Displaying Structural Fragments inside a Spectrum View
Basic molecule view
functions are also applied here, but some additional functions are required
for IR/RAMAN Spectrum Analysis.
Here, structural fragments need to be displayed according to investigated
functional groups. Molecule fragments are shown and they might have undefined
residuals representing an unknown rest of a molecule. It is also possible,
that more than one structural representation is available for a functional
group. In this case each molecule fragment can be displayed alone or all
can be shown together.
A typical Imine molecule fragment view looks like this.
It represents all kinds of molecules containing an Imine functional group.
As described above some residuals or atoms in the molecule
fragments might be undefined in order to give a representation of a chemical
environment for a set of various molecules. In Chemistry some well known
abbreviations for such atoms or residuals are given in the following:
Alkyl Groups
Alkyl-groups are indicated by a super atom "R".
Aromatic Groups
Aromatic residues are represented by "Ph" for phenyl or "Ar"
for general aromatic residual.
Any Generic Groups
Generic groups, either alkyl, aromatic, cyclic or non-cyclic, etc.
are represented by "G".
Halogen Atoms
Halogen atoms are indicated by "X"
Molecule View Display Options
Some functional group representations cannot be depicted by only one
particular molecule, but a set of various molecule fragments representing
all possible chemical environments. In this case multiple molecules are
displayed in the view:
The navigation toolbar in the top left corner provides convenient control
of visible molecule items. It will be shown automatically, whenever more
than one molecules is displayed and the molecule view is activated or
the mouse pointer resides in the view. The toolbar will be shown for navigation
purposes. The molecule view offers two display modes:
Overview Mode
All available molecules are visible at once.
Single View Mode
Only one molecule is visible and maximized to the molecule view. The
user can toggle between all available molecules.
View mode can be altered clicking the button
in the navigation toolbar. Single view mode and overview mode will be
toggled.
In the single view mode, only one molecule is displayed at a time. In
order to toggle between all available molecules, move forwards and backwards
in the list of all molecules clicking
the and the buttons
Previous
Shows previous molecule.
Next
Shows next molecule.
Displaying Functional Groups in a Spectrum View
In the spectrum interpretation result, a molecular representation of
the active functional group is displayed in the spectrum view:
All functions described above are also available for the molecule item
shown inside a spectrum view.
Click with the
Left
mouse button
onto the molecule in the spectrum view to activate and select the molecule
item.
Move the molecule
item around in the spectrum view with Drag & Drop.
Resize the molecule
display by dragging and dropping the tracker symbols.
Click somewhere
outside the molecule item to leave selection.
and the 
