NanoShaper 1.5

NanoShaper is a tool aimed at computing the molecular surface and pockets of a biomolecular system. It does that through a ray tracing technique which renders NanoShaper compatible with patch-based, implicit surface or triangulated surfaces. NanoShaper is GPL licensed software. The 1.5 version parallelizes completely the SES build-up and bears many optimizations which support increased accuracy, improved speed, and a significantly reduced memory footprint.

1. Contents

   A. Files and folders to compile NanoShaper

   • "\src" C++ sources
   • "\src_client" C++ sources and example main for API usage
   • "setup.py" script to support the compilation

   B. Example input files for standalone NanoShaper

   • "\example"

   C. Docker file and image

   • "Dockerfile"

2. Installation

   NanoShaper can be compiled on Linux for x86-64 with gcc, tested from 8 to 9.5. Pre-requisites libraries are: boost, gmp, mpfr. To install please run the setup.py script and select if a standalone, or .so (for API usage) is required.

   git clone https://gitlab.iit.it/sdecherchi/nanoshaper
   git checkout NanoShaper_PatchBased
   python setup.py

3. Execution

   Running the NanoShaper executable file if you installed as described above

   cd <Path of the directory where input files are>
   NanoShaper  <Surface Configuration file>

   To use NanoShaper in VMD please add NanoShaper path to your $PATH variable.
   In order to use nanoshaper docker image inside VMD, please rename NanoShaper_Docker_VMD.sh into NanoShaper and add its path to your $PATH environment variable. Also please be sure that in the .sh file the correct Docker image in your system is referenced. In some OS X systems (e.g., Big Sur) you may need to change the VMD default temporary folder using the VMDTMPDIR env variable because of permission issues.