| Name | bemm-gen JSON |
| Version |
2024.7.26
JSON |
| download |
| home_page | None |
| Summary | Biomolecular Environment Mimicking Model GENerator |
| upload_time | 2024-07-26 01:56:10 |
| 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="./bemm-gen_logo_horizontal.png" width="512px"><br><br>
Biomolecular Environment Mimicking Model GENerator <br><br><br></p>
# Welcome to BEMM-GEN
<p align="center"><br><img src="./bemm-gen_main.png" width="800px"></p>
## What is BEMM-GEN?
<img src="./bemm-gen_scheme.png" align="right" width="400px">
BEMM-GEN is a new tool aiming to generate biomolecular environment mimicking model for molecular dynamics simulation. BEMM-GEN generates spherical and cylindrical models with user-specified chemical properties, allowing the integration of arbitrary protein structures into the generated models. Consequently, the model and protein complex structures, along with the corresponding parameter files for MD simulations (AMBER or GROMACS), are provided as output files.
<br><br><br><br><br><br><br><br><br>
## Requirements
Python >= 3.8, conda, openbabel, psi4, resp, ambertools, scikit-learn, rdkit, parmed
## Installation
### For Linux/MacOS
- Follow the instructions below to install BEMM-GEN.
### For Windows
- Install Windows Subsystem for Linux (WSL), then follow the instructions below to install BEMM-GEN on WSL.
Using a Conda environment (such as Miniforge, or Miniconda) is recommended for BEMM-GEN. If you use only the pip package manager, please adjust the commands accordingly.
```sh
conda create -n bemm-gen-env
conda activate bemm-gen-env
conda install -c conda-forge openbabel psi4 resp ambertools
pip install bemm-gen
```
## Basic Usage
```sh:available_sub-commands
# Make a cylindrical model
bemm-gen cylinder --proteinseq GASGASGASGAS --proteinSS HHHHHHHHHHHH --resnames MTY:HYD --composition 1:2.5
# Make a spherical model
bemm-gen sphere --proteinpdb protein.pdb --resnames MTY:HYD --composition 0.3:0.7
# Make parameters for a new residue
bemm-gen makeparam --smiles CCC --resname MTY --description "Methyl group"
```
**Please see the documentation [English](https://github.com/y4suda/BEMM-GEN/blob/main/tutorial_en.md) / [日本語](https://github.com/y4suda/BEMM-GEN/blob/main/tutorial_ja.md)**
## Cite Us
T. Yasuda, R. Morita, Y. Shigeta and R. Harada. "BEMM-GEN : A toolkit for generating a biomolecular 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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