| Name | cemm-gen JSON |
| Version |
2024.7.23
JSON |
| download |
| home_page | None |
| Summary | Cellular Environment Mimicking Model GENerator |
| upload_time | 2024-07-22 07:34:53 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License Copyright (c) 2024 y4suda Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
bioinfomatic
molecular dynamics
biology
chemoinformatics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<p align="center"><br><img src="./cemm-gen_logo_horizontal.png" width="512px"><br><br>
Cellular Environment Mimicking Model GENerator <br><br><br></p>
# Welcome to CEMM-GEN
<p align="center"><br><img src="./cemm-gen_main.png" width="800px"></p>
## What is CEMM-GEN?
<img src="./cemm-gen_scheme.png" align="right" width="400px">
CEMM-GEN is a new tool aiming to generate cellular environment mimicking model for molecular dynamics simulation. CEMM-GEN provides a configuration with any modification group added to the spherical or cylinder-like interior.
<br><br><br><br><br><br><br><br><br>
## Requirements
Python >= 3.8, conda, openbabel, psi4, resp, ambertools, scikit-learn, rdkit, parmed
## Instllation
```sh
conda create -n cemm-gen-env
conda activate cemm-gen-env
conda install -c conda-forge openbabel psi4 resp ambertools
pip install cemm-gen
```
## Basic Usage
```sh:available_sub-commands
# Make a cylindrical model
cemm-gen cylinder --proteinseq GASGASGASGAS --proteinSS HHHHHHHHHHHH --resnames MTY:HYD --composition 1:2.5
# Make a spherical model
cemm-gen sphere --proteinpdb protein.pdb --resnames MTY:HYD --composition 0.3:0.7
# Make parameters for a new residue
cemm-gen makeparam --smiles CCC --resname MTY --description "Methyl group"
```
**Please see the documentation [English](https://github.com/y4suda/CEMM-GEN/blob/main/tutorial_en.md) / [日本語](https://github.com/y4suda/CEMM-GEN/blob/main/tutorial_ja.md)**
## Version History
See the [version history](./version_history.md) for the latest updates.
## Cite Us
T. Yasuda, R. Morita, Y. Shigeta and R. Harada. "Cellular Environment Mimicking Model GENerator: A tool for generating a cellular environment mimicking model."*XXXX*,2024,XXXX,[doi](https://XXX)
## Authors
Takunori Yasuda, Doctoral Program in Biology, University of Tsukuba
Rikuri Morita, Center for Computational Sciences, University of Tsukuba
Yasuteru Shigeta, Center for Computational Sciences, University of Tsukuba
Ryuhei Harada, Center for Computational Sciences, University of Tsukuba
yasuda.takunori.tkb_gb@u.tsukuba.ac.jp
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