Properties Estimation: How to Use PirikaLight JAVA applet
2009.09.15
This program calculate Tb, Tc, Pc, Vc, MP, SP, Antoine A, B, C. Web version have some limitations. Total Heavy atoms are below 8 and Oxygen atom below 2 and nitrogen atom below 1.
(Figures are HSPLight. But usage is same.)
Please run the PirikaLight program on the sub-window.（If you are using IE, please allow to run blocked contents) Then you will see see the above JAVA Applet. look&Feel is depend on type of browser. Please put smiles molecular structure into Text field above of the applet. If you are not familiar to Smiles, please search in the Net.
This Light version can calculate heavy 8 atoms. And can use Carbon, Nitrogen, Oxygen. For example, please enter CCCOC (Methyl Propyl Ether) to Text Field and push Convert button. Then the pane automatically change to “Smiles Viewer” and structure of molecule (without Hydrogen) appear. Sometime, atoms are overlapped and hard to recognize.(The calculations are not affect by look so you need not worry about it) In that case, please push mouse on one atom and (keep mouse down) drag, then the only that atom move. please push Stop button if you get good structure. If you need not viewer, please deselect Smiles viewer on check box. Calculation result already come to appear.
If you push Stop button, the Snap to Draw appear. If you push this button, the Draw pane is selected and it become completely same with depict molecule from scratch.
From Smiles, or from Depict molecule, the results come immediately. Y-MB text area, it listed which Functional Groups, how many. This Y-MB is the official method for molecular breaking for HSPiP. And if breaking are finished without error, molecular properties are calculated.
If you select “Line” tool, and set mouse on C2, then red circle is appear on C2 atom. Then push mouse on that atom (and keep mouse button pushed), and drag. When you release mouse button, then C5 atom appear. The functional group listed in Y-MB is change from propyl to 2-butyl and calculated values are all changed. And Smiles scheme also changed to new molecule. There are several way of depict molecule. Push mouse where there is no atom and drag, release mouse button where exist atom. Or Push mouse where there is no atom and release immediately. Then push mouse on one atom and drag to that new atom then release. (This is make bond procedure.)
If you select “Eraser” tool, you set mouse on one atom (red circle appear) then push, that atom will erase.
If you set mouse middle of bond, then 2 red circle appear on correspond 2 atoms. And push mouse, then bond will disappear. If you want to make double bonds or triple bonds, set mouse on one atom(red circle appear) then push mouse, keep mouse down, and drag to the other atom(red circle appear both) then release mouse.
Please select Oxygen atom and set mouse on C4 atom (red circle appear).
Then push mouse and release immediately. Then the C4 atom change to O4 atom.
Or, push on one atom and drag (line appear), then release mouse, new selected atom will appear.
Select cross cursor, push somewhere without atom, and drag, then you can translate molecular.
With cross cursor, push on one atom, you can move only that one atom.
Please paste mol file to “Mol file” text area from atom number line to bond matrix line.
Then push convert.
After convert, it is same with depict procedure.
Please try!
Caution:This sketch molecule routine is not implemented into HSPiP.
