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BOAConstructor_Tutorial
Note to Editors: Note, this page belongs to the ballaxy server, do not remove!
Click on Shared Data in the top level bar, select Data Libraries.
A list with data libraries will be shown. Select BOA Constructor Input Examples by clicking onto the name.
The content of the library will be shown (6 files).
Under that list actions for the selected dataset are provided. Select the entire dataset, then select the action Import to current history (the default) and add all these files to your history by clicking on the Go button.
The upload is confirmed.
Click on Analyze Data in the top level menu, to return to the main page.
The History on the right hand side now contains all six files: 3 molecular files in mol2 format and the corresponding structure diagram (SD) files. All bond orders in these files are set to one and need to be computed. :-)
This step is not really necessary, but helps to understand the input data.
Lets have a look on the example file 5: BOA_nontrivial_example_1 in the history. Click on the name, and more information to the file like its format (mol2) is provided.
To display the file in the browser click on the eye icon at the right of the file name.
The paragraph “@BOND” stores the bond orders and in this case all bond orders are set to one.
If you prefer an SD of the molecule, select in the history 3: Structure diagram for nontrivial input example 1 and click on the eye icon to display the SD in the browser.
If you are logged in, the input mask for BOA Constructor can be accessed via the menu Workflow in the top level menu. A list will show all provided workflows (currently, only BOA Constructor). Click the arrow next to the workflow and then click run.
If not, return to the main page by clicking on the ballaxy logo (upper left corner).
Click on the BOA Constructor label on the light green box.
The BOA Constructor workflow is a combination of 3 tasks or tools: MolecularFileConverter, BOAConstructor and the StructureDiagramGenerator.
Select the file 5: BOA_nontrivial_example_1 as input file for Step 1: MolecularFileConverter and start the workflow with Run workflow.
The workflow computes 9 additional files and adds them directly into your history (please note that due to caching reason, sometimes the browser initially only shows 5 results; reloading the page fixes this).
File 7: MolecularFileConverter on data 5 is the input file converted in to mol2 file format.
File 8: BOA Constructor on data 7, file 10: ... to 15: ... are the different bond order assignments in mol2 format, all equally possible.
File 9: ... is an SD file for the first solution (file 8: ...).
Click on the file named 8: BOA Constructor on data 7 and display the file via the eye-tool (eye icon right besides the name).
The paragraph “@BOND” contains the bond orders and we have single and double bond orders. To download the resulting file, click on the disc icon in the files history item.
If you prefer a structure diagram for visualization, select file 9: Structure Diagram on data 8 from the history and use the eye tool to have a look at the bond order assignment.
Given an input file in mol2 format (as we have created in the previous example or can be done using the MolecularFileConverter tool), we can now create more or even sup-optimal bond order assignments if needed.
Select the BOAConstructor tool from the tool bar on the left hand side.
You can adapt 4 parameters:
- the input mol2-file: select 5: BOA_nontrivial_example_1
- maximal number of assignment solutions: upper bound of 10 is reasonable
- compute sub-optimal assignments as well: this is interesting, we try true (click on the box and a tip appears)
- penalty score rules: we try the default BALL
This run will produce 10 solutions.