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AntiPatch
testdata
README.md
config_example
makefile
produceResults.sh

README.md

PatchInference

This repository contains the source code source code for AntiPatch, a software for inference of antigenicity-altering patches of sites on a protein structure. For reference, please cite "C. Kratsch, L. Mümken, L. Steinbrück, T.R. Klingen, A.C. McHardy; Determination of antigenicity-altering patches of sites on the major surface protein of human influenza A/H3N2 viruses (in review)".

The source code is located under AntiPatch/src/.

How to install

To use antipatch your system must have installed make and g++. If you do not want to use the g++ compiler, that is found in your path, you have to change it in the makefile. Otherwise open a console, change to the root path (where you found this README too) and type 'make'.

This will produce a path named AntiPatch/bin, where all compiled src will lay in and the programm 'antipatch'.

The command 'make dist-clean' will delete all exept the program 'antipatch' and the src files.

How to run

To run antipatch you have the choice to edit the config file or to type the parameter in your system.

  • use config: ./antipatch config_surfaceOnly
  • use parameter option: ./antipatch -g testdata/oneValue.onlyInternal -z 1.1 -u false -s testdata/3hmg -b testdata/3HMG.pdb -c "A" -p 1 -k true

Alternatively, you can run the bash script produceResults.sh to infer patches for the reference hemagglutinin structure (PDB identifier 3HMG).

  • just type: bash produceResults.sh

With the -h option you can request help to start the program.

Questions

Please ask questions and report faults to tkl15@helmholtz-hzi.de