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

See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.

## To run
### Requirements
- Python > 3.9
- gcc
- g++

### Install via
```
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**.

See [Format overview — MDAnalysis User Guide documentation](https://userguide.mdanalysis.org/stable/formats/index.html)

### 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) (AMBER NETCDF or GROMACS TRR). You will need to output the **coordinates** and **forces** to the **same file** | Require at least 2 file: a topology and a trajectory file | 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` | 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 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 <ul><li>1 : pLogP method (will separate between backbone and side chain)</li><li>2: Corr. pLogP method (will separate between backbone and side chain)</li><li>3: Corr. pLogP after adaptive enumeration of states</li></ul> | `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
You need to clone this repository to download example trajectories.
```
# 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
```

## Units
The program assumes the following default unit
| Qunatity | Unit |
| ------------- | ------------- |
| Length | Å |
| time | ps |
| charge | *e* |
| mass | u |
| force | kJ/(mol·Å) |

## Copyright

Copyright (c) 2022, DonaldChung-HK, CCPBioSim
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