Table 1

STRAP HotSwap Plugin Types. This table gives an overview of some of the plugins that are already available in STRAP and can be used as examples for development new plugins. STRAP plugins are defined by a Java interface with functions that users can implement in order to have their plugin interact with STRAP. Protein Protein Distance returns values for all pairs of proteins in a set of proteins. The values can be used for distance matrices. Sequence Aligner is used as a wrapper around programs such as clustalW to perform multiple alignments and display them in the STRAP GUI. Likewise Protein Viewer is a wrapper around external protein viewers such as rasmol or pymol. Superimpose3D is an interface for methods that superimpose one protein structure onto another by calculating a 3 × 3 rotation matrix and a {dx, dy, dz} translation matrix. Value Of Residue is an interface for methods that return a float value for each residue of a protein in order to plot a profile along the sequence of the protein. Value Of Protein is for plugins that calculate a float value for individual proteins; the STRAP GUI will display these values as a bar chart. Fuller documentation of these and other plugin types is available online. Each example plugin is already included in the main STRAP distribution, and source code can be seen from within the STRAP GUI. The last column explains the purpose of the most important methods of the respective plugins. In general, these methods are designed to interact with the rest of the STRAP GUI to display the results of the plugin's analysis. See text for further details.

Plugin Type

Example

Methods in Interface


SoR

CoiledCoil

See text


Protein Protein Distance

SequenceDisSimilarity-AsAligned

get Value Returns a real number representing the degree of dissimilarity between two or more proteins. In the example class, it returns the proportion of aligned residues that are identical. This information is then used by the STRAP GUI to display a graph or table with the results.


Sequence Aligner

A variety of well-known algorithms are implemented as plugins, for example "Multiple AlignerClustalW"

Get AlignedSequences Returns the results of the alignment algorithm for display in the STRAP GUI.


Protein Viewer

Interfaces to rasmol, pymol, others

getProtein Returns a reference to the associated STRAP protein object.

getSelectedAminoAcids Causes selected residues to be shown as selected by the protein viewer.


Superimpose3D

SuperimposeGoede

getRotation Returns a 3 × 3 rotation matrix.

getTranslation Returns a {dx, dy, dz} translation vector.


Value Of Residue

Solvent Accessibility

get Values Returns the values for each residue which are then displayed by the STRAP GUI as a profile.


Value Of Protein

countResidues

get Value Returns a value for the protein which is then displayed by the STRAP GUI as a bar in a bar chart.


Gille and Robinson BMC Bioinformatics 2006 7:64   doi:10.1186/1471-2105-7-64

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