11. Transformation
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11. Transformation

11.1. Transformation editing window

Transformations can be defined between structurally equivalent (up to differences with regard to internal bonds) complexes. Given a source complex the modeler application will identify the complexes that meet this equivalence condition as potential result complexes.

  1. The window for transformation editing:

  2. "Source" complex

    The source complex of the transformation.

    • Complex Name

      The name of the current "From" complex. If the "Complex ID" is empty, this field is editable for the user to give a customized name for a new complex. Otherwise, the field is readonly.

    • Species Name

      The short name of the complex species.

    • "Select Complex" button

      If the complex species associated with the current complex has a list of complexes defined, the user can select a complex by clicking this button.

    • "Save Complex" button

      If a new complex is detected based on the current molecule component tag states and binding status, the user can click this button to save it to the model file with the name.

    • graphical layout window section

      The graphical layout of the current complex, including molecule component state tags. Similar to the graphical layout window section in the complex editing window.

    • Molecule component tag states and binding status window section

      This window section contains the information of the molecule component states, similar to the tree window section in the complex editing window. The user can customize the states and the modeler application will update the complex accordingly based on the "Species ID", the combination of the molecule component tag state(s) and the combination of binding status.

      Similar to the complx editing window, the user can also change the molecule component tag state(s) and binding site status through the graphical window section by mouse right-click.

      The change of binding site status in the source complex invokes the same change of the status of the mapped binding site in the result complex.

  3. "Result" complex

    This window section for the "Result" complex has the same features as the window section for the "Source" complex.

    But editing statuses of binding sites is disabled. The result complex must always have consistent binding status with the source complex.

    Note

    See the note about result complex binding status in the "Getting Started" section.

  4. Transformation information

    • Transformation Short Name

      The short name of the transformation.

    • Transformation Full Name

      The full name of the transformation

      Note

      Also see "Display Full Name Fields" in the preference section.

    • Transformation Rate

      The rate for the tranformation in units of "/s"

    • Transformation Annotation

      Free text field for the user to provide annotation.

  5. Control buttons

    • "Save" button

      When this button is clicked, a saving request is sent to the modeler application. The moder will first check the completeness of the transformation data and give warning message(s) if necessary. If the check is passed, the modeler application saves the data to the model file.

      The modeler application will detect if there is any conflicting data. If the modeler application finds a conflict, a message window displays to ask the user to decide how to handle the conflict.

      • Conflicting case 1: a complex has been changed for an existing transformation and the transformation with the changed complex has not been defined yet. The user will be asked whether the current transformation should be updated using the new complex or whether the transformation with the new complex should be treated as a new transformation.

      • Conflicting case 2: a complex has been changed for an existing transformation and the transformation with changed complex is defined.

      • Conflicting case 3: the current transformation is created as new, but it has been defined before.

    • "Back" button

      When this button is clicked, the modeler application goes back to the previous window.

    • "Create A Copy" button

      Similar to the function of the "Create A Copy" button in the complex species editing window.

    • "Delete" button

      This button is provided for convenience. It is equivalent to the "Delete" button in the complex relationship side window section when a transformation is highlighted.

  6. Transformations between different but (for the modeler application) equivalent complexes

    Transformations can be defined between complexes that are either fully structurally equivalent (same molecules in same binding relationships and the same binding site status except the binding site pair for open-ring relationship) or that differ only with regard to internal bonds. The open and closed ring structures below are an example for the latter case. Since transformations can be used to transform one complex into another with completely different component states it can be important to define exactly which molecule (or molecule component) within a complex is transformed into which molecule (with its specific component states) in the result complex. To allow the user to define this the modeler application permits to choose from (if applicable) the different possible mappings (see below).

    A message window will appear if more than one "equivalent" complexes are found and the user can choose one from the list in the window.

    The user can choose a molecule mapping relationship from a list of all possible mappings detected by the modeler application.

    When the "Show Molecule Mapping" checkbox is checked/unchecked, the modeler application displays/hides the molecule mapping.

    The user can select the mapping relationship by clicking the "<" button or the ">" button for "Change Mapping".

    The user can choose the orientation from "No orientation", "trans-binding" and "cis-binding"

    Note

    The two binding sites involved in open<-->ring binding/unbinding have the fixed reverse binding status in the result complex compared with that in the source complex. It is an exception from the general note about binding status before.

11.2. Creating/editing a transformation

  1. Creating a new transformation

    The user can create a new transformation using the "New" button in the "Relations" side window section in either the complex species editing window or the complex editing window.

    If the transformation is created from an complex species, the modeler application will set "Don't care" as the default value for all molecule component tags and binding sites (except those involved in in-complex binding and open-ring relationship) to initialize a complex and the user can make change(s) later.

  2. Load an existing transformation

    An existing transformation can be loaded:

  3. Edit

    The fields which can be edited include:

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10. Complex Home 12. Complex association