Updated 2014-11-25 22:44:01 by RLE

What: tsurf: tcl extension to compute an isosurface given a set of points/atoms. tsurf is an enhanced version of the polyr program written by Jesper James Jensen.
Where: http://www.lbgi.fr/~moumou/TclTk
Description: Tcl extension to compute an iso-surface givent a set of points/atoms. The original program (the 'marching cube' part) was written by Jesper James Jensen, and it has been adapted to support expansion/contraction/smoothing.
Updated: 11/2014
Contact: luc.moulinier at unistra.fr

Description :  edit

This command will compute the iso-surface associated with a set of atoms or points. This extension is based upon the polyr program by Jesper James Jensen. It has been adapted to add the -contract, -smooth, -expand options.

It first creates a mesh and places the atoms on it given their radii (Van der Waals radius). It then creates the isosurface using the "marching cube" algorithm. It outputs two lists, one containing all triangles describing the surface, and one containing all normals associated with each triangle vertices.

Usage :  edit

The minimal form of the tsurf command is :

tsurf ?options? pointsList

where pointsList is of the form :
set pointsList {{x1 y1 z1 na1 id1} {x2 y2 z2 na2 id2} .... }

where (x,y,z) is the 3d-coordinates of the points, na is the atomic number, and id is an id of the point, not used at present.

Several options can control the shape of the resulting surface (see Documentation) :

  • -sample
  • -contract
  • -expand
  • -smooth
  • -asa

Documentation is available here : http://www.lbgi.fr/~moumou/TclTk/tsurf.html and the source code (and some binaries) either as a zip file (http://www.lbgi.fr/~moumou/TclTk/Downloads/tsurf0.1.zip) or a tar-gzipped (http://www.lbgi.fr/~moumou/TclTk/Downloads/tsurf0.1.tar.gz)