Structure Edit Dialog
Applicability: Cranium, Synapse

Many estimation techniques require knowledge of a chemical's molecular structure. Some techniques require only information about the chemical's family, e.g., does the chemical contain silicon atoms. Other techniques, e.g., group contribution techniques, require a chemical's structure to be completely dissected into molecular fragments.

Cranium and Synapse use a simple connectivity model to represent molecular structure. Atoms and bonds are connected into a simple graph. Our goal is not to produce structures for publication but to provide Cranium and Synapse with the structural information needed for estimations and analyses.

The Structure Edit dialog is used to enter molecular structure:

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The dialog's elements section displays a control listing all the elements available in the current document. The selected element will be used when new atoms are created. Several "shortcut" buttons are also avaliable in this section listing commonly used elements. Pressing one of these shortcut buttons will make that element the current element.
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The dialog's Bond Type section displays a control listing all the bond types available for the current type of structure being edited. (Different bond types are available when editing chemical structures than when editing group structures.) The selected bond type will be used when creating new bonds.
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The buttons on the left side of the dialog's Structure Entry section control the editor's "mode". For example, when the atom button, the button with the letter "A" on it, is depressed, clicking on the editor pane will add atoms. When the bond button, the button with the diagonal line, is depressed, clicking on the editor pane will bond atoms together.
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The dialog's large central pane is used for drawing molecular structures. For example: atoms are placed in the pane by selecting the atom button and clicking the left mouse button in the pane; bonds are added by selecting the bond button and clicking the left mouse button on the first atom to be bonded and then on the second atom to be bonded.
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The right side of the edit dialog displays several buttons used to select atoms, arrange atoms and insert molecular structures for further editing.
Element Section

The Structure Edit dialog's Element section is used to specify the current element. You many select an element using the dropdown menu or by clicking on one of the element buttons.

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The dropdown elements menu
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Shortcut element buttons
Tip: Use a template document when creating new knowledge bases

The Structure Edit dialog's elements section only shows those elements present in the document's Elements chapter. This is one of the reasons that you should almost always used the MKS Template Knowledge Base when creating a new knowledge base. The template knowledge base already contains elements.

Bond Type Section

The Structure Edit dialog's Bond Type section is used to specify the current bond. Bonds of the selected type are used to connect two atoms together.

Tip: Bonds for chemicals and groups are different

The bond types available for chemical structures and group structures are different. Because groups represent only part of a molecular structure, they can contain additional bond types:

  • Ring Single Bond: a bond type used to denote a single bond that occurs in a ring.
  • Ring Double Bond: a bond type used to denote a double bond that occurs in a ring. (Note that Cranium and Synapse differentiate between aromatic bonds and ring double bonds.)
  • Ring Triple Bond: a bond type used to denote a triple bond that occurs in a ring.

Modes and Options Buttons

The toolbar buttons located on the Structure Edit dialog's left side is used to specify the various operating modes of the edit pane. For example, depressing the atom button, the button with the large "A", places the edit pane in "atom mode", i.e., clicking the left mouse button within the pane will add atoms made using the current element.

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Selection Tool: this button sets the editor pane's mode to "selection". Individual atoms can be selected by clicking on them with the left mouse button. Multiple atoms can be selected by clicking and holding the left mouse button down and then dragging the mouse. All atoms within the rectangle formed will be selected.
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Eraser Tool: this button sets the editor pane's mode to "deletion". Clicking on an atom or bond will delete (erase) that item.
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Atom Tool: this button sets the editor pane's mode to "atom". Clicking on blank space within the editor pane will create a new atom, using the current element, and place it at the mouse's location.
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Bond Tool: this button sets the editor pane's mode to "bonding". Clicking on one atom and then another will bond the two atoms using the current bond type.
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Grid Option: this option button places a grid on the editor pane. The center of new atoms will be placed on a grid point.
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Autoconnectivity Option: this option button causes each new atom placed into the editor pane to also be selected as the first bonding atom. Thus, when the next atom is placed in the editor pane, it will be bonded to the previous atom. (Note that the Atom mode button must also be pushed to enable autoconnectivity.)
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Subtractability Option: this option button causes each new atom placed into the editor pane to be subtractable (if not pushed) or non-subtractable (if pushed). This button is only displayed when group structures are being edited. (See below for more details on atom subtractability.)
Dialog Commands

The right side of the edit dialog displays several buttons used to select atoms, arrange atoms and insert molecular structures for further editing.

