Thanks,
I will try with the standard pdbatomtypes file. It would have also been interesting to overload the function based in the supplied type of molecule. I.e. if a IBioPolymer is supplied then the standard pdbatoms typing is used. However, I think the way you have done should give more freedom to the user.
Is this already in CVS? I cannot acces it with CVS grab (firewall :-((() so I have to ask ...
Cheers
Nik
| Rajarshi Guha <[EMAIL PROTECTED]>
09.02.2006 16:19
|
To: Nikolaus Stiefl/PH/[EMAIL PROTECTED] cc: [email protected] Subject: Re: [Cdk-user] error in PDBReader Category:
|
On Thu, 2006-02-09 at 09:24 +0100, [EMAIL PROTECTED] wrote:
> 2. When calculating the numerical surface with NumericalSurface.java
> on a read in PDB file I get a CDK exception :
> org.openscience.cdk.exception.NoSuchAtomTypeException when the VDW
> radii should be configured (line 318). I circumvented this by
> assigning the VDW radii to the Protein as in the
> ProteinPocketFinder.java file (function assignVdwRadiiToProtein) prior
> to calling NumericalSurface(). However, I was wondering if there is an
> easy way to use the configVDW of the NumericalSurface class?
I've just committed some changes to NumericalSurface and now there is a
constructor in which you can supply a filename of a file that contains
VDW radii. So one way to use this is to make a copy of the Jmol atom
types file (org/openscience/cdk/config/jmol_atomtypes.txt), edit it to
whatever you want and specify the new file.
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