9. Complex species
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9. Complex species

9.1. Complex species editing window

  1. The window for editing complex species

  2. "Complexes" side window section

    The window section has the following control buttons:

    • "New" button:

      Clicking this button brings up the "Molecules" side window section and initializes/resets all window sections and fields in the complex species editing window.

    • "View" button:

      If this button is clicked and a complex species is highlighted in the complex species/complex tree, the modeler application loads the complex species to the complex species editing window. If a complex is highlighted, the modeler application loads the complex to the complex editing window.

    • "Delete" button:

      If this button is clicked and a complex is hightlighted in the complex species/complex tree, a request is sent to the modeler application to delete the highlighted complex species/complex. The modeler application checks if there are any related entities such as complex associations. If there are no related item(s), the modeler application deletes the complex from the model file. Otherwise, a window will prompt the user to confirm performing a cascading deletion.

    • "Show Complexes and Species" / "Show Compex Speces Only" radio buttons:

      Indicate if complexes show in the list.

    • "Display Hidden Complexes" check box:

      Indicate if displaying hidden complexes. Similar to "Display Hidden Complexes" in model summary page.

    • Preview window section

      When a complex species or a complex is highlighted in the list, the modeler application shows the graphical layout in the preview window section.

  3. "Add Molecule" side window section

    The molecules listed in this window section can be used to build complexes. This window section has the same layout as the "Add Molecule" side window section in the molecule interaction editing window. Double clicking on a molecule in the list or clicking "Add" button sends the request to the modeler application to add the selected molecule to the current complex species.

  4. "Relations" side window section

    This window section contains "New", "View", "Delete" buttons, "Show Hidden Complexes" checkbox, and a list of entities in tree hiearchy format including "Complex", "Transformation", "Association" and "Dissociation"

    • "New" button

      When this button is clicked, the user will be prompted to specify what (complex, transformation, association) to create for the current complex species.

    • "View" button

      When this button is clicked and there is an item highlighted in the list, the modeler application will load the item to the corresponding editing window (complex species or complex).

    • "Delete" button

      When this button is clicked and there is an item hightlighted in the list, a request is sent to the modeler application to remove the item from the model file. Similar to the "Delete" action in the complex species/complex list window, the modeler application will check the related items and delete the complex/transformation/association/dissociation if is has no related items (otherwise, the user will be prompted to confirm cascading deletion of the related database entries).

    • "Complex" in the list

      The complexes related to the current complex species are listed under the "Complex" list item.

    • "Transformation" in the list

      The transformations that contain a complex related to the current complex species are listed in the "Transformation" list. If the related complex is the "Source" complex, the transformation will be listed in the "As Source" list. Otherwise, it will be a "As Result" list item.

    • "Association" in the list

      The associations that have a complex related to the current complex species are listed in the "Association" list. If the related complex is a "Source" complex, the association will be a "As Source" list item. Otherwise, it will be a "As Result" list item.

    • "Dissociation" int the list

      The dissociations that have a complex related to the current complex species are listed in "Dissociation" list. If the related complex is the "Source" complex, the dissociation will be a "As Source" list. Otherwise, it will be a "As Result" list item.

    • "Display Hidden Complexes" check box.

      It has the similar function as the "Display Hidden Complex" checkbox in the model summary page.

  5. Graphical layout window section

    If "Move" is selected in the "Edit Options", the user can move all items directly and indirectly connected to the item (binding site or molecule component) as a whole. If "Change Layout" is select, the user can change the layout of the molecules as long as the relative position relationships within the components of the molecule remain valid.

    If two binding sites from different molecules get into contact and neither is involved in other binding site interactions, the modeler application adds the interaction as an binding interaction within the complex species. If the interaction has not been defined as a molecule interaction, a message window asks the user to " Confirm to add a new molecule interaction". The user can remove this interaction from the complex species by highlighting and removing it from the "Binding Site Interaction" window section.

  6. "Edit Options" window section

    The "Move" and "Change Layout" modes control the mouse behavior in the graphical layout window section (see the decription about the graphical layout window section).

    If a molecule is highlighted and has no interaction with any other molecule yet, the user can rotate it by clicking the "Rotate +90o" or "Rotate -90o" button, or flip it by clicking the "Flip" button.

  7. "Composition" window section

    This window section shows the hiearchy structure of the current complex species.

    If a molecule is highted, the user can click the "Remove" button to remove the molecule and all related bindings from the current complex species.

    The property window section on the right side of this "Composition" window section shows properties of the highlighted item in this "Composition" window section.

  8. "Binding Site Interactions" window section

    This window section displays a list of bindings within the current complex species.

    If a binding is selected, the user can remove the binding from the complex species by clicking the "Remove" button.

  9. Property window section: Complex Species

    The modeler application displays this window section when the complex species item is highlighted or there is no item highlighted in the "Composition" window section.

    The properties of a complex species include:

  10. Property window section: Molecule

    Similar to the molecule property window section in the molecule editing window, it is readonly for the complex species.

  11. Property window section: Molecule Component.

    Similar to the molecule component property window section in the molecule editing window, it is readonly for the complex species.

  12. Property window section: Binding Site

    Similar to the binding site property window section in the molecule editing window, it is readonly for the complex species.

  13. Control buttons

    • "Save" button

      When this button is clicked, the modeler application will check the if all molecules are connected and then save the data to the model file. If short name is not assigned, the modeler application will assign default one during this saving process. When the modeler detects unsaved content, this button displays "Save*" (with a start) to alter the user.

      When an existing complex species is loaded, the editing window is "readonly" and and this button displays the text "Enable Editing". Click it to enable editing functions.

    • "Clear" button

      Clear all the fields in the complex species editing window section.

    • "Center" button

      See "Display 'Center' buttons" in preference settings.

    • "Delete" button

      This button is provided here for convenience. It is equivalent to the "Delete" button in the complex side window section when a complex species is selected.

    • "Create A Copy" button

      This is a convenient button to create a copy of current complex species and set properties to empty or default. Then the user may continue to modify and create a new complex species.

    • "New" button

      This button is provided here for convenience. It is equivalent to the "New" button in the complex side window section.

9.2. Creating/editing complex species

9.2.1. Creating a new complex species

  1. Start

    Click "New" button in the "Complexes" side window section.

  2. Add a molecule

    To add a molecule to the current complex, double click the selected molecule in the "Add Molecule" side window section.

  3. Connect molecules

    To connect molecules within the complex, move or change the layout in the graphical layout window section to have the desired binding site pair contacted. The user can also change the layout before a molecule is connected by rotating or flipping.

  4. Save data

    Click the "Save" button.

9.2.2. Editing an existing complex species

  1. Loading a complex species

  2. Editing the data

    Edit the data in the complex species property window section

9.2.3. Creating a complex species from association window.

See the corresponding section in "Getting Started".

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8. Molecule interaction Home 10. Complex