The model summary page is the default page being displayed after creating/loading a model.
The summary window has 2 sections, "Model Info" and "Model
Summary".
The user may use this section as a text editor to add description about the model.
Click the "Save" button to save the content being edited to the model
file (in html format).
The summary contents display in tree view including "Molecule",
"Molecule Interaction", "Complex Species",
"Transformation", "Association", and
"Dissociation". The Number in the square bracket
indicates the number of items under that category.
If the item is corresponding to an editable entity such as a molecule, double clicking on the item in the tree view loads the item into the corresponding window. If the double clicked item is the root of a Molecule or Complex Species, the application will be directed to the molecule editing window or complex species editing window.
More details:
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"
Details" or "Standard View"Click the "
Details" button on the top to expand and show all detailed model information.Click the "
Standard View" button to show the concise view of the model.
Note
The model summary uses a tree view. The user can click the "+" sign to expand the corresponding section and "-" to collapse the corresponding section.
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"
Display Hidden Complexes"The user may specify whether a complex is hidden or not in the summary window.
When the "
Display Hidden Complexes" checkbox is checked, all complexes are listed. The user may check off a complex, for example in the below screenshot, the "A_2" complex is checked off and set to be hidden.
Whe the "
Display Hidden Complexes" checkbox is unchecked, the hidden complex(es) will not appear in the list of each complex species. The complex species item displays number of its complex(es) in the format "[n] (Shown) / [all] (All)". For example in the screenshot below, the "A_2" complex does not appear in the list under complex species "A". The number of complexes is "3 (Shown) / 4 (All)", which means there are total 4 complexes under "A" and 3 of them are not hidden. The "A_2" complex is also involved in one transformation and its name is replaced with a "*" and the display is grayed out.
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"
Filter Model Summary"The user may use certain conditions to filter the content of the summary. Click the "
+" button to expand the window section "Filter Model Summary".
The button changes its icon to "-". Click it and the window section "
Filter Model Summary" collapses.The user may specify the filtering type, select the name of entity and apply. The filtering condition also appears on the top of the summary.
Click "x" button besides the filtering condition on the top and remove the filtering condition.
The "
Display Hidden Complexes" checkbox also impact the way to display complex number under a complex species.When the "
Display Hidden Complexes" is unchecked, the number of complexes under a complex species is in the format "[n1] (Shown) / [n2] (After Filtering) / [n3] (All)", for example, "3 (Shown) / 4 (After Filtering) / 4 (All)" in the sreenshot below. Under the complex species "A", 3 complexes are shown, 4 complexes satisfy the filtering condition (related to molecule "A") and there are total 4 complexes.
When the "
Display Hidden Complexes" is checked, the number of complexes under a complex species is in the format "[n1] (After Filtering) / [n2] (All)", for example, "4 (After Filtering) / 4 (All)" in the sreenshot below.