[Cdk-devel] RFC: Proposed changes to pdb_atomtypes.xml

[Andreas S. <asc...@bi...>]

Hi All,

This is the last of my set of emails.

There are some bugs - probably of the copy/paste type - in 
org/openscience/cdk/config/data/pdb_atomtypes.xml:

<atomType id="TRP.HH2" ><atom elementType="C"/>
<atomType id="TRP.CZ2" ><atom elementType="N"/>
<atomType id="TRP.CZ3" ><atom elementType="O"/>
<atomType id="TRP.N"   ><atom elementType="C"/>
<atomType id="GLN.2HE2"><atom elementType="C"/>
<atomType id="GLN.CD"  ><atom elementType="N"/><scalar 
dataType="xsd:double" dictRef="emboss:vdwrad">1.7</scalar></atomType>
<atomType id="GLN.N"   ><atom elementType="O"/>
<atomType id="GLN.NE2" ><atom elementType="O"/>

In each of these lines the elementType is incorrect and in one case also 
the vdwrad. Correct would be:

<atomType id="TRP.HH2" ><atom elementType="H"/>
<atomType id="TRP.CZ2" ><atom elementType="C"/>
<atomType id="TRP.CZ3" ><atom elementType="C"/>
<atomType id="TRP.N"   ><atom elementType="N"/>
<atomType id="GLN.2HE2"><atom elementType="H"/>
<atomType id="GLN.CD"  ><atom elementType="C"/><scalar 
dataType="xsd:double" dictRef="emboss:vdwrad">1.9</scalar></atomType>
<atomType id="GLN.N"   ><atom elementType="N"/>
<atomType id="GLN.NE2" ><atom elementType="N"/>


Best,
Andreas


-- 
Dr. Andreas Schueller
Depto. Genética Molecular y Microbiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile