Contributed Code

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Code contributed from community members

sphgen.cpp

Sphgen_cpp is a C++ version of the DOCK suite program sphgen, used for generating spheres around a receptor from a molecular surface file.

author

Andrew Magis, University of Florida andrewmagis@gmail.com Developed in the Department of Physiology and Functional Genomics, Peter Sayeski, Ph.D.

description

Sphgen_cpp is a modified form of the DOCK suite program Sphgen. It has been translated from the original Fortran into C++, and the following improvements have been made:

  • Sphgen frequently crashed on large inputs. This was caused by either the hard-coded upper limit of surface points being exceeded, or irregularities in the column spacing of molecular surface file atom numbers, which were used as indices into arrays. Sphgen_cpp does not have these problems, as most of the arrays have been eliminated, and all memory is dynamically allocated.
  • Some calculations have been optimized to improve performance, and most of the disk ccesses have been eliminated. As a result, sphgen_cpp runs approximately 2X to 2.5X as fast as Sphgen, depending on the input size.
  • Use of the INSPH file is now optional, as command-line arguments are now accepted.

Sphgen_cpp.1.1.tar.gz

sphere_select

Sphere_select is designed to allow much more flexibility in selecting spheres. Users can select spheres based on ligand coordinates in MOL2 and PDB format, or around specific atoms in the receptor file, or around a specific sphere. Sphere_select can also automatically write out the sphere PDB file for easy visualization.

author =

Andrew Magis, University of Florida andrewmagis@gmail.com Developed in the Department of Physiology and Functional Genomics, Peter Sayeski, Ph.D.

description

Sphere_select allows the user to select spheres in several different ways. MOL2 coordinate files can be used as inputs to select spheres around a known binding ligand, as with the original sphere_selector. Sphere_select also reads coordinate files in PDB format, and automatically detects the file format. Spheres can also be selected around a specific atom in either the MOL2 or PDB coordinate file. This is somewhat different than selecting spheres based on a ligand. In this case, the user knows or suspects a binding site, but lacks a MOL2 ligand coordinate file with which to select spheres. In this case the original PDB (or MOL2) file of the receptor can be provided as a coordinate file, and an atom can be specified around which to select spheres. The atom number exists in column 1 of the TRIPOS MOL2 format and column 2 of the PDB file format. Finally, the user can specify a specific sphere around which to select other spheres. In this case the coordinate file is ignored. This might be useful in a situation where the user knows or suspects a binding site that has been populated with spheres, and simply picks a sphere in approximately the correct place to select a group of spheres for DOCKing calculations.

Sphere_select.1.0.tar.gz