[Open Babel] Get atom force field types

[John Doe]

Hi Users,

If I use one of the preloaded force fields, I'm guessing openbabel assigns 
appropriate force field atom types.  Is there away to access those atom types?  
I would like to use openbabel to assign UFF atom types for full MD simulations.

Thanks
  --
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Get atom force field types

[Nicolas Cheron]

Hi,

Did you try something such as:

OpenBabel::OBMol obMol; // Then load your molecule in obMol
OpenBabel::OBAtom *atom;
for (unsigned int i=1; i<=obMol.NumAtoms() ; i++ ) {
 atom = obMol.GetAtom(i);
 cout << "Atom type: " << atom->GetType() << endl;
 }

Nicolas


2014-05-01 9:46 GMT-04:00 John Doe :
> Hi Users,
>
> If I use one of the preloaded force fields, I'm guessing openbabel assigns
> appropriate force field atom types.  Is there away to access those atom
> types?  I would like to use openbabel to assign UFF atom types for full MD
> simulations.
>
> Thanks
>
> --
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Get atom force field types

[John Doe]

Hi Nicolas,

Thanks for the suggestion but I failed to mention I am using Python.

Thanks

> From: nicolas.cheron.bou...@gmail.com
> Date: Thu, 1 May 2014 11:21:44 -0400
> Subject: Re: [Open Babel] Get atom force field types
> To: helstr...@hotmail.com
> CC: openbabel-discuss@lists.sourceforge.net
> 
> Hi,
> 
> Did you try something such as:
> 
> OpenBabel::OBMol obMol; // Then load your molecule in obMol
> OpenBabel::OBAtom *atom;
> for (unsigned int i=1; i<=obMol.NumAtoms() ; i++ ) {
>  atom = obMol.GetAtom(i);
>  cout << "Atom type: " << atom->GetType() << endl;
>  }
> 
> Nicolas
> 
> 
> 2014-05-01 9:46 GMT-04:00 John Doe :
> > Hi Users,
> >
> > If I use one of the preloaded force fields, I'm guessing openbabel assigns
> > appropriate force field atom types.  Is there away to access those atom
> > types?  I would like to use openbabel to assign UFF atom types for full MD
> > simulations.
> >
> > Thanks
> >
> > --
> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> > unparalleled scalability from the best Selenium testing platform available.
> > Simple to use. Nothing to install. Get started now for free."
> > http://p.sf.net/sfu/SauceLabs
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
  --
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Get atom force field types

[Dimitri Maziuk]

On 05/01/2014 11:18 AM, John Doe wrote:
> Hi Nicolas,
> 
> Thanks for the suggestion but I failed to mention I am using Python.

pybel molecule:

for a in molecule.atoms :
  print a.OBAtom.GetType()

Element:

et = openbabel.OBElementTable()
elt = et.GetSymbol( a.OBAtom.GetAtomicNum() )

NOTE: elt.lower() can be "xx"

HTH,
-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



signature.asc
Description: OpenPGP digital signature
--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss