https://github.com/akohlmey/topotools
VMD plugin for manipulating topology information
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary
Repository
VMD plugin for manipulating topology information
Basic Info
- Host: GitHub
- Owner: akohlmey
- License: other
- Language: Tcl
- Default Branch: master
- Size: 373 KB
Statistics
- Stars: 36
- Watchers: 6
- Forks: 17
- Open Issues: 1
- Releases: 5
Metadata Files
README.md
VMD TopoTools package. Version 1.10
Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2022,2023,2024,2025 by Axel Kohlmeyer akohlmey@gmail.com
This package contains contributed features from: - Josh Vermaas (fully working gromacs topology files for CHARMM) - Konstantin W (replicatemols for non-orthogonal cells)
New TopoTools Maintainers
After over 16 years, I have lost interest in developing and maintaining TopoTools. Jake Gissinger and Josh Vermass have volunteered to continue developing it. The new home of TopoTools is https://github.com/NanoCIPHER-Lab/topotools
Overview
TopoTools is a plugin for VMD providing a collection of Tcl commands to manipulate, build, read and write topologies (i.e. bonds, angles, dihedrals, etc. and their corresponding properties (type, order, etc.).
Updates
The public git repository is at https://github.com/akohlmey/topotools
TopoTools version 1.10 is the final release created by me. I have no more plans to further develop and maintain this package. It is therefore available for "adoption". Please contact me via email or PM if you want to take over.
Installation
TopoTools is written entirely in the Tcl scripting language for use as a plugin with VMD. A version of TopoTools is already bundled with VMD, to update it with the newer, downloaded version unpack the TopoTools archive, which will create a directory containing that various Tcl script files. If the directory is not named topotools1.10, please rename it accordingly. Now, find the plugin folder in your VMD installation where it already has a topotools1.x directory and move the folder with the new version next to it. If it already has the topotools1.10 folder, overwrite the files inside with the new version. VMD should use the new version automatically at the next start.
Owner
- Name: Axel Kohlmeyer
- Login: akohlmey
- Kind: user
- Location: Philadelphia PA
- Company: Temple University
- Website: http://goo.gl/1wk0
- Repositories: 8
- Profile: https://github.com/akohlmey
I work as Associate Dean for High-Performance Computing at Temple University in Philadelphia, PA and am head of a small team that manages HPC clusters.
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 7
- Push event: 4
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 7
- Push event: 4
- Fork event: 1
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 19
- Total pull requests: 8
- Average time to close issues: 2 months
- Average time to close pull requests: 3 months
- Total issue authors: 16
- Total pull request authors: 5
- Average comments per issue: 2.58
- Average comments per pull request: 0.5
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 3 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 5.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MamtaMohan (2)
- EfremBraun (2)
- Movaffaq (1)
- jeffcomer (1)
- shuxiansheng2 (1)
- Bellsthescientist (1)
- xu139411 (1)
- BrianMoths (1)
- sizmailov (1)
- jonas-feldt (1)
- S30194 (1)
- akohlmey (1)
- gandhiforbes (1)
- allotrust (1)
- kpounot (1)
Pull Request Authors
- jvermaas (4)
- jrgissing (1)
- BrianMoths (1)
- koniweb (1)
- EfremBraun (1)