ACD/Structure Drawing Applet

A Quick Reference

The structure drawing applet appears in the right-hand part of the page.
The toolbar contains several buttons and features that are numbered as shown and described below:

1. Pin - switches between two modes: "attached mode", when the applet is placed inside the browser window; and "floating mode", when the applet has its own window that can be dragged anywhere on the screen.
2. Clear - clears the drawing area.
3. Undo - cancels the last action performed.
4. Redo - cancels the last Undo command.
5. Copy as Image - copies the drawn structure as a graphical image to the clipboard.
6. Copy as Mol Text - copies the drawn structure as MDL molfile contents to the clipboard.
7. Paste from Mol Text - pastes a structure from the clipboard containing any MDL molfile text.
8. Normal bond - connects atoms, i.e., draws chemical bonds in a simple fashion. Click on this button, then on an atom button, then click-drag away from the atom. Release the mouse button and you have just drawn a molecule!
   1. Up stereo bonds - draws stereo bonds that come out of the plane of the screen, towards the viewer.
   2. Down stereo bonds - draws stereo bonds that go out of the plane of the screen, away from the viewer.
9. Delete - erases the atom, bond, or selection from the drawing area.
   To delete an atom or bond:
   1. Choose the Delete tool.
   2. Place the mouse pointer over the atom or bond you want to delete. (You will see the item become highlighted.)
   3. Click on the atom or bond to delete it.
   To delete a structure or fragment:
   1. Choose the Delete tool.
   2. Click-drag to select the fragment or the structure that you want to delete. (You will see the fragment become highlighted.)
   3. Click once more on the highlighted structure or fragment to remove it.
10. Select/Move - selects/moves the atom, bond or selection.
    To move an atom or bond:
    1. Choose the Select/Move tool.
    2. Place the mouse pointer over the atom or bond you want to move (the item will be highlighted).
    3. Click-drag the atom or bond to a new position.
    4. Release the mouse button.
    To move a structure or fragment:
    1. Choose the Select/Move tool.
    2. Click-drag over the molecule until you select the fragment or the structure that you want to move. Release the mouse button.
    3. Place the mouse cursor over the highlighted fragement or structure so that the hollow blue squares appear.
    4. Click-drag the selected structure or fragment to a new position.
    5. Release the mouse button.
11. Charge Plus - increases the charge (+) of a chosen atom or ion.
12. Charge Minus - decreases the charge (-) of a chosen atom or ion.
13. Reaction Plus - allows you to draw a reaction plus. Select this tool, move the cursor to the place where you want a plus to be inserted and click once.
14. Reaction Arrow - inserts a reaction arrow. The applet considers all structures to the left of the reaction arrow as reactants and to the right as products. Only one reaction arrow is allowed in the drawing area.
15. Templates - contains the most frequently needed structures and structural fragments. Click on this button to call up the template window where you can choose a set of templates from the list by clicking on one of the template titles shown on the left-hand side. Select one of the template structures by clicking on it, and then click once in the structure drawing applet to place the template structure there.
    To insert the chosen template into the drawing area you can do one of the following:
    1. To insert an unattached template click on an empty space in the drawing area.
    2. To insert a template attached to an existing atom click on this atom. The template is attached to an atom with the atom chosen in the Template window.
    3. To insert a template fused to an existing bond click on that bond. The template is fused to a bond with the bond chosen in the Template window.
16. Add Polymer - adds a polymer brackets to the selection or to the whole structure if no fragment is selected. Click on this button to call up the Polymer Options dialog box up where you can choose choose polymer index, type of connectivity, and brackets style.
    1. Remove from Polymer - removes the polymer brackets above the selected fragment.
17. Markush Bond - connects a Markush bond to the selection or the whole structure if no fragment is selected. A markush bond can be connected to a solid fragment that does not contain another markush bonds.
18. Zoom In - expands the structure in the (x,y) directions.
19. Zoom Out - reduces the size of structure in the (x,y) directions.
20. Fit to Page - use this tool to fit the structure exactly to the drawing area.
21. I-Lab - opens the ACD/Interactive Laboratory (ACD/I-Lab) Web page in a new browser window.
22. Button Name - when the cursor is placed over a button, this area displays the name of the button.
23. Query Atom - allows you to specify query options for atoms when performing a sub-structure search, allowing you to look for the specified type of atom in a given location:

    A (Any) - the marked atom may be any atom except hydrogen.
    Q (Hetero) - any atom except hydrogen or carbon.
    HO (without hydrogen) - no hydrogens may be attached to this atom.
    L (list) - creates a list of atoms to be allowed.
    NL (not list) - creates a list of atoms to be excluded.

    To specify query atoms for a sub-structure search, click on any of these query options and then on an atom in the drawn structure.
24. Query Bond - allows you to specify query options for bonds when performing a sub-structure search, allowing you to look for the specified type of bond in a given location:

    A (Any) - accepts any bond (single, double, triple or aromatic).
    Ar (Aromatic) - accepts only aromatic bonds.
    S/D (Single/Double) - accepts single or double bonds.
    Rn (Ring) - the bond must be part of a ring (cancels chain).
    Cn (Chain) - the bond must be part of a chain (cancels ring)

    To specify query bonds for a sub-structure search, click on any of these query options and then on a bond in the drawn structure.
25. Periodic Table of Elements - opens the Periodic Table of Elements window where you can choose a new element for the drawing. When your cursor passes over an element, detailed information about it (symbol, name, atomic number, density, mass, typical valence or oxidation states and electron configuration) appears. To choose the desired element, just click on it. You can do one of the following with the chosen element:
    
    
    1. Click on an empty space to insert the atom at that point.
    2. Or click on top of any atom in the drawing area to replace it with the chosen atom.
       
       When an atom is chosen from the Periodic Table of Elements window, its corresponding button is automatically added to the Atoms Toolbar, if space permits. (There are certain default atoms always listed.) Next time you can use this button for faster drawing.
    
    
26. Atoms Toolbar - lists atoms frequently used in drawing. This Toolbar is displayed as a vertical column on the left of the drawing area. This Toolbar self-customizes to include buttons for atoms you have recently selected, thereby permitting you to draw more quickly.
27. Edit Atom Label - this tool allows you to replace any atom in a structure with a group abbreviation or a label which then can be expanded. Clicking sequentially this tool and the needed atom, displays the Edit Label dialog box where you should specify the label to be inserted.
28. Atom Properties - changes valence, charge, and isotope of a chosen atom.
29. Radicals Table - opens the Radicals Table window where you can choose a new radical for the drawing. Radicals are divided into six basic groups. When your cursor passes over a radical, its image appears in the special subwindow. Note that the "R" in the radical structure denotes the position of attachment to other structures in the drawing area. To choose the desired radical, just click on it. You can do one of the following with the chosen radical:
    
    
    1. Click on an empty space to insert a non-bonded structure of the chosen radical.
    2. Or click any atom to sprout the chosen radical from it.
       
       When a radical is chosen from the Radicals Table window, its corresponding button is automatically added to the References Toolbar, if space permits. Next time you can use this button for faster drawing.
    
    
30. References Toolbar - lists radicals frequently used in drawing. This Toolbar is displayed as a vertical column on the right of the drawing area. This Toolbar self-customizes to include buttons for radicals you have recently selected, thereby permitting you to draw more quickly.