Re: [Joelib-devel] molecular weight

[Joerg K. W. <we...@in...>]

Hello,

two initial comments:
1. this is an easy example and i will be glad to help you
2. This topic would be better placed in the help mailing list (for
future request). 

Look at the appended descriptor class. Copy this file to
joelib/src/joelib/desc/types
and add 
joelib.descriptor.9.representation        
=joelib.desc.types.MolecularWeight

to line 102 in joelib/src/joelib.properties
The descriptor is accessible by "Molecular_weight".

A little bit of programming experience would not be a bad choice.
1. abstract - means that this class needs a child ! That's not the case
for this class.
2. The rest seems to be o.k., but the parent class (this is an abstract
one)
forces you to implement the double value calculation in
public double getDoubleValue(JOEMol mol)
{
  double aValue=Double.NaN;
  return aValue;
}

if you want it to use with your scheme you can use
public double getDoubleValue(JOEMol mol)
{
  return getMolWt(mol);
}

Regards, Joerg


Pekka Suomalainen wrote:
> 
> Trying to use getMolWt to calculate molecular weight.
> The code below fails. I have no programming experience so any help would be
> appreciated.
> 
> public abstract class MW extends SimpleDoubleDesc
> {
>      /*
>       *
> -------------------------------------------------------------------------*
>       *  public static member variables
>       *
> -------------------------------------------------------------------------
>       */
>          *  Obtain a suitable logger.
>       */
>      private static Category logger =
> Category.getInstance("joelib.desc.types.MW");
> 
>      /*
>       *
> -------------------------------------------------------------------------*
>       *  constructor
>       *
> -------------------------------------------------------------------------
>     */
>      /*
>       *  Constructor for the MW object
>       */
>      public MW()
>      {
>          descInfo = DescriptorHelper.generateDescInfo("MW",
>                  this.getClass(),
>                  "topological",
>                  2,
>                  null,
>                  "joelib.desc.result.AtomDoubleResult");
>      }
> 
>      /*
>       *
> -------------------------------------------------------------------------*
>       *  public methods
>       *
> -------------------------------------------------------------------------
>       */
>         *  Gets the molWt attribute of the <tt>JOEMol</tt> object
>       *
>       * @return   The molWt value
>       */
>      public double getMolWt(JOEMol mol)
>      {
>          double molwt = 0.0f;
>          JOEAtom atom;
>          AtomIterator ait = mol.atomIterator();
>                  while (ait.hasNext())
>          {
>              atom = ait.nextAtom();
>              molwt += JOEElementTable.instance().getMass(atom.getAtomicNum());
>          }
> 
>          return molwt;
>      }}
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen,
Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de