| Name | FlatProt JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | None |
| Summary | Python package for creating simplified 2D protein visualisations. Specialised on showing differences and similaritys between proteins from the same protein family. |
| upload_time | 2024-10-07 21:09:04 |
| maintainer | None |
| docs_url | None |
| author | constantincarl |
| requires_python | <3.13,>=3.10 |
| license | Apache-2.0 |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# FlatProt
<img width="910" alt="image" src="https://github.com/ConstantinCarl/prot2d/assets/156075124/34d415d3-55be-4784-a96d-035e40fc5afe">
FlatProt is a tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations. FlatProt focuses on creating highly comparable representations for same-family proteins. In this case FlatProt was used to generate comparable representatoins for 3 3FTx structures.
## Contents
- [Getting Started](#getting-started)
- [First Experiences with Google Colab](#first-experiences-with-google-colab)
- [Documentation](#documentation)
- [Data](#data)
- [Example Visualizations](#example-visualizations)
- [Domain Annotation File Format](#domain-annotation-file-format)
- [Runtime for Protein Sizes](#runtime-for-protein-sizes)
- [Reference](#reference)
## Getting Started
FlatProt needs python version: python= ">=3.10,<3.13"
### Download FlatProt via pip or poetry
- pip:
```shell
pip install FlatProt
```
- Poetry:
```shell
poetry add FlatProt
```
### Install Foldseek
Instructions for downloading the Foldseek software can be found in Foldseek's GitHub
- [Foldseek GitHub](https://github.com/steineggerlab/foldseek)
--> FlatProt needs the path to the foldseek executable passed as argument to the main function to be used by the program.
### Install dssp
Instructions for downloading dssp can be found here:
- [dssp instructions](http://biskit.pasteur.fr/install/applications/dssp)
!The program runs on the mkdssp version 4.4.0! (some sources dont provide that (brew does!))
_An example download workflow for usage can also be found in the google colab_
## First experiences with Google Colab
For users to get to know prot2d we've prepared a Google Colab notebook with a quick tutorial through the major functions/possibilities of prot2d. Therefore the exmample protein 1kt1 is used and visualized in different ways. This allows for basic understanding of the functionalities:
- [Google Colab tutorial](https://colab.research.google.com/drive/17u0twE81kYYspNFsdXUHrCyP33hj0dO6?usp=sharing)
Instructions in the Colab help with the first hands-on.
For direct usage of prot2d including all paramters the following Collab provides functionalitys for using prot2d withput locally downloading anything.
Users can upload theri own proteins to the Collab and visualize them as wanted.
The runtime of the Collab is way longer than local usage. Therefore we dont advise using it for big amounts of data:
- [Google Colab usage](https://colab.research.google.com/drive/1pJHMagKgpTJ1cfBHkBSh2hMlkzQk263d?usp=sharing)
## Documentation
FlatProt's documentation can found here:
- [FlatProt documentation!](https://constantincarl.github.io/FlatProt/)
**important notes:**
- input PDB files need a header to work (important for predicted structures)
- FlatProt's methods can also be used via command line commands (cli)
## Data
This project uses datasets that can be found on Zenodo. Additional example files can be found here aswell. You can access and download the data using the following link or DOI:
- [Zenodo Data](https://doi.org/10.5281/zenodo.10674045)
## Example visualizations
### 3FTx: None|Anca_10|Anolis_carolinensis
<img width="409" alt="image" src="https://github.com/ConstantinCarl/prot2d/assets/156075124/a315fd49-74cc-456e-b0d2-c6b63333b22b">
### 3FTx - Family Overlay
### 1kt1 - domain visualization (family vis)
<img width="1000" alt="image" src="https://github.com/ConstantinCarl/prot2d/assets/156075124/1f8ac748-09d1-464c-9e42-c6fd93bfeddc">
### 1kt1 - full protine visualization
<img width="450" alt="image" src="https://github.com/ConstantinCarl/prot2d/assets/156075124/854a89a7-e91c-4ec5-b81d-d33b4f1b96ec">
## Domain Annotation File Format:
The domain annotation is needed in the following format to be procceced by prot2d (methods for converting chainsaw annotations are included in the package documentation)
## Runtime for protein sizes
<img width="750" alt="image" src="https://github.com/ConstantinCarl/prot2d/assets/156075124/ff033992-3339-43ab-a7d4-dd71a26dddc4">
<br>
The runtimes are measured on a local lightweight device.<br>
## Reference
In the following document one can find more information on the tools methodogy, result analysis and references of the shown proteins and used software.
[BachelorThesis_ConstantinCarl_Enhancing-Protein-Comparability-with-Standardized-2D-Visualization.pdf](https://github.com/ConstantinCarl/prot2d/files/14605102/BachelorThesis_ConstantinCarl_Enhancing-Protein-Comparability-with-Standardized-2D-Visualization.pdf)
Raw data
{
"_id": null,
"home_page": null,
"name": "FlatProt",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.13,>=3.10",
"maintainer_email": null,
"keywords": null,
"author": "constantincarl",
"author_email": "ge37goy@mytum.de",
"download_url": "https://files.pythonhosted.org/packages/45/1b/0634e34d75f94e701da89eb9b047617bf224f8a91bf37111b19a3429af19/flatprot-0.2.0.tar.gz",
"platform": null,
"description": "# FlatProt\n\n<img width=\"910\" alt=\"image\" src=\"https://github.com/ConstantinCarl/prot2d/assets/156075124/34d415d3-55be-4784-a96d-035e40fc5afe\">\n\nFlatProt is a tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations. FlatProt focuses on creating highly comparable representations for same-family proteins. In this case FlatProt was used to generate comparable representatoins for 3 3FTx structures.\n\n## Contents\n\n- [Getting Started](#getting-started)\n- [First Experiences with Google Colab](#first-experiences-with-google-colab)\n- [Documentation](#documentation)\n- [Data](#data)\n- [Example Visualizations](#example-visualizations)\n- [Domain Annotation File Format](#domain-annotation-file-format)\n- [Runtime for Protein Sizes](#runtime-for-protein-sizes)\n- [Reference](#reference)\n\n## Getting Started\n\nFlatProt needs python version: python= \">=3.10,<3.13\"\n\n### Download FlatProt via pip or poetry\n\n- pip:\n\n```shell\npip install FlatProt\n```\n\n- Poetry:\n\n```shell\npoetry add FlatProt\n```\n\n### Install Foldseek\n\nInstructions for downloading the Foldseek software can be found in Foldseek's GitHub\n\n- [Foldseek GitHub](https://github.com/steineggerlab/foldseek)\n\n--> FlatProt needs the path to the foldseek executable passed as argument to the main function to be used by the program.\n\n### Install dssp\n\nInstructions for downloading dssp can be found here:\n\n- [dssp instructions](http://biskit.pasteur.fr/install/applications/dssp)\n\n!The program runs on the mkdssp version 4.4.0! (some sources dont provide that (brew does!))\n\n_An example download workflow for usage can also be found in the google colab_\n\n## First experiences with Google Colab\n\nFor users to get to know prot2d we've prepared a Google Colab notebook with a quick tutorial through the major functions/possibilities of prot2d. Therefore the exmample protein 1kt1 is used and visualized in different ways. This allows for basic understanding of the functionalities:\n\n- [Google Colab tutorial](https://colab.research.google.com/drive/17u0twE81kYYspNFsdXUHrCyP33hj0dO6?usp=sharing)\n\nInstructions in the Colab help with the first hands-on.\n\nFor direct usage of prot2d including all paramters the following Collab provides functionalitys for using prot2d withput locally downloading anything.\nUsers can upload theri own proteins to the Collab and visualize them as wanted.\nThe runtime of the Collab is way longer than local usage. Therefore we dont advise using it for big amounts of data:\n\n- [Google Colab usage](https://colab.research.google.com/drive/1pJHMagKgpTJ1cfBHkBSh2hMlkzQk263d?usp=sharing)\n\n## Documentation\n\nFlatProt's documentation can found here:\n\n- [FlatProt documentation!](https://constantincarl.github.io/FlatProt/)\n\n**important notes:**\n\n- input PDB files need a header to work (important for predicted structures)\n- FlatProt's methods can also be used via command line commands (cli)\n\n## Data\n\nThis project uses datasets that can be found on Zenodo. Additional example files can be found here aswell. You can access and