# GaussParse
  
GaussParse is a versatile Python package designed for parsing output files generated by Gaussian software, a widely used computational chemistry tool. This package enables users to efficiently extract essential information and perform various analytical tasks directly from Gaussian output files. Whether you need to visualize energy profiles, analyze IRC (Intrinsic Reaction Coordinate) curves, retrieve summary results, or extract molecular orientations, GaussParse provides a streamlined interface to accomplish these tasks with ease.
Key Features:
* Energy Profile Plotting: Visualize and analyze energy profiles directly from Gaussian output files.
* IRC Curve Plotting: Generate plots of IRC curves to study reaction pathways.
* Summary Results Extraction: Extract and summarize key computational results from Gaussian calculations.
* Molecular Orientation Analysis: Retrieve detailed information about molecular orientations and configurations.
* Publication-Ready Data: Extract molecular orientation data into a Word file formatted for publication as supplementary information.
* GaussParse simplifies the process of post-processing Gaussian output, making it an invaluable tool for computational chemists and researchers working in molecular dynamics, quantum chemistry, and related fields.
## Installation
Install this project
```bash
pip install GaussParse
```
## Documentation
Import GaussParse
```python
import GaussParse as gp
```
Available methods
```python
# collect all files
# excel file
xls_file = r'...\\TS2-data.xlsx'
gp.collect_files_from(xls_file, sheet_name="Sheet1")
```
List all the Gaussian log files in an excel file,
All the Gaussian log files are saved in a folder:
```python
# Save result summary to Excel
# file
gaussian_log = r"...\1,2LO.txt"
# save in excel
gp.result_summary_to_excel(gaussian_log)
```
Results summary as:
The data are saved in an excel file:
```python
# Save input orientation to txt
# folder
gaussian_log = r"...\\acetone-limonene-mechanism-1"
# save in txt
gp.input_orientation_to_txt(gaussian_log)
# Transform input orientation to xyz
# file
gaussian_log = r"...\g09_exp.log"
# save in txt
gp.txt_orientation_to_xyz(gaussian_log)
```
Gaussian log files (saved in a folder)
The molecular orientation are saved in a text file (Notepad),
```python
# Save IRC profile
# file path
plt_data = "...\\g09_exp.log"
# save IRC profile
gp.plot_irc_profile(plt_data)
```
IRC profile:
```python
# Save energy profile
# file path
plt_data = '...\\energy.xlsx'
# plot energy profile and save it
gp.plot_energy_profile(plt_data)
```
Load data in an excel file:
Energy profile:
## License
[MIT](https://choosealicense.com/licenses/mit/)
## Citation
If you use this Python package in your research, please cite it as follows:
Sina Gilassi, (2024). GaussParse: A Python package for parsing Gaussian software output. GitHub repository. https://github.com/sinagilassi/GaussParse
## FAQ
For any question, contact me on [LinkedIn](https://www.linkedin.com/in/sina-gilassi/)
## Authors
- [@sinagilassi](https://www.github.com/sinagilassi)
