CodeEntropy

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

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

• Computational Molecular Science Python Cookiecutter version 1.6.
• arghya90/CodeEntropy version 0.3
• jkalayan/PoseidonBeta