openfreeenergy / konnektor Goto Github PK

Improve Unit Test coverage.
needs to be seperated into more subtasks.

Collecting Visualization ideas here:

• Build Network graph visualization
• make bottlenecks visible
• interactive visualization (checkout swensons solution fo this)
• large number of nodes?
• [ ]

Add documentation:

• Small theoretic analysis of different networks
• Tutorial
• API Ref

Network Graph Generators are generating networks from compounds, using mappers and scorers.

general method signature of the main functionality:

def generate_ligand_network(self, ligands: Iterable[SmallMoleculeComponent]) ->LigandNetwork

Implement/transfer the following Graph Generator Algorithms:

• MST
• Redundant MST
• Star / Radial Map
• Starry Sky
• Cyclic Graph
• Maximal Graph

here we should define some helping functions for the analysis of networks.

generall function should look like:
def ana(Network) -> any

Functions:

• isConnected->bool
• edgeRedundancy->float
• nodeConnectivity->dict{int, float}
• cyclesForNode(network, cycleSize)->dict{int, float} - Difficult!
• getGraphScore(network, scorer)->float
• getGraphRobustness(network)->float

new ideas, please add

General ideas for tools:

Tools (Helper Functions):

• concatenate(networks: Iterable[LigandNetwork], _concatenator:NetworkConcatator) ->LigandNetwork
• merge(networks: Iterable[LigandNetwork]) ->LigandNetwork
• appendCompound(network: LigandNetwork, compound:Iterable[Compound], _concatenator:NetworkConcatator)-> LigandNetwork
• removeCompound(network: LigandNetwork, compound:Iterable[Compound], _concatenator:NetworkConcatator)-> LigandNetwork

Concatenator Implementations:

• MST Concatenator(networks: Iterable[LigandNetwork], _concatenator:NetworkConcatator) ->LigandNetwork
• Cyclic Concatenator(networks: Iterable[LigandNetwork], _concatenator:NetworkConcatator) ->LigandNetwork

Build Userstories, that help understanding how the Konnektor functionality can be used to solve problems.

ToDo:

• Build Design Usersheet
• Add to the docs.

Here i need help from the team, giving feeback on repo structures and names

Todos:

• Refactor algorithms folder (remove them and merge the files into the folder structure)
• is the Graph generator and bi-partite graph concatentor seperation needed?

This is one clustering approach.

Content:

• Paper: https://pubmed.ncbi.nlm.nih.gov/32584031/
• JNB example: https://github.com/greglandrum/rdkit_blog/blob/master/notebooks/Scaffold%20Network%20-%20Interactive%20Views%20and%20Exploring%20the%20Options.ipynb

Is your feature request related to a problem? Please describe.
add code bit to Cyclic graph planner, making node connections more diverse

Something like

network = generate_explicit_network([mapper1, mapper2], [(ligand1, ligand2), (ligand2, ligand3), ...])

(Based on meeting with Joe Bluck, this might be useful, especially when benchmarking against other tools.)

remove:

  plt.figure... 
   fig.gca()

maybe replace plt.figure with plt.subplots

additionalExample: https://github.com/dwhswenson/contact_map/blob/7fbb0b037db01831f8fd9ddd8710e9e0d23a25c5/contact_map/contact_count.py#L274

https://github.com/OpenFreeEnergy/konnektor/blob/9a091c03254d605dc917df3408a6e95f7a3aa27f/src/konnektor/visualization/visualization.py#L44C15-L44C41

Enable selecting one node and build cylces around it.

Is your feature request related to a problem? Please describe.
flex it such we can use different ways connecting clusters.

Here we could start adding a heuristic Maximal Network Lister. This one tries N random mappings for the ligands.

Add feature as a new clustering class.

Todo:

• Make scorer passable
• Make Distance matrix passable

Implement different Clustering Algorithms:

• allow featurization and clustering in one go.

same pattern as:
https://github.com/OpenFreeEnergy/konnektor/blob/main/src/konnektor/network_tools/cluster_molecules.py

is already part of GUFE

Todo:

• make Konnektor importable into Openfe
• replace old ligand network planners.
• make Konnektor Options accessible from CLI

General Idea:

• Build a network planner, that clusters nodes, builds sub networks and then concatenates the sub networks.
• each edge is labelled accordingly.

This abstract class will be transferred to Gufe in the end.

Thoughts:

• Use Scaffold Network Class from RDkit.
• what can we do about 3D?