Getting Started¶

Requirements¶

Python > 3.9
gcc
g++

Installation¶

Run the following at the root directory of this repository

pip install CodeEntropy

Input¶

For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the coordinates and forces to the same file.

For unsupported format see 1. Loading data for ideas on how to load custom data into MDanalysis universe and convert to supported format.

Units¶

The program assumes the following default unit

Units¶
Qunatity	Unit
Length	Å
Time	ps
Charge	e
Mass	u
Force	kJ/(mol·Å)

Quick start guide¶

Warning

This doesn’t work on Windows!!!

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

For help¶

CodeEntropyPoseidon -h

Arguments¶

Arguments¶
Arguments	Description	Default	Type
`-f`, `--top_traj_file`	Path to Structure/topology file(`AMBER PRMTOP`, `GROMACS TPR` or topology file with MDAnalysis readable dihedral information (not officially supported)) followed by Trajectory file(s) (`GROMAC TRR` or `AMBER NETCDF`) You will need to output the coordinates and forces to the same file .	Required	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	`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`	Steps between frame	`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 and translational 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. pLogP after adaptive enumeration of states	`0` : no topographical analysis	`int`
`--solwm`	Do solution entropy calculation at residue level (The whole molecule is treated as one single bead.).	Flag, activate when included	Flag
`--solres`	Do solution 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 3

# 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