GAPS

GAPS is a software toolkit for Geometric Analysis of Protein Structures.

It contains the following six packages ...

• RNBasics - Simple common stuff (e.g., memory allocation, error reporting, dynamic arrays, etc).
• R2Shapes - 2D geometry and images (e.g., points, vectors, lines, images, etc.).
• R3Shapes - 3D geometry (e.g., points, vectors, lines, planes, boxes, etc.).
• R3Graphics - 3D display utilities (e.g., cameras, viewports, grdfs, textures, etc.)
• R3Grids - 2D/3D grids (e.g., cartesian, spherical, harmonics, etc.)
• PDB - PDB molecules (e.g., parsing, analysis, etc.)

.. and several example applications:

• rinit - Test initialization and error reporting functions in RNBasics package.
• rarray - Test the dynamic array class in the RNBasics package.
• off2grd - Convert a mesh file (.off) to a grid file (.grd).
• pdb2pdb - Convert a PDB file (.pdb) to another PDB file (.pdb), possibly extracting only part of the file.
• pdb2grd - Convert a PDB file (.pdb) to a grid file (.grd).
• pdb2off - Convert a PDB file (.pdb) to a mesh file (.off).
• pdb2shd - Convert a PDB file (.pdb) to a spherical harmonic descriptor (.shd).
• pdb2map - Convert a list of PDB files (.pdb) to a map describing atom distributions around a point (.map).
• pdb2chd - Convert a list of PDB files (.pdb) to a map describing atom distributions along chords (.chd).
• pdbalign - Align a pair of PDB files (.pdb).
• pdbinfo - Print information about a PDB file (.pdb).
• pdbview - View a PDB file (.pdb) interactively with OpenGL.
• grd2grd - Convert a grid file (.grd) to another grid file (.grd), possibly performing a series of operations.
• grd2shd - Convert a grid file (.grd) to a spherical harmonic descriptor (.shd).
• grd2txt - Convert a grid file (.grd) to an ASCII text file (.txt).
• grdinfo - Print information about a grid file (.grd).
• grdview - View a grid file (.grd) interactively with OpenGL.
• map2grd - Convert a PDB file (.pdb) and map file (.map) to a grid file (.grd).
• mapview - View a map file (.map) interactively with OpenGL.
• chd2grd - Convert a PDB file (.pdb) and chord file (.chd) to a grid file (.grd).
• chdview - View a chd file (.chd) interactively with OpenGL.
• hst2mat - Convert a list of descriptor histogram files (.shd) to a distance matrix file (.mat).
• hst2txt - Convert a descriptor histogram file(.shd) to an ASCII text file (.txt).
• mat2txt - Convert a distance matrix file (.mat) to an ASCII text file (.txt)..

Please view the README file for more information about compiling and linking.