Plugins Guide

Brief introduction/tutorial for plugins.

Plugins

Plugins are graphical user interfaces with three main functions: enabling the specification of inputs, running calculations, and displaying results.

In the SBL, plugins are developed using the following generic framework, proposed in the package AutoCLIP. This framework makes it possible to handle coherently all targeted platforms, including PyMOL, VMD, and NGLViewer.

VMD Multi-Instance Limitation: Each VMD plugin communicates with VMD through a fixed network port (default: 5555). If two VMD instances are opened simultaneously, the plugin may send commands to the wrong VMD instance. To avoid this issue, ensure only one VMD instance with an active plugin is running at a time.

List of available plugins

Below is a brief overview of the currently available plugins.

• Short videos are available from the SBL-plugins youtube channel.

• A self-contained toy example illustrating the complete plugin-generation workflow is available as Toy Example.

• See also the installation guide

Surfaces, volumes, interfaces, contacts

• sbl_vorlume_pdb from the package Space_filling_model_surface_volume : computes molecular surfaces, volumes, and packing properties.

• sbl_intervor_ABW_atomic from the package Space_filling_model_interface : detects pairs of interface particles, either between partners in a complex or via mediators (e.g., interfacial water molecules).

• sbl_bif_chainsW_atomic from the package Space_filling_model_interface_finder : analyzes interfaces and interactions within macromolecular complexes.

• sbl_misa from the package Multiple_interface_string_alignment : combines MSA with interface models to yield Multiple Interface String Alignments (MISA) that encode properties of amino acids at protein–protein interfaces.

Alignments and decompositions

• sbl_kpax from the package Kpax : provides a generic implementation of the Kpax algorithm, a reference structural aligner.

• sbl_spectraldom from the package Spectral_domain_explorer : identifies structural domains by maximizing intra-domain and minimizing inter-domain interactions.

Conformational analysis

• sbl_tripeptide_loop_closure from the package Tripeptide_loop_closure : generates or modifies tripeptide segments using Tripeptide Loop Closure (TLC).

Structure prediction analysis

• sbl_alphafold_dbrun from the package Alphafold_analysis : characterizes the fragmentation of AlphaFold predictions.

Misc

• sbl_alpha_complex_of_molecular_model from the package Alpha_complex_of_molecular_model : analyzes the alpha complex of a molecular model.