download the data using the following link or DOI:\n\n- [Zenodo Data](https://doi.org/10.5281/zenodo.10674045)\n\n## Example visualizations\n\n### 3FTx: None|Anca_10|Anolis_carolinensis\n\n<img width=\"409\" alt=\"image\" src=\"https://github.com/ConstantinCarl/prot2d/assets/156075124/a315fd49-74cc-456e-b0d2-c6b63333b22b\">\n\n### 3FTx - Family Overlay\n\n\n### 1kt1 - domain visualization (family vis)\n\n<img width=\"1000\" alt=\"image\" src=\"https://github.com/ConstantinCarl/prot2d/assets/156075124/1f8ac748-09d1-464c-9e42-c6fd93bfeddc\">\n\n### 1kt1 - full protine visualization\n\n<img width=\"450\" alt=\"image\" src=\"https://github.com/ConstantinCarl/prot2d/assets/156075124/854a89a7-e91c-4ec5-b81d-d33b4f1b96ec\">\n\n## Domain Annotation File Format:\n\nThe domain annotation is needed in the following format to be procceced by prot2d (methods for converting chainsaw annotations are included in the package documentation)\n\n\n\n## Runtime for protein sizes\n\n<img width=\"750\" alt=\"image\" src=\"https://github.com/ConstantinCarl/prot2d/assets/156075124/ff033992-3339-43ab-a7d4-dd71a26dddc4\">\n<br>\nThe runtimes are measured on a local lightweight device.<br>\n\n## Reference\n\nIn the following document one can find more information on the tools methodogy, result analysis and references of the shown proteins and used software.\n\n[BachelorThesis_ConstantinCarl_Enhancing-Protein-Comparability-with-Standardized-2D-Visualization.pdf](https://github.com/ConstantinCarl/prot2d/files/14605102/BachelorThesis_ConstantinCarl_Enhancing-Protein-Comparability-with-Standardized-2D-Visualization.pdf)\n",
"bugtrack_url": null,
"license": "Apache-2.0",
"summary": "Python package for creating simplified 2D protein visualisations. Specialised on showing differences and similaritys between proteins from the same protein family.",
"version": "0.2.0",
"project_urls": {
"Documentation": "https://constantincarl.github.io/FlatProt/",
"Example-Collab": "https://colab.research.google.com/drive/17u0twE81kYYspNFsdXUHrCyP33hj0dO6?usp=sharing",
"Repository": "https://github.com/ConstantinCarl/FlatProt",
"Zenodo": "https://doi.org/10.5281/zenodo.10674045"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "c654352c30bb8179fdc9cbf703c46eb60c78466b1c92cdf6812062df273cc2a6",
"md5": "ec860b5d934c90eab25c10a45ec327a8",
"sha256": "30fb062c75b0b93dd55fa38edb985e972f9e31feebde16e651b9e68dee7ac46d"
},
"downloads": -1,
"filename": "flatprot-0.2.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "ec860b5d934c90eab25c10a45ec327a8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<3.13,>=3.10",
"size": 2874816,
"upload_time": "2024-10-07T21:08:59",
"upload_time_iso_8601": "2024-10-07T21:08:59.287908Z",
"url": "https://files.pythonhosted.org/packages/c6/54/352c30bb8179fdc9cbf703c46eb60c78466b1c92cdf6812062df273cc2a6/flatprot-0.2.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "451b0634e34d75f94e701da89eb9b047617bf224f8a91bf37111b19a3429af19",
"md5": "ba96d5df11514b3da6e3abe1b2e01046",
"sha256": "03cfa03af226cbe2594f8f64b8717a754e89f8493ffc4e75819edf882013709d"
},
"downloads": -1,
"filename": "flatprot-0.2.0.tar.gz",
"has_sig": false,
"md5_digest": "ba96d5df11514b3da6e3abe1b2e01046",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.13,>=3.10",
"size": 5575607,
"upload_time": "2024-10-07T21:09:04",
"upload_time_iso_8601": "2024-10-07T21:09:04.371008Z",
"url": "https://files.pythonhosted.org/packages/45/1b/0634e34d75f94e701da89eb9b047617bf224f8a91bf37111b19a3429af19/flatprot-0.2.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-07 21:09:04",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "ConstantinCarl",
"github_project": "FlatProt",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"requirements": [],
"lcname": "flatprot"
}
