fegrow - 2.0.1

• a fix to conformer generation including R atom during position generation (#75)

- Jupyter Notebook
Published by bieniekmateusz over 1 year ago

fegrow - 2.0.0

The major release 2.0.0 contains two major features: Active Learning and Parallelisation Acceleration.

The best way to familiarise yourself is going to be via using the Jupiter notebooks. Please get in touch if you spot any errors, or if you'd like to see any improvements.

Active learning is carried out with scipy and supports multiple models and querying strategies. This is further parallelised with Dask, which can split the work across CPUs, different PCs (over -ssh), cluster (PBS, SLURM, etc), and more.

The major changes have been encoded in the new class called ChemSpace. However, some of the previous minute functions were modified to simplify the interactions between Dask and them. This means that not all previous functions have the same interface.

This release also contains a number of small fixes.

What's Changed

• Daskify rlist by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/69

Minor

• Libraries initiated on request by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/34
• Single SDFs for libraries by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/37
• library order by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/38
• Gnina error handling by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/39
• Wording: Wrong Atoms picking for building a molecule by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/40
• ANI - exploded conformers by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/42
• A scaffold: allow the use of a previously minimised structure as a starting scaffold by default. by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/43
• Builder: growing not just from hydrogens by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/44
• We don't need the hydrogens. by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/45
• Make more use of openmm pdbfile by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/46
• A growing vector splits the molecule into several components by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/47
• Saving MDAnalysis-readable .pdb files by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/49
• Keeping original scaffold by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/52
• update HBD/HBA calc for Lipinski by @RPirie96 in https://github.com/cole-group/FEgrow/pull/51
• No Hs in RMS to avoid the wrong hydrogens being compared by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/55
• Present gnina "CNNAffinity->IC50" as Kd [nM] with pint-pandas by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/59
• Linkers and RGroups are now dataframes - easier API access by @bieniekmateusz in https://github.com/cole-group/FEgrow/pull/62
• CLI high throughput scoring by @jthorton in https://github.com/cole-group/FEgrow/pull/64

Full Changelog: https://github.com/cole-group/FEgrow/compare/v1.3.0...v2.0.0

- Jupyter Notebook
Published by bieniekmateusz over 1 year ago

fegrow - 1.3.0

• Compatibility with openff-toolkit >=0.11 (thanks to @jeeberhardt for #29 #30)

- Jupyter Notebook
Published by bieniekmateusz almost 3 years ago

fegrow - 1.2.1

• library dataset has better coordinates (Ben)
• visualisations with pandas work better
• error handling

- Jupyter Notebook
Published by bieniekmateusz almost 3 years ago

fegrow - 1.2.0

• Adding the ability to work with linkers in addition to R-groups,
• Embedding a linker library (see and cite https://www.sciencedirect.com/science/article/abs/pii/S0968089623000421)

See the log for more.

- Jupyter Notebook
Published by bieniekmateusz about 3 years ago

fegrow - 1.0.2

• conda ready release

- Jupyter Notebook
Published by bieniekmateusz over 3 years ago

fegrow - 1.0.1

Updates: - embeds the openmm-ml plugin - optimisation now allows you to specify whether to use the cpu or gpu (which also fixes the bug due to both being deployed as the same time)

- Jupyter Notebook
Published by bieniekmateusz over 3 years ago

fegrow - 1.0.0

An Open-Source Molecular Builder and Free Energy Preparation Workflow by Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, and Daniel J. Cole.

Further Information Please see cole-group.github.io/fegrow for full installation instructions, documentation and acknowledgements.

And see the tutorial to get started.

- Jupyter Notebook
Published by bieniekmateusz almost 4 years ago