  • Undo Button: pressing this button will undo the effect of the last command.
  • Align Atoms: when two or more atoms are selected, pressing this button will activate the Align Atoms dialog. This dialog enables you to align the selected atoms along their X centers, Y centers or to the grid.
  • Set Grid: when the Grid Option dialog is pressed, all new atoms will be placed on grid points. The X and Y placement of these grid points can be changed by this command. Pressing the button activates the Set Grid Spacing dialog. Grid spacing must be a number between 8 and 32.
  • Select All: pressing this button will select all atoms within the editor pane. Selected atoms can aligned, moved as a group and cleared.
  • Clear: pressing this button will delete all atoms currently selected within the editor pane. (Note that when and atom is deleted, all attached bonds are also deleted.)
  • Std Structures: pressing this button activates the Standard Structures dialog. This dialog enables you to insert common ring structures, fused ring structures and hydrocarbon chains. These structures are often good starting points when entering new structures. See the Standard Structures Dialog documentation for more details.
  • Import: the Structure Edit dialog can read structures from mol files and add them to the editor pane. Pressing the Import button activates the Open File dialog. Selecting a mol file will cause the application to read the file, create the associated atoms and bonds, assign positions to these atoms and copy these atoms and bonds to the editor pane. See the Mol Files Export Dialog for more details on mol files.
  • Insert: using this command you can insert the molecular structure of other chemicals present in the current knowledge base. Pressing the Insert button activates the Insert Chemical's Structure dialog.
    Selecting a chemical and pressing the OK button will insert that chemical's molecular structure into the edit pane.
Example: Enter a new chemical's molecular structure

In this example we will create a new chemical and enter its molecular structure. The chemical is 5-butyl-4-methyloxolan-2-one also commonly known as whiskey lactone.

  1. Open a knowledge base document. (Open a "working" document or create a copy of a document (see here) if you are just experimenting with this functionality.)
  2. Using the tabs at the top of the document, change to the Chemicals Chapter by clicking the left mouse button on Chemicals tab.
  3. Press the Add toolbar button (the large plus sign). Alternatively you can choose the Add New Page command from the Edit menu or use the crtl-a keyboard accelerator. A new, blank Chemical page will be added to the current document.
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    Add Button: pressing this toolbar button will add a new, blank page to the current chapter.
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    Delete Button: pressing this toolbar button will delete the current page from the current chapter. IMPORTANT: the deletion of a page cannot be undone.
  4. Click the left mouse button on the Identifier Pane's edit control and enter the chemical's name: 5-Butyl-4-methyloxolan-2-one. (See documentation on the Chemical Chapter for details on the layout of Cranium and Synapse documents.)
  5. Scroll the data pane down to the Chemical Structure section. Click click the left mouse button in the section's Structure field. The application will activate the Structure Edit dialog.
  6. Press the Std Structs button to activate the Standard Structures dialog. Select Rings as the Category and then cyclopentane as the Ring Choice. Finally press the OK button to copy the standard structure to the edit pane. (See the Standard Structures Dialog documentation for more details.)
  7. Drag the inserted structure toward the center of the edit pane by clicking and holding the left mouse button on a selected atom and then move the mouse toward the center of the window.
  8. Double click the left mouse button on the top, center carbon atom of the cyclopentane structure. The application will display the Edit Atom Attributes dialog. Select Oxygen as the element and press the OK button.
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    Edit Pane: imported and inserted structures will be placed in the edit pane's upper left corner.
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    Atom Editing: double-clicking the left mouse button on an atom will activate the Edit Atom Attributes dialog.
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    Element Replacement: selecting a new element and pressing the dialog's OK button will replace the element in the selected atom.
  9. Click the left mouse button on the Oxygen button, the "O" button, in the Element section. The dialog will automatic select oxygen in the element dropdown list and press the Atom Tool.
  10. Click the left mouse button to the upper left of the carbon to the left of the top oxygen atom in the current ring structure. The dialog will create an oxygen atom and add it to the editor pane.
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    Pressing the oxygen shortcut button selects oxygen as the current element in the Element dropdown list.
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    Pressing the oxygen shortcut button also activates the Atom Tool button.
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    When the Atom Tool is activated, clicking the left mouse button within the editor pane will create a new atom. (Note that you cannot place one atom on top of another atom.)
  11. Select the Double Bond type from the Bond Types dropdown list.
  12. Click the left mouse button on the Bond Tool - the button with the diagonal line. Then, click the mouse button on the newly added oxygen and on the carbon atom to the left of the ring oxygen.
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    The Bond Type dropdown list is used to select the current bond type.
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    Select the Bonding Tool button to begin bonding atoms together.
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    Click sequentially on the two atoms to be bonded.
    The order does not matter except for ionic bonds. When bonding two atoms with an ionic bond, the first atom's charge will be increased by 1, i.e. it will receive a positive charge, and the second atom's charge will be decreased by 1, i.e., it will receive a negative charge.
  13. Press the Autoconnectivity Tool and the Carbon Shortcut button.
  14. Add four connected carbon atoms near carbon atom in the top right of the current ring structure.
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    The Carbon Shortcut button selects carbon as the current element.
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    The Autoconnectivity Option will automatically connect subsequent atoms to the prior atom.
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    Clicking the left mouse button four times adds four carbon atoms each automatically bonded to the prior carbon atom.
  15. Add another carbon atom near the lower right ring carbon.
  16. Finally, bond the second and third carbon atoms to the adjacent carbon atoms.
  17. Pressing the Save button causes the dialog to check that the entered structure is valid, e.g., all atoms are bonded into a single structure, and then store the entered structure into the current document.
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