Vol. 1/2, November 2004
4
jectIOListener interfaces, this class has the function
of containing information about the IO setting, and
store the active value.
CDK currently has four IOSetting implementa-
tions: BooleanIOSetting, IntegerIOSetting, Strin-
gIOSetting and OptionIOSetting. The first three
classes can only take specific settings: yes or no, in-
tegers, and Strings respectively.
The OptionIOSetting is a special class; besides
one default, it contains a list of suggestions. The
ChemObjectIOListeners, i.e. all current implemen-
tations, will offer this list of options to the user, as
depicted in Fig. 1.
If you plan to add IOSettings to existing or new
IO classes, please have a look at the source code of
the GaussianInputWriter or the CMLWriter.
I hope you appreciate the simplicity of the whole
architecture.
Egon Willighagen
Radboud University Nijmegen, The Netherlands
e.willighagen@science.ru.nl
First steps in the implementation of a
force field for the CDK package
Development of a 3D-structure model builder tool.
by Christian Hoppe
Introduction
As mentioned in the CDK News 1.1[1] we recently
started to work on a CDK implementation of a force
field. Force fields are widely used in the area of
chemoinformatics, e.g. to optimize the 3D geome-
try of a molecule, in conformational search or stud-
ies in molecular dynamics[2]. A force field of a
molecule describes with a set of equations the po-
tential energy surface of that molecule. Since those
equations are not based on first principles empir-
icaly or quantenmechanicaly precalculated data is
needed. This parameterisation limits the applica-
tion of force fields and over the years several differ-
ent sets of equations with corresponding data have
been developed[2, 3]. In general one can differenti-
ate these force fields in two classes, one for macro-
molecules and one for small organic molecules (usu-
ally less than 200 heavy atoms)[2]. We are aiminig at
the latter and plan to provide at least a couple of min-
imization alogorithms which can be used in comb