Molecule Set

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 JOELib 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.

Estimate logS

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.

Browse Molecules

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 logS

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.