diff --git a/README.md b/README.md index e146e28..47390ca 100644 --- a/README.md +++ b/README.md @@ -1,84 +1,17 @@ -CodeEntropy -============================== [//]: # (Badges) -[![GitHub Actions Build Status](https://github.com/CCPBioSim/CodeEntropy/workflows/CI/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions?query=workflow%3ACI) - +[![ci](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/CI.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/CI.yaml) +![PyPI - Version](https://img.shields.io/pypi/v/codeentropy?logo=pypi&logoColor=white) +![PyPI - Status](https://img.shields.io/pypi/status/codeentropy?logo=pypi&logoColor=white) +![PyPI - Downloads](https://img.shields.io/pepy/dt/codeentropy?logo=pypi&logoColor=white&color=blue) +[![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/CodeEntropy/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/CodeEntropy?branch=main) +[![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest) +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 | `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