[Cdk-user] error in PDBReader

[nikolaus . stiefl]

Hi,

I just started playing around with CDK and during my first 'simple learning examples' I also tested the calculation of surfaces on PDB files ...

Here I had two problems arising which might actually eb bugs (however, I don't know exactly since I don't know if I am doing something wrong ;-)

1. When reading in PDB files one sometimes has files for which the RMEARK line includes empty lines, i.e something like:

REMARK   0
REMARK   0
REMARK   2   DATE OF DEPOSITION ...
REMARK   2   X-RAY DATA ...
REMARK   2
REMARK   2   STRUCTURE SOLVED BY ...

where often the 'spacefiller' REMARK   2 line has only 10 fields. when reading these kind of PDB files PDBReader.java will throw an 'String index out of range: -1' error since in line 263 of PDBReader field entry 11 is tried to be accessed without any check. Now I was wondering if I am using a wrong function or if this is just something which has not occured before since most people don't use any PDB files?!?

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?

Many thanks,
Nik