konnektor

Algorithms for various Network Layouts and Tooling for planning FE Calculations

https://github.com/openfreeenergy/konnektor

Science Score: 67.0%

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Keywords

free-energy-calculations network-planning openfe python

Last synced: 6 months ago · JSON representation ·

Repository

Algorithms for various Network Layouts and Tooling for planning FE Calculations

Basic Info

Host: GitHub
Owner: OpenFreeEnergy
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage: https://konnektor.readthedocs.io/
Size: 70.4 MB

Statistics

Stars: 19
Watchers: 1
Forks: 5
Open Issues: 30
Releases: 2

Topics

free-energy-calculations network-planning openfe python

Created almost 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

Konnektor: Tools for Networks in your FE Calculations

Konnektor is a package supporting you in planning your free calculations. It contains multiple algorithms and tools for network planning, that make setting up the calculation plans much easier. As an example imagen you are given a set of drug candidates that shall be ranked with relative binding free energies. In theory you could calculate all the possible network transformations, in order to get your ligand ranking (we call this a Maximal Network). However this leads to an explosion in time and compute cost, therefore we need more efficient ways on how to caluclate a drug candidate ranking. From a thermodynamic perspective not all transformations are actually required to retrieve a ranking. In fact you only need one conection per small molecules to the others in order to get the ranking, like for example in Star Networks or Minimal Spanning Tree (MST) Networks. However we found the very efficient networks to be sensitive to transformation failures, this can be solved with network building algorithms, that are slightly more redundant.

Ontop of the described ligand network planners, Konnektor gives access to tools, that allow for example to concatenate networks or delete transformations of a network. Analysis of networks, like calculating graph scores, getting the connectivities of network nodes or calculating the network robustness are available too. Last we want to bring to your attention our Network visualization tools and the provided interactive network visualization widget for IPython like in Jupyter-Lab/Notebooks.

Check out our article on Konnektor in the Journal of Chemical Information and Modeling: 𝐊𝐨𝐧𝐧𝐞𝐤𝐭𝐨𝐫: 𝐀 𝐅𝐫𝐚𝐦𝐞𝐰𝐨𝐫𝐤 𝐟𝐨𝐫 𝐔𝐬𝐢𝐧𝐠 𝐆𝐫𝐚𝐩𝐡 𝐓𝐡𝐞𝐨𝐫𝐲 𝐭𝐨 𝐏𝐥𝐚𝐧 𝐍𝐞𝐭𝐰𝐨𝐫𝐤𝐬 𝐟𝐨𝐫 𝐅𝐫𝐞𝐞 𝐄𝐧𝐞𝐫𝐠𝐲 𝐂𝐚𝐥𝐜𝐮𝐥𝐚𝐭𝐢𝐨𝐧𝐬 - Benjamin Ries*, Richard J. Gowers, Hannah M. Baumann, David W. H. Swenson, Michael M. Henry, James R. B. Eastwood, Irfan Alibay, and David Mobley.

You can find our pre-print on ChemRxiv.

Try our interactive demo:

Content

Implemented Network Layouts

Several Network layout generating algorithms are implemented in Konnektor, with different advantages and disadvantages. From an algorithmic perspective most of the algorithms are actually a reduction method of the Maximal Network. To speed-up the Maximal Network Algorithm we implemented an parallelization scheme to it. Below you can find some of our layouts:

Tools for handling Networks

Konnektor implements tools, that allow for example to merge (if a node is shared in the networks) or concatenate (if no node is shared) networks, append single molecules (nodes) to a network or delete transformations/molecules from a network.

Enable More Complex Higher Order Networks

Another goal of Konnektor is to go beyond the standard network layout algorihtms and allow easy implementation of more complex network algorithms. This is achieved by combining the Tools and Network Generator Algorithms, to build up to more advanced workflows.

