Python version (slower than Julia version)

• To use code: python gauss_linking.py -f TRAJ -p TOP -b BEGIN -e END -skip SKIP_FRAME -nproc NUMTHREAD

Notes about |G|c values: G>=1: entanglement exist (see original paper for details)

For single frame (pdb file), use single_frame.py for short and more detailed

For trajectory, run caller.py, which will automatically divided trajectory in multiple parts and call ent_calculations for each part (multiple frames) ./run_caller.sh is perfect for short, but you need to modify the input params.

Julia version (prefer to use):

• requirement packages: MDToolbox, Distances
• To reduce precompute time, run pre_compile.jl to generate image and load into environment (this take so long, ~7 mins) but worth to do so. This is run only one. Full command:
  julia -J SYS_IMAGE.so -t NUM_THREADS gauss_linking.jl -f TRAJ -p TOP -b START_FRAME -e END_FRAME -s SKIP_FRAME

simple command: julia gauss_linking.jl -f PDBFILE

Analyze single PDB file:

For single PDB file, another option is use GE_BioStructures_v4.jl which employed BioStructures.jl package version 4, which will work with Julia 1.10.

Command is similar to above: julia GE_BioStructure_v4.jl -f PDB_FILE

The benifit of this file is using newer version of Julia and dependence packages so it improves loading time.

Note:

MDToolbox is not able to load structure contains HEATATM like ions. Find different library