Overview

This module wraps the fast molecular surface calculation library (MSMS) developed by Michel Sanner at the Molecular Graphics Laboratory (TSRI).

The basic functionality of this library is to create compute solvent excluded surfaces of molecules. The input is a set of spheres for which a 3D position can be specified (x,y,z) along with a radius (r) as well as an optional name (n). In a first step, a probe sphere representing a solvent molecule is rolled over the set of spheres, defining the Reduced Surface (RS) (see manual reference below). The radius of the probe sphere is a user specified parameter. From the reduced surface the analytical model of the Solvent Excluded Surface (SES) is computed. This analytical surface can be triangulated with a user specified vertex density.In addition this library allows to,

- compute and report surface areas that can be computed analytically or numerically.

- compute the surface patches buried by a second set of spheres.

- upadate the surface after a subset of atoms assume new positions or radii.

- add/remove atoms to the molecule and recompute the surface partially.