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CHANGELOG
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Authors: Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, Daniel J. Cole
**version 2.0.1 **
- The scaffold's R atom breaks the constrained embedding. The R atom is now omitted. (#74)
**version 2.0.0 **
- The new FEgrow with ChemSpace (AL) and Dask support
**version 1.4.0 **
- rmol.to_file now writes all conformers into the PDB using the "MODEL / ENDMDL" flavour which can be ready by
MDAnalysis.
- ANI in some cases explodes. Remove the bad conformers with bonds that have lengths larger than 3A.
- The user now has to import the libraries (RGroupGrid) and instantiate first.
- Libraries (linkers, rgroups) are now single .sdf files to avoid problems on clusters with many small files
- A growing vector can now be any molecule-separating atom in the molecule.
- Lipinski now uses the initial definitions of HBD: "sum of Ns and Os" and HBA: "sum of OHs and NHs",
(thanks to @RPirie96)
- When growing a molecule C multiple time in the same session (e.g. +linker +R), the .template attribute will
always be the original C
- Lipinski now uses the initial definitions of HBD: "sum of Ns and Os" and HBA: "sum of OHs and NHs",
(thanks to @RPirie96)
- R-group without coordinates are now using by default Chem.rdDistGeom.EmbedMolecule
- Do not cache openff parameters into db.json which right now crashes when multiple threads are used (same filename)
- using a tempfile with the anipotential .pt model file for for thread safety
- gnina column is renamed from "CNNaffinity->IC50s" to "Kd" with nM unit. We added pint-pandas package for units.
- rgroups and linkers are now dataframe (simpler API access)
**version 1.3.0**
- Compatibility with openff-toolkit >=0.11 (thanks to @jeeberhardt for #29 #30)
**version 1.2.1**
- refined library coordinates (Ben)
- visualisations with pandas
- error handling
**version 1.2.0**
- [Feature] Linkers with a library, with simpler searchable SMILEs
- Fix: [PR#20] Using the conda-forge package openmm-ml
**version 1.1.0**
- Fix: [RP] ExactMolWt used in the lipinski Ro5 is for mass spec/crystallography for specific isotopes. Moving on to the more appropriate MolWt.
**version 1.0.2**
- adjusting the files for the conda-release
**version 1.0.1**
- Fix+Feature: optimise_in_receptor function now takes platform_name argument allowing to use cuda or cpu for non-ani or ani optimisation.
- Fix: embedding openmm-ml into fegrow in order to create a conda package
**version 1.0**
- Initial release