Science Score: 44.0%
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○Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary
Keywords
Repository
Nonlocal Electrostatics in Structured Solvents
Basic Info
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 23
Topics
Metadata Files
README.md
Nonlocal Electrostatics in Structured Solvents
NESSie.jl is a software package for the popular Julia language,
providing efficient numerical solvers for local and nonlocal protein electrostatics
computations in structured solvents.
Installation
In the Julia shell, switch to the Pkg shell by pressing ] and enter the following command:
sh
pkg> add NESSie
Analogously, the NESSie.jl can be removed at any time using the following command in the
Pkg shell:
sh
pkg> rm NESSie
Usage
Modules
All functionality is organized into separate modules:
| Module | Description |
|--------|-------------|
| NESSie | Models and utility functions
| NESSie.BEM | Local and nonlocal BEM solvers
| NESSie.Format | Input and output file formats
| NESSie.TestModel | Test models with analytical solutions
Example
The following Julia code shows how to compute and print the nonlocal reaction field energy of a single Na+ ion (modeled as a spherically-symmetric, vacuum-filled system) in water:
```julia using NESSie using NESSie.BEM using NESSie.Format: readoff, readpqr
I. Create model
model = readoff("data/born/na.off") model.charges = readpqr("data/born/na.pqr") model.params.εΩ = 1 # dielectric constant for vacuum model model.params.εΣ = 78 # dielectric constant for water
II. Apply nonlocal solver
bem = solve(NonlocalES, model)
III. Apply postprocessor
val = rfenergy(bem)
println("Reaction field energy: $val kJ/mol")
``
More examples are available in thedocs/examples/` directory.
Documentation
A detailed documentation of NESSie.jl is available
online.
You can also build the same documentation manually using the following command in the
docs/ directory:
sh
shell> julia make.jl
Please note that this additionally requires the
Documenter.jl package to be installed. This can be achieved by using the following command in the Pkg shell:
sh
pkg> add Documenter
After the build process has finished successfully, the documentation can be
found in the docs/build/ directory.
Testing
NESSie.jl provides tests for most of its functions. You can run the test suite with the
following command in the Pkg shell:
sh
pkg> test NESSie
Tools
NESSie.jl ships with the following extra tools:
- Converter.jl, a simple Julia script to convert surface and volume meshes into different formats
- Mesher, a wrapper application for the GAMer library to create surface and volume meshes from PDB files
Please refer to the respective tool's README file for more details.
Citing
If you use NESSie.jl in your research, please cite the following publications:
Kemmer, T, Rjasanow, S., Hildebrandt, A (2018). NESSie. jl - Efficient and Intuitive Finite Element and Boundary Element Methods for Nonlocal Protein Electrostatics in the Julia Language. Journal of Computational Science 28, 193-203.
Kemmer, T (2021). Space-efficient and exact system representations for the nonlocal protein electrostatics problem. Ph. D. thesis, Johannes Gutenberg University Mainz. Mainz, Germany.
Citations items for BibTeX can be found in CITATION.bib.
Owner
- Name: Thomas Kemmer
- Login: tkemmer
- Kind: user
- Location: Germany
- Company: University of Mainz
- Repositories: 5
- Profile: https://github.com/tkemmer
Computer scientist and Gentoo Linux enthusiast
Citation (CITATION.bib)
@phdthesis{cunessie-2021,
author = {Kemmer, Thomas},
title = {{Space-efficient and exact system representations for the nonlocal protein electrostatics problem}},
year = {2021},
school = {Johannes Gutenberg University Mainz},
address = {Mainz, Germany},
doi = {10.25358/openscience-5689}
}
@article{nessie-2018,
author = {Kemmer, Thomas and Rjasanow, Sergej and Hildebrandt, Andreas},
title = {{NESSie.jl -- Efficient and Intuitive Finite Element and Boundary Element Methods for Nonlocal Protein Electrostatics in the Julia Language}},
year = {2018},
journal = {Journal of Computational Science},
volume = {28},
pages = {193-203},
doi = {10.1016/j.jocs.2018.08.008}
}
GitHub Events
Total
- Create event: 51
- Commit comment event: 9
- Release event: 3
- Issues event: 12
- Watch event: 1
- Delete event: 56
- Issue comment event: 6
- Push event: 426
- Pull request event: 60
Last Year
- Create event: 51
- Commit comment event: 9
- Release event: 3
- Issues event: 12
- Watch event: 1
- Delete event: 56
- Issue comment event: 6
- Push event: 426
- Pull request event: 60
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Thomas Kemmer | t****s@b****e | 553 |
| CompatHelper Julia | c****y@j****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 69
- Average time to close issues: about 8 hours
- Average time to close pull requests: 2 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 0.44
- Average comments per pull request: 0.0
- Merged pull requests: 54
- Bot issues: 0
- Bot pull requests: 3
Past Year
- Issues: 8
- Pull requests: 67
- Average time to close issues: about 9 hours
- Average time to close pull requests: 2 days
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 53
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- tkemmer (8)
- JuliaTagBot (1)
Pull Request Authors
- tkemmer (66)
- github-actions[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- julia 1 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
juliahub.com: NESSie
Nonlocal Electrostatics in Structured Solvents
- Documentation: https://docs.juliahub.com/General/NESSie/stable/
- License: MIT
-
Latest release: 1.5.0
published 8 months ago
Rankings
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