topoly 0.1.0

This package provides a set of tools for modeling protein knots, lassos and other.

Requirements

• cmake 3.8 or later**
• make
• CUDA toolkit - nvidia-toolkit (nvcc CUDA compiler)
• gcc 4.8 or later
• boost 1.50-1.65
• Python 3 (3.4 or later)
• Cython 0.26 or later - use "pip3 install Cython" to install
• Xcode 9.4 or OLDER (on Mac OS X - Nvidia does not support newer Xcode)

** You can download binary distributions of cmake from: https://cmake.org/download/ Just unzip and add the cmake-XXX/bin to the PATH, for example:

export PATH=~/cmake-3.13.0-Linux-x86_64/bin:$PATH

Build and test C++ code

1. Setup the build directory:

mkdir build && cd build && cmake .. 2. Build the binaries: make 3. Run the tests* make test

• The build may be done on a computer without a CUDA supported GPU provided that the nvidia-toolkit is installed. The knotnet tests, however, will require a CUDA supported GPU to pass.

• if tests fail you can look into build/Testing/Temporary for details.

Generate distribution

After building in the build directory run:

make package

This will produce 3 distribution packages:

• ZIP package
• DEB package for Debian and Ubuntu
• RPM package for RedHat, Scientific Linux and CentOS

Generate Python Package for PIP

1. In the main folder run:

python3 setup.py bdist_wheel 2. The output should be a wheel (whl) package located in: dist 3. If you want to clean and rebuild the package delete the directory rm -rf _skbuild

Documentation:

See topoly\graph.py and topoly\doc_example.py

Generate API documentation as HTML:

1. sudo apt install doxygen graphviz
2. cd topoly
3. doxygen topoly.doc.cfg or run doxygen.sh
4. The API documentation will be generated to topoly-web\api

Readme for the end user is located in docs/README.md

Install C++ support (plugin) for Apache Netbeans 9.0:

Tools->Plugins->Settings->Add

http://updates.netbeans.org/netbeans/updates/8.2/uc/final/distribution/catalog.xml.gz

Based on:

https://stackoverflow.com/questions/51493882/netbeans-9-c-support

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