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"description": "\r\n# GaussParse\r\r\n\r\r\n  \r\r\n\r\r\nGaussParse is a versatile Python package designed for parsing output files generated by Gaussian software, a widely used computational chemistry tool. This package enables users to efficiently extract essential information and perform various analytical tasks directly from Gaussian output files. Whether you need to visualize energy profiles, analyze IRC (Intrinsic Reaction Coordinate) curves, retrieve summary results, or extract molecular orientations, GaussParse provides a streamlined interface to accomplish these tasks with ease.\r\r\n\r\r\nKey Features:\r\r\n\r\r\n* Energy Profile Plotting: Visualize and analyze energy profiles directly from Gaussian output files.\r\r\n\r\r\n* IRC Curve Plotting: Generate plots of IRC curves to study reaction pathways.\r\r\n \r\r\n* Summary Results Extraction: Extract and summarize key computational results from Gaussian calculations.\r\r\n \r\r\n* Molecular Orientation Analysis: Retrieve detailed information about molecular orientations and configurations.\r\r\n \r\r\n* Publication-Ready Data: Extract molecular orientation data into a Word file formatted for publication as supplementary information.\r\r\n \r\r\n* GaussParse simplifies the process of post-processing Gaussian output, making it an invaluable tool for computational chemists and researchers working in molecular dynamics, quantum chemistry, and related fields.\r\r\n\r\r\n## Installation\r\r\n\r\r\nInstall this project\r\r\n\r\r\n```bash\r\r\n pip install GaussParse\r\r\n```\r\r\n \r\r\n## Documentation\r\r\n\r\r\nImport GaussParse\r\r\n\r\r\n```python\r\r\nimport GaussParse as gp\r\r\n```\r\r\n\r\r\nAvailable methods\r\r\n\r\r\n```python\r\r\n# collect all files\r\r\n\r\r\n# excel file\r\r\nxls_file = r'...\\\\TS2-data.xlsx'\r\r\ngp.collect_files_from(xls_file, sheet_name=\"Sheet1\")\r\r\n\r\r\n```\r\r\n\r\r\nList all the Gaussian log files in an excel file,\r\r\n\r\r\n\r\r\n\r\r\nAll the Gaussian log files are saved in a folder:\r\r\n\r\r\n\r\r\n\r\r\n```python\r\r\n# Save result summary to Excel\r\r\n\r\r\n# file\r\r\ngaussian_log = r\"...\\1,2LO.txt\"\r\r\n# save in excel\r\r\ngp.result_summary_to_excel(gaussian_log)\r\r\n```\r\r\n\r\r\nResults summary as:\r\r\n\r\r\n\r\r\n\r\r\nThe data are saved in an excel file:\r\r\n\r\r\n\r\r\n\r\r\n```python\r\r\n# Save input orientation to txt\r\r\n\r\r\n# folder\r\r\ngaussian_log = r\"...\\\\acetone-limonene-mechanism-1\"\r\r\n# save in txt\r\r\ngp.input_orientation_to_txt(gaussian_log)\r\r\n\r\r\n# Transform input orientation to xyz\r\r\n\r\r\n# file\r\r\ngaussian_log = r\"...\\g09_exp.log\"\r\r\n# save in txt\r\r\ngp.txt_orientation_to_xyz(gaussian_log)\r\r\n\r\r\n```\r\r\n\r\r\nGaussian log files (saved in a folder)\r\r\n\r\r\n\r\r\n\r\r\nThe molecular orientation are saved in a text file (Notepad), \r\r\n\r\r\n\r\r\n\r\r\n```python\r\r\n# Save IRC profile\r\r\n\r\r\n# file path\r\r\nplt_data = \"...\\\\g09_exp.log\"\r\r\n# save IRC profile\r\r\ngp.plot_irc_profile(plt_data)\r\r\n\r\r\n```\r\r\n\r\r\nIRC profile:\r\r\n\r\r\n\r\r\n\r\r\n```python\r\r\n# Save energy profile\r\r\n\r\r\n# file path\r\r\nplt_data = '...\\\\energy.xlsx'\r\r\n\r\r\n# plot energy profile and save it\r\r\ngp.plot_energy_profile(plt_data)\r\r\n``` \r\r\n\r\r\nLoad data in an excel file:\r\r\n\r\r\n\r\r\n\r\r\nEnergy profile:\r\r\n\r\r\n\r\r\n\r\r\n## License\r\r\n\r\r\n[MIT](https://choosealicense.com/licenses/mit/)\r\r\n\r\r\n## Citation\r\r\n\r\r\nIf you use this Python package in your research, please cite it as follows:\r\r\n\r\r\nSina Gilassi, (2024). GaussParse: A Python package for parsing Gaussian software output. GitHub repository. https://github.com/sinagilassi/GaussParse\r\r\n\r\r\n## FAQ\r\r\n\r\r\nFor any question, contact me on [LinkedIn](https://www.linkedin.com/in/sina-gilassi/) \r\r\n\r\r\n\r\r\n## Authors\r\r\n\r\r\n- [@sinagilassi](https://www.github.com/sinagilassi)\r\r\n\r\r\n",
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