The molecule set screen allows you to view a set of molecules
from a file and calculate the solubilities of these molecules.
To open a set of molecules choose Molecule Set -> open from
the menu. Then choose a filename to load. At the moment only
.mol2 and .sdf files have been tested. However all file
formats supported by
should function correctly.
If successfull, a new tab will appear in the window. To close
the tab click on the red cross in the top right corner.
The application stores various details about every file opened.
To delete these details click on the 'DELETE MOLSET' button at
the top of an open molecule set tab.
Choosing an Algorithm
An algorithm is used to calculate solubilities for a molecule
set. The solubility results displayed are those that were
calculated from the current selected algorithm. When browsing
and viewing single molecules in the molecule set, the current
selected algorithm is used to estimate the solubility.
Underneath the progress bar in a molecule set tab the file name
loaded is displayed. To the right of this there is a list of
algorithms that are avaliable. If you have recently added/removed
an algorithm, click on the 'Reset List' button to refresh the
list of avaliable algorithms. To change the algorithm used, just
select a different algorithm name from the combo box.
The first tab that is displayed allows you to estimate the
solubilities of the entire set of molecules. Once this is
done the results can be viewed in the next tab, the Results
tab. These results can be sorted by the molecule's order
in the file, the molecule's CAS number, or the estimated
logS value. If you just want to estimate the solubility of
a single molecule, use the Browse Molecules tab.
The 'start' button starts the calculation using the
currently selected algorithm. If the 'index molecules first'
check box is checked the molecule set file will be
first indexed before calculating solubilities. This
allows you to quickly access molecule information from
the results, only usefull for large files.
The 'pause' button pauses the calculation, which then
can be restarted with the 'start' button. Once the application
is closed, the calculation must be restarted from the beggining.
The 'stop' button cancels the rest of the calculation. If
the calculation is started again it will begin with the first
molecule in the file.
The Results tab allows you to browse through the estimated logS
values of the molecule set. The values are the ones calulcated
by the currently selected algorithm.
Use the buttons to browse through the results. The stats button
calculates some statistics about the estimation but this only
works is experimental solubility values are avaliable. The delete
(rubbish bin picture) button deletes all the results for
the molecule set for the selected algorithm.
You can change the field on which the results are sorted and
also print all the results to a file.
Double-clicking on one of the displayed results in the table
will bring up a new tab displaying the details about the
molecule and the calculation.
The Browse Molecules tab allows you to view the molecules in
the molecule set file. They can only be accessed in an
iterative fashion. Double-click on any of the molecules
in a displayed table to view the details of the molecule,
estimate logS for that molecule, and view the structure
of the molecule. If there is no selected algorithm logS
will not be estimated.
Experimental solubility values are used to calculate
statistics on the solubility calculation. Some file
formats such as .sdf can embed this information in with
the molecule structure and this information will be loaded
by the application if it recognises it. Otherwise
you must specify the experimental logS files in
a test file and read this into the program.
Click on 'LOAD logS FILE' to choose the filename of a
file containing experimental solubility values. The
standard deviation of these values can be calculated by
clicking on the 'STANDARD DEVIATION' button.