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1 | | -CodeEntropy |
2 | | -============================== |
3 | 1 | [//]: # (Badges) |
4 | | -[](https://github.com/CCPBioSim/CodeEntropy/actions?query=workflow%3ACI) |
5 | | - |
| 2 | +[](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/CI.yaml) |
| 3 | + |
| 4 | + |
| 5 | + |
| 6 | +[](https://coveralls.io/github/CCPBioSim/CodeEntropy?branch=main) |
| 7 | +[](https://codeentropy.readthedocs.io/en/latest/?badge=latest) |
6 | 8 |
|
| 9 | +CodeEntropy |
| 10 | +============================== |
7 | 11 | CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for calculating entropy |
8 | 12 |
|
9 | 13 | See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information. |
10 | 14 |
|
11 | | -## To run |
12 | | -### Requirements |
13 | | -- Python > 3.9 |
14 | | -- gcc |
15 | | -- g++ |
16 | | - |
17 | | -### Install via |
18 | | -``` |
19 | | -pip install CodeEntropy |
20 | | -``` |
21 | | - |
22 | | -### Input |
23 | | -For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the **coordinates** and **forces** to the **same file**. |
24 | | - |
25 | | -See [Format overview — MDAnalysis User Guide documentation](https://userguide.mdanalysis.org/stable/formats/index.html) |
26 | | - |
27 | | -### Command-line tool |
28 | | -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!!!) |
29 | | -#### For help |
30 | | -``` |
31 | | -CodeEntropyPoseidon -h |
32 | | -``` |
33 | | -#### Arguments |
34 | | -| Arguments | Description | Default | type| |
35 | | -| ------------- | ------------- |----------- |--------------| |
36 | | -| `-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` | |
37 | | -| `-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` | |
38 | | -| `-b`, `--begin` | Start analysing the trajectory from this frame index. | `0`: From begining | `int` | |
39 | | -| `-e`, `--end` | Stop analysing the trajectory at this frame index | `-1`: end of trajectory | `int` | |
40 | | -| `-d`, `--step` | Steps between frame | `1` | `int` | |
41 | | -| `-k`, `--tempra` | Temperature for entropy calculation (K) | `298.0` | `float` | |
42 | | -| `-t`, `--thread` | How many multiprocess to use. | `1`: for single core execution | `int` | |
43 | | -| `-o`, `--out` | Name of the file where the text format output will be written. | `outfile.out` | `str` | |
44 | | -| `-v`, `--csvout` | Name of the file where the total entropy output will be written. | `outfile.csv` | `str` | |
45 | | -| `-r`, `--resout` | Name of the file where the residue entropy output will be written. | `res_outfile.csv` | `str` | |
46 | | -| `-m`, `--mout` | Name of the file where certain matrices will be written. | `None` | `str` | |
47 | | -| `-n`, `--nmd` | Name of the file where VMD compatible NMD format files with mode information will be printed. | `None` | `str` | |
48 | | -| `-a`, `--rotationalaxis` | The 3 atom name in each residue for rotational axis. | `['C', 'CA', 'N']` : for protein | list of `str` | |
49 | | -| `-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` | |
50 | | -| `-p`, `--pureAtomNum` | Reference molecule resid for system of pure liquid. | `1` | `int` | |
51 | | -| `-x`, `--excludedResnames` | Exclude a list of molecule names from nearest non-like analysis. | `None` | list of `str` | |
52 | | -| `-w`, `--water` | Resname for water molecules. | `WAT` | list of `str` | |
53 | | -| `-s`, `--solvent` | Include resname of solvent molecules (case-sensitive). | `None` | list of `str` | |
54 | | -| `--wm` | Do entropy calculation at whole molecule level (The whole molecule is treated as one single bead.). | Flag, activate when included | Flag | |
55 | | -| `--res` | Do entropy calculation at residue level (A residue as a whole represents a bead.). | Flag, activate when included | Flag | |
56 | | -| `--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 | |
57 | | -| `--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` | |
58 | | -| `--solwm` | Do water entropy calculation at residue level (The whole molecule is treated as one single bead.). | Flag, activate when included | Flag | |
59 | | -| `--solres` | Do water entropy calculation at residue level (A residue as a whole represents a bead. | Flag, activate when included | Flag | |
60 | | -| `--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 | |
61 | | -| `--solContact` | Do solute contact calculation. | Flag, activate when included | Flag | |
62 | | -#### Example |
63 | | -You need to clone this repository to download example trajectories. |
64 | | -``` |
65 | | -# example 1 DNA |
66 | | -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 |
67 | | -
|
68 | | -# example 2 lysozyme in water |
69 | | -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 |
70 | | -``` |
71 | | - |
72 | | -## Units |
73 | | -The program assumes the following default unit |
74 | | -| Qunatity | Unit | |
75 | | -| ------------- | ------------- | |
76 | | -| Length | Å | |
77 | | -| time | ps | |
78 | | -| charge | *e* | |
79 | | -| mass | u | |
80 | | -| force | kJ/(mol·Å) | |
81 | | - |
82 | 15 | ## Copyright |
83 | 16 |
|
84 | 17 | Copyright (c) 2022, DonaldChung-HK, CCPBioSim |
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