Biomedical Engineering Reference
In-Depth Information
Figure 6.4
Outline of a workfl ow for comparing two SD fi les
there are new structures that should be purchased. This task can be
accomplished with the following KNIME workfl ow. As the workfl ow is
too big to be shown on a single page in readable form, we have divided it
into four different parts. The overall process is depicted in Figure 6.4.
The fi rst part is shown in Figure 6.5 and is quite simple: fi rst, it reads
two SD fi les (e.g. the fi rst containing the new structures from the vendor
and the second containing the corporate database) with the SDF Reader,
then adds a column indicating the source of each molecule with a Java
Snippet node, and fi nally concatenates both tables.
This small workfl ow already shows two interesting concepts in
KNIME. First, the SDF Reader has two output ports: the upper port
provides a table with all the structures that have been successfully parsed
and the second port contains a (possibly empty) table with structures that
could not be parsed due to syntactic errors in the SD fi le. The reader node
Figure 6.5
Reading and combining two SD fi les
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