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CodeEntropy

!!! This repo is now moved to CCPBioSim/CodeEntropy. Please check there for the latest version.

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CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for calculating entropy

See CodeEntropy’s documentation for more information.

To run

Requirements

  • Python > 3.9
  • gcc
  • g++

Install via

pip install .

Command-line tool

A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing CodeEntropyPoseidon (Note: this doesn't work on Windows!!!)

For help

CodeEntropyPoseidon -h

Arguments

Arguments Description Default type
-f, --top_traj_file Path to Structure/topology file (AMBER PRMTOP or GROMACS TPR) followed by Trajectory file(s) Requires either --top_traj_file or --pickle list of str
-l, --selectString Selection string for CodeEntropy such as protein or resid, refer to MDAnalysis.select_atoms for more information. "all": select all atom in trajectory for CodeEntropy analysis for trajectory without solvent str
-b, --begin Start analysing the trajectory from this frame index. 0: From begining int
-e, --end Stop analysing the trajectory at this frame index -1: end of trajectory int
-d, --step Stop analysing the trajectory at this frame index 1 int
-k, --tempra Temperature for entropy calculation (K) 298.0 float
-t, --thread How many multiprocess to use. 1: for single core execution int
-o, --out Name of the file where the text format output will be written. outfile.out str
-v, --csvout Name of the file where the total entropy output will be written. outfile.csv str
-r, --resout Name of the file where the residue entropy output will be written. res_outfile.csv str
-m, --mout Name of the file where certain matrices will be written. None str
-n, --nmd Name of the file where VMD compatible NMD format files with mode information will be printed. None str
-a, --rotationalaxis The 3 atom name in each residue for rotational axis. ['C', 'CA', 'N'] : for protein list of str
-c, --cutShell Include cutoff shell analysis, add cutoff distance in angstrom. None : will ust the RAD Algorithm. See Higham, Jonathan, and Richard H Henchman. “Locally adaptive method to define coordination shell.” The Journal of chemical physics vol. 145,8 (2016): 084108. doi:10.1063/1.4961439 list of str
-p, --pureAtomNum Reference molecule resid for system of pure liquid. 1 int
-x, --excludedResnames Exclude a list of molecule names from nearest non-like analysis. None list of str
-w, --water Resname for water molecules. WAT list of str
-s, --solvent Include resname of solvent molecules (case-sensitive). None list of str
--wm Do entropy calculation at whole molecule level (The whole molecule is treated as one single bead.). Flag, activate when included Flag
--res Do entropy calculation at residue level (A residue as a whole represents a bead.). Flag, activate when included Flag
--uatom Do entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). Flag, activate when included Flag
--topog Compute the topographical entropy using
  • 1 : pLogP method (will separate between backbone and side chain)
  • 2: Corr. pLogP method (will separate between backbone and side chain)
  • 3: Corr. density function (only output LamdaRho)
  • 4: Phi Coeff method (not functional!!)
  • 5: Corr. pLogP after adaptive enumeration of states
 0: no topographical analysis int
--solwm Do water entropy calculation at residue level (The whole molecule is treated as one single bead.). Flag, activate when included Flag
--solres Do water entropy calculation at residue level (A residue as a whole represents a bead. Flag, activate when included Flag
--soluatom Do solution entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). Flag, activate when included Flag
--solContact Do solute contact calculation. Flag, activate when included Flag

Example

# example 1 DNA
CodeEntropyPoseidon -f "Example/data/md_A4_dna.tpr" "Example/data/md_A4_dna_xf.trr" -a "C5'" "C4'" "C3'" -l "all" -t 8 --wm --res --uatom --topog 5

# example 2 lysozyme in water
CodeEntropyPoseidon -f "Example/data/1AKI_prod_60.tpr" "Example/data/1AKI_prod_60.trr" -l "protein" -b 1 -e 30 -d 2 --wm --res --uatom --topog 1 --solwm --solres --soluatom --solContact

Units

The program assumes the following default unit

Qunatity Unit
Length Å
time ps
charge e
mass u
force kJ/(mol·Å)

Script Examples

See Example folder You can add your own trajectories by editing the path in the python script to point to your own trajectories

create_new_universe.py

This repo uses MDAnalysis to parse values and it can only parse force natively for GROMACS TRR and AMBER NETCDF. This scripts shows you how to create a new universe from unsuppported data so that you can use trajectories created from other simulation software or reduce the size of universe to focus on a section of simulation.

CodeEntropy_non_topo.py

Calculate entropy of target trajectory non topographical level with a no water lysozyme trajectory

CodeEntropy_topo.py

Calculate entropy of target trajectory based on different method with a no water lysozyme trajectory

Poseidon_GROMACS

Run POSEIDON analysis for a GROMACS trajectories with a lysozyme in water

Poseidon_LAMMPS

A LAMMPS example for POSEIDON this is a capped amino acid example (note the force unit of this trajectory is based on KCal not KJ)

mcc_mdanalysis

A DNA example for CodeEntropy without using function to show the inner working of CodeEntropy

mcc_mdanalysis_multiprocess

mcc_mdanalysis with multiprocess parallelization

CodeEntropy_DNA.py

the DNA strand example but with updated generalized CodeEntropy functions

Copyright

Copyright (c) 2022, DonaldChung-HK

Acknowledgements

Project based on the