybel didn't allow the user to set the title, just read
> the title.

Correct me if I'm wrong, but shouldn't a Pybel molecule still be an  
OBMol? Since Pybel includes the Open Babel wrapper, the C++ methods  
should still be exposed.

mol.SetTitle("Foo!")

Does that work?

Cheers,
-Geoff

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

On 05/09/2008, Geoffrey Hutchison <ge...@ge...> wrote:
>
>  On Sep 5, 2008, at 7:50 AM, Noel O'Boyle wrote:
>
>
> > I can't easily check at the moment (I'm on holidays), but earlier
> > versions of Pybel didn't allow the user to set the title, just read
> > the title.
> >
>
>  Correct me if I'm wrong, but shouldn't a Pybel molecule still be an OBMol?
> Since Pybel includes the Open Babel wrapper, the C++ methods should still be
> exposed.
>
>  mol.SetTitle("Foo!")
>
>  Does that work?

Actually, it would be mol.OBMol.SetTitle("Foo!"), where mol is the
Pybel Molecule.

See line 225 of
http://code.google.com/p/cinfony/source/browse/trunk/cinfony/pybel.py
for the current pybel code using this.

>  Cheers,
>  -Geoff
>