3.0.0

What's Changed

Summary

• SDF support
• Repaired MCS due to testing with combined scoring system
• FEgrow scripts for MCS-based docking
• "modules" for docking, prepping, perturbation map, and dg calculation (cinnabar).
• Thoroughly tested

log

• Lots of permutations by @bieniekmateusz in #345
• Logging by @bieniekmateusz in #346
• Align by default (CLI) by @bieniekmateusz in #347
• Specific and minimum logging by @bieniekmateusz in #348
• Taking net-q from MOL2 files. by @bieniekmateusz in #349
• Minor Logging by @bieniekmateusz in #350
• Feature: Logs are broken down per pair by @bieniekmateusz in #351
• Empty suptops by @bieniekmateusz in #352
• Switch to a rectangular cuboid by @bieniekmateusz in #353
• Non-unique atom named creating issue for NAMD tagings (B-factor for alchemical transformation) by @bieniekmateusz in #354
• MCS and RMSD weights in CLI by @bieniekmateusz in #355
• By default, ignore RMSD in the scoring of overlaps. by @bieniekmateusz in #356
• Adding indices of atoms into the meta.json file. by @bieniekmateusz in #357
• Heuristic in CLI by @bieniekmateusz in #358
• Fix: during merging of paths, the initial solutions are dropped. by @bieniekmateusz in #359
• One H was missing from the solution - due to different defaults (coor… by @bieniekmateusz in #360
• A logger print with args. by @bieniekmateusz in #361
• Feature: allow setting multiple starting pairs in CLI. by @bieniekmateusz in #362
• Fix propagating weights everywhere by @bieniekmateusz in #363
• Add the problem with the kink issue to the dataset by @bieniekmateusz in #364
• Adding WDR91 for the kink issue by @bieniekmateusz in #365
• Too much logging in the DEBUG mode. by @bieniekmateusz in #366
• Check if atom names are unique, but do not worry if atom names do not… by @bieniekmateusz in #367
• Alignment using the original lager MCS before cutting down by @bieniekmateusz in #368
• Measuring the alchemical region overlap by @bieniekmateusz in #369
• Leaving only fully matched rings. Anything else is unmatched. by @bieniekmateusz in #370
• Allowing for sensible partial rings - which originated from the perfect overlap but differ in partial charges by @bieniekmateusz in #371
• Feature: support RDKit molecules and SDF files by @bieniekmateusz in #372
• Utils for SDF<->Mol2 by @bieniekmateusz in #373
• Scripts for MCS docking pipeline by @bieniekmateusz in #374
• Formatting and checks with ruff by @bieniekmateusz in #375
• Setting 0.6 superimposition search which has been behaving well. by @bieniekmateusz in #376
• Feature: Introducing RDKit MCS by @bieniekmateusz in #377
• Parmed can read GAFF atom types correctly now by @bieniekmateusz in #378
• Overlay factored out by @bieniekmateusz in #379
• Remove unused by @bieniekmateusz in #380
• Feature: docking modules by @bieniekmateusz in #381
• Migrated to the standardised property naming. by @bieniekmateusz in #382
• About the environment for docking by @bieniekmateusz in #383
• Reuse the existing parmed object for conversion rather than rewriting it by @bieniekmateusz in #384
• Handle the case when there is no conformers (ie from smiles) by @bieniekmateusz in #385
• Convert a ligand to an RDKit molecule. Towards RDKit MCS. by @bieniekmateusz in #386
• Use GAFF2 by default by @bieniekmateusz in #387
• Conformer fitting: allow using disconnected components in superimposition by @bieniekmateusz in #388
• RDKit MCS upgraded to use heavy atoms for scoring. by @bieniekmateusz in #389
• SDF can be used directly by @bieniekmateusz in #390
• Bond (a, b) can be represented as (b, a). Use sets to account for order by @bieniekmateusz in #391
• When suptops have the same length, select one with lower RMSD. by @bieniekmateusz in #392
• Tolerate bad molecule - print the exception but avoid breaking the pipeline by @bieniekmateusz in #393
• Handle MCS bad cases. by @bieniekmateusz in #394
• Expose the MCS threshold for deciding whether the fit should proceed. by @bieniekmateusz in #395
• Expand to enable indices use in -seed (MCS search) by @bieniekmateusz in #396
• Ext modules finalising documenting + Network module. by @bieniekmateusz in #397
• When a file exists already, reuse it. by @bieniekmateusz in #398
• cinnabar dg from ddg by @bieniekmateusz in #399
• docker moved to be a module by @bieniekmateusz in #400
• cleaning up after the old ties version. by @bieniekmateusz in #401

Full Changelog: v2.1.0...v3.0.0