| Name | pandamap JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | A Python package for visualizing protein-ligand interactions with 2D ligand structure representation |
| upload_time | 2025-03-28 23:13:02 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT License
Copyright (c) 2025 Pritam Kumar Panda
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 |
bioinformatics
protein-ligand
interactions
visualization
drug-design
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# PandaMap
**P**rotein **AND** lig**A**nd interaction **MAP**per: A Python package for visualizing protein-ligand interactions with 2D ligand structure representation
## Overview
PandaMap is a lightweight tool for visualizing protein-ligand interactions from PDB files. It generates intuitive 2D interaction diagrams that display both the ligand structure and its interactions with protein residues.
Key features:
- Visualization of protein-ligand interactions with minimal dependencies
- 2D representation of ligand structure without requiring RDKit
- Detection of multiple interaction types (hydrogen bonds, π-stacking, hydrophobic)
- Command-line interface for quick analysis
- Python API for integration into computational workflows
## Installation
```bash
pip install pandamap
```
## Dependencies
- NumPy
- Matplotlib
- BioPython
## Basic Usage
### Command Line Interface
```bash
# Basic usage
pandamap protein_ligand.pdb --output interactions.png
# Specify a particular ligand by residue name
pandamap protein_ligand.pdb --ligand LIG
```
### Python API
```python
from pandamap import HybridProtLigMapper
# Initialize with PDB file
mapper = HybridProtLigMapper("protein_ligand.pdb", ligand_resname="LIG")
# Run analysis and generate visualization
output_file = mapper.run_analysis(output_file="interactions.png")
# Or run steps separately
mapper.detect_interactions()
mapper.estimate_solvent_accessibility()
mapper.visualize(output_file="interactions.png")
```
## Example Output
## Citation
If you use PandaMap in your research, please cite:
```
Pritam Kumar Panda. (2025). Protein AND ligAnd interaction MAPper: A Python package for visualizing protein-ligand interactions with 2D ligand structure representation. GitHub repository. https://github.com/pritampanda15/PandaMap
```
## License
This project is licensed under the MIT License - see the LICENSE file for details.
Raw data
{
"_id": null,
"home_page": null,
"name": "pandamap",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": null,
"keywords": "bioinformatics, protein-ligand, interactions, visualization, drug-design",
"author": null,
"author_email": "\"Dr. Pritam Kumar Panda\" <pritam@stanford.edu>",
"download_url": "https://files.pythonhosted.org/packages/e2/1d/7fa21e1c1111ac7cb799d492f5e269f78abc919c0ad2d1b69cce9810e9da/pandamap-1.0.1.tar.gz",
"platform": null,
"description": "# PandaMap\n\n**P**rotein **AND** lig**A**nd interaction **MAP**per: A Python package for visualizing protein-ligand interactions with 2D ligand structure representation\n\n## Overview\n\nPandaMap is a lightweight tool for visualizing protein-ligand interactions from PDB files. It generates intuitive 2D interaction diagrams that display both the ligand structure and its interactions with protein residues.\n\nKey features:\n- Visualization of protein-ligand interactions with minimal dependencies\n- 2D representation of ligand structure without requiring RDKit\n- Detection of multiple interaction types (hydrogen bonds, \u03c0-stacking, hydrophobic)\n- Command-line interface for quick analysis\n- Python API for integration into computational workflows\n\n## Installation\n\n```bash\npip install pandamap\n```\n\n## Dependencies\n\n- NumPy\n- Matplotlib\n- BioPython\n\n## Basic Usage\n\n### Command Line Interface\n\n```bash\n# Basic usage\npandamap protein_ligand.pdb --output interactions.png\n\n# Specify a particular ligand by residue name\npandamap protein_ligand.pdb --ligand LIG\n```\n\n### Python API\n\n```python\nfrom pandamap import HybridProtLigMapper\n\n# Initialize with PDB file\nmapper = HybridProtLigMapper(\"protein_ligand.pdb\", ligand_resname=\"LIG\")\n\n# Run analysis and generate visualization\noutput_file = mapper.run_analysis(output_file=\"interactions.png\")\n\n# Or run steps separately\nmapper.detect_interactions()\nmapper.estimate_solvent_accessibility()\nmapper.visualize(output_file=\"interactions.png\")\n```\n\n## Example Output\n\n\n\n## Citation\n\nIf you use PandaMap in your research, please cite:\n\n```\nPritam Kumar Panda. (2025). Protein AND ligAnd interaction MAPper: A Python package for visualizing protein-ligand interactions with 2D ligand structure representation. GitHub repository. https://github.com/pritampanda15/PandaMap\n```\n\n## License\n\nThis project is licensed under the MIT License - see the LICENSE file for details.\n",
"bugtrack_url": null,
"license": "MIT License\n \n Copyright (c) 2025 Pritam Kumar Panda\n \n Permission is hereby granted, free of charge, to any person obtaining a copy\n of this software and associated documentation files (the \"Software\"), to deal\n in the Software without restriction, including without limitation the rights\n to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n copies of the Software, and to permit persons to whom the Software is\n furnished to do so, subject to the following conditions:\n \n The above copyright notice and this permission notice shall be included in all\n copies or substantial portions of the Software.\n \n THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n SOFTWARE.\n ",
"summary": "A Python package for visualizing protein-ligand interactions with 2D ligand structure representation",
"version": "1.0.1",
"project_urls": {
"Bug Tracker": "https://github.com/yourusername/pandamap/issues",
"Homepage": "https://github.com/yourusername/pandamap"
},
"split_keywords": [
"bioinformatics",
" protein-ligand",
" interactions",
" visualization",
" drug-design"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "bd4d9e8fa30e47436d3c3e7d3d5fbc700a0d0e3422b794a275d254c431346b9d",
"md5": "64795ef81585f65fc72331a9acd414ae",
"sha256": "f905124adc611f6f3180016bf5e196c1baa5409a3dd0458b95dbea96a701ed35"
},
"downloads": -1,
"filename": "pandamap-1.0.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "64795ef81585f65fc72331a9acd414ae",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 12763,
"upload_time": "2025-03-28T23:13:01",
"upload_time_iso_8601": "2025-03-28T23:13:01.411830Z",
"url": "https://files.pythonhosted.org/packages/bd/4d/9e8fa30e47436d3c3e7d3d5fbc700a0d0e3422b794a275d254c431346b9d/pandamap-1.0.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "e21d7fa21e1c1111ac7cb799d492f5e269f78abc919c0ad2d1b69cce9810e9da",
"md5": "9f8f7cba0c9be7f2a5fb2fe29a82d1cb",
"sha256": "a4704bb95b3cba2ad6b6851b4f09e1427e7704b3f9773f80364ddc3206d8bc23"
},
"downloads": -1,
"filename": "pandamap-1.0.1.tar.gz",
"has_sig": false,
"md5_digest": "9f8f7cba0c9be7f2a5fb2fe29a82d1cb",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 13264,
"upload_time": "2025-03-28T23:13:02",
"upload_time_iso_8601": "2025-03-28T23:13:02.528770Z",
"url": "https://files.pythonhosted.org/packages/e2/1d/7fa21e1c1111ac7cb799d492f5e269f78abc919c0ad2d1b69cce9810e9da/pandamap-1.0.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-03-28 23:13:02",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "yourusername",
"github_project": "pandamap",
"github_not_found": true,
"lcname": "pandamap"
}
