NanoShaper 0.3.1 user guide in pdf format

Bugfix:

When changing the Probe radius for the Connolly Surface, NanoShaper 0.7 will output always the same surface with probe radius set at 1.4 Angstrom. With this fix the Probe_Radius keyword is not ignored and the surface accordingly changes.

To apply the fix replace ConnollySurface.cpp into the src directory and recompile (running 'make' inside build directory is sufficient). Also a pre-compiled 32 bit version for Windows is given.

This bugfix is cumulative and it is a superset of the previous one.

Bugfix description:

This bugfix allows NanoShaper to save the status map if requested. The previous version ignored the Save_Status_map flag. To apply the patch overwrite the given source files in the src folder and type make (Linux) or recompile in Visual Studio (Windows). 

This bug fix increases the version number to 0.7.5

Additionally we provide precompiled 32/64 bits versions of NanoShaper for Windows.The 32 bit version should run almost everywhere, included older Windows XP based machines.

The 64 bit version requires Windows 7 or above, the shipped .dll in the path (or the running directory) and the Visual Studio 2013 redistributable package installed.

NanoShaper 0.7 statically linked for Linux 64. It comes with some bug fixes. Upon unzip please assure to make the file executable: chmod +X NanoShaper. This version is adapted to be used together with VMD, just make it reachable by placing the executable in a path covered by the PATH variable like usr/bin in some Linux distributions, or update the PATH variable according to the directory where NanoShaper is placed

NanoShaper 0.3.1 comes with two significant performance improvements: Skin Surface build-up time has been reduced by a factor of 5x-12x depending on the molecule. Ray casting for triangulated surfaces now uses the 2D acceleration grid that leads to a 3x performance speed-up. Additionally NanoShaper has an automated installer, called setup.py, that allows to install the required packages on Linux/Mac, and compile the code. The supported distributions/packet managers pairs are: apt-get/Ubuntu-Debian, yast/Suse, yum/RedHat-Centos, fink/Mac.

In the script and utilities section the pdb2xyzr.py script is given: this script translates a pdb file to a .xyzr using Amber99 radii set.

NanoShaper 0.3.2 provides a bug fix for the Solvent Excluded Surface Module

In this version new tools and several improvements are present:

• This version of NanoShaper, using the DelPhiPatcher, can be interfaced to DelPhi Fortran 77 solver.
• The first grid operator is introduced, namely the minus operator. By grid operator we mean a function that takes as input one or more grids and produces an output grid. The minus operator is introduced because it is used to support pocket/cavity detection. To support cavity/pocket detection the keyword Operative_Mode is introduced; pockets detection is carried instead of the usual flow when the keyword is set to "pockets".
• Normals to vertices can be computed, analytically where possible. Meshes can now be saved in the, here introduced, OFF+N, OFF+N+A formats. These new formats save the nearest atom index (A) and the normals (N). Now meshes can be saved in MSMS format too when explicitly requested.
• Octree are now used when collecting the analytical intersections for the triangulation. This leads to a significant memory saving, in particular when an high resolution is used for triangulation. A parallel version of the Marching Cubes algorithm is present. It is a major change with respect to the previous version in that the algorithm has been significantly reformulated; often it gives a linearly scaling performance.
• Load balancing (during ray-tracing) is significantly improved..
• The flood-fill algorithm for closed cavity detection can lead to significant performance improvements wrt to previous version (4x) in particular when the number of detected cavities is relatively small (< 10).
• An algorithm to convert a mesh to a set of approximating atoms (balls) is developed. This can be useful for those codes which, for instance, use as input only a set of atoms (e.g. DelPhi Fortrant 95 code) and are not able to directly manipulate an arbitrary mesh.
• The classes that derive from Surface can be very easily registered. It is sufficient to add the .cpp and .h files of the new surface in src directory and recompile to make the surface available to the rest of the framework. To make clear how the surface derived classes should be written the ExampleSurface class is provided.