Gaussdal Node
The Gaussdal node is for treating molecule data retrieved
from a SQL query in a Gaussdal database. The node is yet
highly experimental, so use it at your own risk. Also, the
documentation for the node will be improved during the
next releases.
To use this node one must connect the input to the Gaussdal
node and then run the diagram. The input should be Gaussdal
files with molecule data consisting of x- y- and z-coordinates,
molecule id's and atomic numbers. Other attributes may also
be provided, but is not mandatory. Also, a mapping matrix can
be set on the ''molecule_mapping'' input port, giving information
on which atom in which molecule is to be mapped to each
other.
Figure 3.3:
Gaussdal molecule mapper dialog
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In the dialog of figure 3.3, the user can set
global and local variables, and choose mapping type.
The different mapping options are:
- Default mapping: generates a mapping based on atom
order in the Gaussdal file, often giving the wanted mapping.
This is set default when creating a new Gaussdal node, and
by connecting a spreadsheet node to the output port on the
Gaussdal node, the result can be viewed without opening the
Gaussdal node.
- Manual mapping: the user creates a mapping by using
the molecule wizard. Press next and follow instructions on
screen. When the mapping process is finished, the user can
choose whether she wants to run the Procrustes routine.
If Procrustes is run, results are illustrated in a window.
Select the wanted molecules from the list and press
''Update''.
- From input port: The mapping is performed according
to a provided matrix on inputport ''mapping_matrix'' in the
Gaussdal node. The matrix might e.g. have Octave format.
The options in the ''File'' and ''Edit'' menu are not working yet,
but will be fixed as soon as possible.
SciCraft Development Team