Code Example

```python3

Here we generate some input data.

from konnektor.data import getbenzeneligands

compounds = list(filter(lambda x: not x.name in ["lig2", "lig3", "lig4", "lig7"], getbenzeneligands()))

Pick your Favourite Network layout with favourite AtomMapper and Scorer

from openfe.setup import KartografAtomMapper, lomapscorers from konnektor.networkplanners import CyclicNetworkGenerator

networker = CyclicNetworkGenerator(mappers=KartografAtomMapper(), scorer=lomapscorers.defaultlomap_score)

Generate Network

network = networker.generateligandnetwork(compounds) network.name = "Cyclic Network"

Visualize the generated network

from konnektor.visualization import drawligandnetwork fig = drawligandnetwork(network=network, title=network.name)

fig.show() ``` example fig

Installation

Latest release

Konnektor can be installed from conda-forge:

shell mamba install -c conda-forge konnektor

Developement version

The developing setup of Konnektor works like this:

```shell git clone https://github.com/OpenFreeEnergy/konnektor.git

cd konnektor mamba env create -f environment.yml

mamba activate konnektor pip install -e .

```

License

This library is made available under the MIT open source license.

Authors

The OpenFE development team.

Acknowledgments

Thanks to Enrico Ruijsenaars, Jenke Scheen and Josh Horton for great discussions!

Owner

Name: Open Free Energy
Login: OpenFreeEnergy
Kind: organization

Website: https://openfree.energy
Repositories: 10
Profile: https://github.com/OpenFreeEnergy

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Ries"
  given-names: "Benjamin"
  orcid: "https://orcid.org/0000-0002-0945-8304"
- family-names: "Gowers"
  given-names: "Richard J."
  orcid: "https://orcid.org/0000-0002-3241-1846"
- family-names: "Baumann"
  given-names: "Hannah M."
  orcid: "https://orcid.org/0000-0002-1736-7744"
- family-names: "Swenson"
  given-names: "David W.H."
  orcid: "https://orcid.org/0000-0001-9922-7923"
- family-names: "Alibay"
  given-names: "Irfan"
  orcid: "https://orcid.org/0000-0001-5787-9130"
- family-names: "Henry"
  given-names: "Michael M."
  orcid: "https://orcid.org/0000-0002-3870-9993"
- family-names: "Eastwood"
  given-names: "James R. B."
  orcid: "https://orcid.org/0000-0003-3895-5227"
title: "Konnektor: A Tool for Planning Free Energy Networks"
version: 1.0
date-released: -
url: "https://openfree.energy/"
repository-code: "https://github.com/OpenFreeEnergy/konnektor"
doi: -

GitHub Events

Total

Issues event: 49
Watch event: 9
Delete event: 40
Issue comment event: 110
Push event: 212
Pull request review comment event: 95
Pull request review event: 107
Pull request event: 77
Fork event: 2
Create event: 39

Last Year

Issues event: 49
Watch event: 9
Delete event: 40
Issue comment event: 110
Push event: 212
Pull request review comment event: 95
Pull request review event: 107
Pull request event: 77
Fork event: 2
Create event: 39

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 79
Total pull requests: 62
Average time to close issues: 3 months
Average time to close pull requests: 15 days
Total issue authors: 6
Total pull request authors: 8
Average comments per issue: 0.42
Average comments per pull request: 1.52
Merged pull requests: 40
Bot issues: 0
Bot pull requests: 4

Past Year

Issues: 34
Pull requests: 46
Average time to close issues: about 2 months
Average time to close pull requests: 16 days
Issue authors: 5
Pull request authors: 6
Average comments per issue: 0.59
Average comments per pull request: 1.39
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 4

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Top Authors

Issue Authors

RiesBen (42)
atravitz (24)
jameseastwood (6)
IAlibay (4)
dwhswenson (1)
mikemhenry (1)

Pull Request Authors

atravitz (31)
RiesBen (29)
IAlibay (9)
richardjgowers (7)
mikemhenry (7)
pre-commit-ci[bot] (4)
Julicancode (2)
LindeSchoenmaker (1)

Top Labels

Issue Labels

Konnektor (30) enhancement (18) refactor (6) documentation (4) openfe (3) help wanted (1) priority:medium (1)

Pull Request Labels

Konnektor (6) documentation (5) enhancement (5) bug (1) refactor (1)

Packages

Total packages: 1
Total downloads:
- pypi 20 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2
Total maintainers: 3

pypi.org: konnektor

Konnektor is a package for calculating networks.

Homepage: https://github.com/OpenFreeEnergy/konnektor
Documentation: https://konnektor.readthedocs.io/
License: MIT License
Latest release: 0.1.0
published over 1 year ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 20 Last month

Rankings

Dependent packages count: 6.6%

Average: 18.6%

Dependent repos count: 30.6%

Maintainers (3)

mmh IAlibay riesb