Software used to compute the classical electric field from a protein structure (or structures) as well as sample the electric field topological data.
System Requirements
- gnuplot (only for plotting)
You can easily install gnuplot on Mac using homebrew
brew install gnuplot
On Linux, gnuplot should be in your package manager repo’s already. For example on Ubuntu
sudo apt-get update
sudo apt-get install gnuplot
Installation
Download Binaries
Binaries (version 0.4.3) are available for MacOSX (ARM 64, ‘Apple Silicon’). Linux binaries are fully statically linked; however, MacOS binaries are still dynamically linked to system libraries. If you receive an error such as
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found
or something similar, you will have to compile from source (see below).
Compile from source
Requirements
- CMake (Version 3.14 or higher)
- A compiler that implements C++17 features or newer
Note, this may not compile or run on Windows.
Compilation Steps
Download or clone this repository using
git clone https://github.com/matthew-hennefarth/CPET.git
Then, go into the project and make a build directory, mkdir build and go into
this directory, cd build. We will then run cmake to build the binary.
cmake ../
make
This should create the executable, cpet, in CPET/bin to be used.
Usage
Calling cpet -h will output the various options available. What is always
needed is a pdb file and an options file. The pdb file should contain the
partial atomic charges in the occupancy column (columns 55-60) for each atom. I
recommend using the Atomic Charge Calculate II for
generating partial atomic charges, and it will place the charges in the
occupancy column automatically. The options file will tell the program what to
compute and how.
Acknowledgements
This code uses the following C++ libraries: