BOAConstructor_Help

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Frequently asked questions about BOA Constructor

For general questions on how to use ballaxy, see here.

• What is the aim of BOA Constructor? Given a molecule _with atomic connectivity information, BOA Constructor computes a _number of possible bond order combinations (integer bond orders 1 to 4) based on atomic valence rules, from which an optimization problem is deduced and solved.

• Where can the results of BOA Constructor be found? The framework offers a full history of input and output data in the bar on the right hand side called "History".

• How can results be visualized? The result of BOA Constructor are _molecular files_ each representing a bond order assignment. A molecular file can be displayed by clicking the preview button symbolized by an eye icon.

In addition, ballaxy is supplemented with a visualization tool “Structure Diagram of a molecule” which generates a structure diagram (SD) in png format for a given molecular file, which can also be viewed by clicking the eye icon.

• What is the difference between the two scoring rule sets BALL and Antechamber? The Antechamber set is taken from the Antechamber approach, we further extended this atomic valence rule set with respect to missing atom types and different preference for atomic valence states, e.g. Antechamber prefers carboxylic groups in a non-standard setting.

• Can BOA Constructor be applied to other file formats than mol2? Ballaxy is supplemented with a file converter tool “MolecularFileConverter”, which allows conversion between mol, hin, pdb, sdf, pdb, xyz and mol2 file formats.

• Where can example data be found? Some test input examples can be found in the “Shared Data Library” in the test set named "BOA Constructor Input Examples" (see https://ballaxy.bioinf.uni-sb.de/library). To access the “Shared Data Library” click “Shared Data” in the top menu and select “Data Library”. Then select the set "BOA Constructor Input Examples" and import them to your history. The corresponding results are discussed BOAConstructor_Examples.

• Is there a tutorial? A tutorial describing how to use BOA Constructor in a step by step manner using the provided example test data can be found here BOAConstructor_Tutorial.

• How can I upload a file? A molecular file can be uploaded via the “Upload File" - tool which you can find in the “Get Data” tool box on the left hand side. A file can be either copied and pasted into the URL/Text - box in ballaxy's "Get Data => Upload File" - tool, or uploaded. It is then entered into the users framework history (seen on the right hand side).

• How can I download a file? Select your file of choice in the history by clicking on its name. Then a disc icon appears, click on that icon to start the download.

• How many solutions can be computed? As many as exist :-) With increasing number, the bond order assignments are less likely.

• Why does BOA Constructor produce equal bond order solutions? BOA Constructor can enumerate all optimal or, if desired, even suboptimal solutions to the bond order assignment problem. In some cases, this results in seemingly identical solutions that are related by a trivial symmetry operation. For example, benzene has two co-optimal solutions that correspond to different kekulizations.

• Why does BOA Constructor not work correctly on xyz files? Xyz files do not contain connectivity information, thus BOA Constructor is not given a valid input.

• Is there a corresponding offline tool? The BALL library (http://www.ball-project.org/) offers a C++ and python interface for BOA Constructor. In addition, BALLView is supplemented with a GUI for BOA Constructor and allows easy usage within the BALL framework (e.g. SMARTS matching, visualization).

• What algorithms are used to solve the Bond Order Assignment problem? We formulate the Bond Order Assignment Problem as an optimization problem, relating atomic valences defined by scoring rules to optimal bond order combinations that fulfilling the specified atomic valences. For solving the optimization problem we use an FPT solver.

• How to cite BOA Constructor?

Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). 
Automated Bond Order Assignment as an Optimization Problem. 
Bioinformatics, 2011