# GlyCONFORMER
**GlyCONFORMERS** is a Python package that assigns labels to glycan conformers, based on their torsion angle values, in order to differentiate various 3D-structures of one single glycan. It enables the automated assignment of the GlyCONFORMER string that was introduced in:
**Grothaus et al. 2022, Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans, J. Chem. Inf. Model. 2022, 62, 20, 4992–5008** https://pubs.acs.org/doi/full/10.1021/acs.jcim.2c01049 for N-glycans.
![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Conformer_string.png?raw=true)
Check the paper or tutorial for a detailed explanation of the GlyCONFORMER string generation. The workflow is not exclusivly designed for N-glycans, but can also be applyied to any other glycan type there is.
## Installation
To use GlyCONFORMER, first install it using pip:
$ pip install GlyCONFORMER
## Tutorial
The tutorial juypter notebook should be run from within the GlyCONFORMER package folder or you have to change the path directing to the TUTORIAL folder.
The tutorial includes different N-glycan types and different complexity levels of how to obtain a GlyCONFORMER label string for custom glycan types and their recorded torsion angle values. The minimum example is given by the high-mannose type N-glycan M5, where only the file **M5_angles.dat** with torsion angle values is used as input:
![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Input.png?raw=true)
It is used by the glyconformer package, whereas remaining necessary information are read from the LIBRARY_GLYCANS folder by specifying the **glycantype = "M5**":
```
conformer = glyconformer(inputfile = "TUTORIAL/M5_example/M5_angles.dat", glycantype = "M5")
```
When executing the run command:
```
binary, population = conformer.run()
```
a **binary** dataframe is produced, where the torsion angles have been converted to letters corresponding to their values and associate them to a certain minima of the free energy profile along that torsion angle.
![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Output.png?raw=true)
Additionally, the occurance of each conformer string is counted and outputted to the **population** dataframe:
![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Count.png?raw=true)
The obtained information can also be used to plot a histogram, displaying the conformer distribution by:
```
conformer.plot()
```
Conformer labels are given on the x-axis and deviations from the most populated conformer indicated by explicit letters, where dots are used when no change in that torsion angle could be detected.
![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/M5_example/Conformer_distribution.png?raw=true)
For more elaborate examples and a detailed explanation of how free energy profiles of each torsion angle are classified, check out the **Tutorial_GlyCONFORMER.ipynb** notebook.
## Documentation
See documentation https://glyconformer.readthedocs.io/en/latest/index.html
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"description": "# GlyCONFORMER\n\n**GlyCONFORMERS** is a Python package that assigns labels to glycan conformers, based on their torsion angle values, in order to differentiate various 3D-structures of one single glycan. It enables the automated assignment of the GlyCONFORMER string that was introduced in:\n\n **Grothaus et al. 2022, Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans, J. Chem. Inf. Model. 2022, 62, 20, 4992\u20135008** https://pubs.acs.org/doi/full/10.1021/acs.jcim.2c01049 for N-glycans. \n\n![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Conformer_string.png?raw=true)\n\nCheck the paper or tutorial for a detailed explanation of the GlyCONFORMER string generation. The workflow is not exclusivly designed for N-glycans, but can also be applyied to any other glycan type there is. \n\n## Installation\n\nTo use GlyCONFORMER, first install it using pip:\n\n$ pip install GlyCONFORMER\n \n## Tutorial\n\nThe tutorial juypter notebook should be run from within the GlyCONFORMER package folder or you have to change the path directing to the TUTORIAL folder.\n\nThe tutorial includes different N-glycan types and different complexity levels of how to obtain a GlyCONFORMER label string for custom glycan types and their recorded torsion angle values. The minimum example is given by the high-mannose type N-glycan M5, where only the file **M5_angles.dat** with torsion angle values is used as input:\n\n![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Input.png?raw=true)\n\nIt is used by the glyconformer package, whereas remaining necessary information are read from the LIBRARY_GLYCANS folder by specifying the **glycantype = \"M5**\": \n\n```\nconformer = glyconformer(inputfile = \"TUTORIAL/M5_example/M5_angles.dat\", glycantype = \"M5\")\n```\n\nWhen executing the run command:\n\n```\nbinary, population = conformer.run()\n```\n\na **binary** dataframe is produced, where the torsion angles have been converted to letters corresponding to their values and associate them to a certain minima of the free energy profile along that torsion angle. \n\n![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Output.png?raw=true)\n\nAdditionally, the occurance of each conformer string is counted and outputted to the **population** dataframe:\n\n![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/Count.png?raw=true)\n\nThe obtained information can also be used to plot a histogram, displaying the conformer distribution by:\n\n``` \nconformer.plot()\n```\n\nConformer labels are given on the x-axis and deviations from the most populated conformer indicated by explicit letters, where dots are used when no change in that torsion angle could be detected. \n\n![](https://github.com/IsabellGrothaus/GlyCONFORMER/blob/v1.0.0-alpha/TUTORIAL/M5_example/Conformer_distribution.png?raw=true)\n\nFor more elaborate examples and a detailed explanation of how free energy profiles of each torsion angle are classified, check out the **Tutorial_GlyCONFORMER.ipynb** notebook. \n\n## Documentation\n\nSee documentation https://glyconformer.readthedocs.io/en/latest/index.html\n",
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