Skip to content

Latest commit

 

History

History
351 lines (278 loc) · 9.98 KB

CHANGELOG.md

File metadata and controls

351 lines (278 loc) · 9.98 KB
Raw

CHANGELOG

Version 0.5.7

Breaking changes

  • Renamed some parameters for compatibility with new node tagging system

Features

  • Allow PDBQT for GNINA receptor
  • Added tags to all nodes

Changes

  • Modified behaviour of Mol2Mol
  • Modifications to allow use of Gaussian and Crest nodes independently from reaction control
  • Sanitization for ADV is now active again by default
  • Keep hydrogens when reading a molecule from an SDF block by default
  • Increased default Schrodinger polling intervals
  • Additional debug info for Schrodinger job submission, increased wait for jobserver restart
  • Added logging of ports in use by Schrodinger job servers
  • Schrodinger nodes now set additional env variable for local job server

Fixes

  • Don't use MPS with GNINA if we don't want to use the GPU
  • Fixed Vina test failure due to missing properties
  • Skip non-created input.pdbqt files for Vina
  • Added explicit job server directory cleanup for Schrodinger

Version 0.5.6

Features

  • Added AEV-PLIG ligand-protein complex scoring
  • Added absolute solvation free energy node using OpenFE

Changes

  • GNINA node now adds hydrogens explicitly post-docking
  • Added query_interval parameter to Schrodinger workflows

Fixes

  • Increased default query_interval value to avoid crashes on very long jobserver wait times

Version 0.5.5

Features

  • Added PoseStability node using a simple MD simulation
  • Added GNINA + pose stability workflows

Changes

  • Added option to specify GNINA reference by name

Fixes

  • Fixed incomplete scalar check when setting scores

Version 0.5.4

Features

  • Added cofactor option to OpenFE

Changes

  • Refactored GNINA into separate single and ensemble nodes
  • Made Ligprep more robust for bad smiles codes

Fixes

  • Fixed reversed merging direction for merge_libraries
  • Only run GNINA with MPS locally, not on batch system
  • Fixed unbound local for result checks
  • Fixed GNINA not using GPUs correctly when running on multi-GPU nodes

Version 0.5.3

Features

  • Added YAML workflows
  • Added early termination option to OpenFE
  • Added option to specify AL n_oracle as a percentage
  • Added complex output to VinaFlex
  • Added GPU flag to GNINA
  • Added GPU / MPS check for GNINA
  • Added tag arithmetic / aggregation nodes (TagAgg, TagMath)
  • Improved node doc rendering
  • Added SetName node
  • Added isomer extraction node
  • Added max_score parameter to Glide + associated workflows
  • Added all GNINA scores
  • Added GNINA ensemble docking

Changes

  • Suppress all NaN warnings for aggregated scores
  • Downgraded Schrodinger download warning to debug
  • Update for OpenFE 1.0
  • Added explicit path inheritance to OpenFE
  • ReinventExit node now returns names
  • Removed GNINA pre-alignment
  • Overhauled library merging
  • Updated Glide REINVENT workflow to avoid writing out un-docked and extraneous poses

Fixes

  • Fixed REINVENT readlog printing everything when nothing changed
  • Fixed bad transform access in OpenFE parsing
  • Fixed missing mapping type in DynamicReference
  • Made isomer name logging consistent (fixes #60)
  • Fixed incomplete parsing of PDBQT output (#63)
  • Improved constraint type input for glide, exposed on the workflow and also allow to be set from keywords
  • Fixed incorrect filename incrementing behaviour in SaveSingleLibrary
  • Fixed off-by-one in Ligprep for weird smiles
  • Fix for Glide score parsing sometimes returning ints
  • Fixed BestConformerFilter to sort NaN scores correctly

Version 0.5.2

Changes

  • Improved node documentation
  • SaveSingleLibrary now increments filenames by default

Fixes

  • Fixed Glide attempting to update with potentially non-existent tag
  • Fixed Glide conformer sorting

Version 0.5.1

Features

  • Added neighbor tags to OpenFE results
  • Added pre-alignment to FEPGNINA subgraph
  • Added ROCSish FlexibleShapeAlign node

Changes

  • ROCS no longer has a scores_only output
  • Added Schrodinger job server query interval parameter
  • Major documentation overhaul

Fixes

  • Added stopped status for Schrodinger job server
  • Fixed error in array property conversion
  • Tentative fix for Reinvent worker not shutting down properly
  • Fix for BestIsomerFilter using incorrect descending value

Version 0.5.0

Features

  • Overhauled scoring (now allows multiple scores to be set)
  • Added tentative flexible PDBQT prep
  • Added BestConformerFilter, removed RMSDFilter
  • Added dynamic FEP references
  • Added redundant-minimal mapping for OpenFE
  • Added LigFilter to LigPrep
  • Added pre-alignment option to GNINA
  • Added LoadSingleRow function node
  • Added scheduled epsilon greedy acquisition
  • Improvements to ReactionControl

Changes

  • Exposed lambdas + replicas in FEP subgraph
  • Improved Glide output parsing
  • Removed InChI saving split strategy

Fixes

  • Fixed BestIsomerFilter not handling empty collections
  • Fixed Glide failing on non-existent docking score
  • Fix for merge_libraries not merging base keys
  • LoadLibrary no longer renumbers atoms by default
  • Fixed potentially inconsistent atom numbering in parsed conformers
  • Documentation fixes
  • Fixed EpsilonGreedy failing when n_random > n_best

Version 0.4.4

Features

  • Added FEP Mapping subgraph
  • Added Kartograf mapping backend for OpenFE
  • Allowed multiple target charges in ChargeFilter
  • Added SMILES tag to Ligprep output
  • Added SaveSingleLibrary to save mols into single SDF

Changes

  • Allowed SetScoreTag to operate on the existing score tag
  • Explicit cast to str when writing Isomer tags to SDF
  • Simplified InChI-based library IO
  • Exposed CNN scoring options for GNINA
  • Glide now sends NaN on failure by default
  • Updated Schrodinger host + n_jobs handling
  • Redesigned additional Glide constraint inputs
  • Schrodinger job submission overhaul, will now use a global jobserver in a temp folder
  • Simplified BestIsomerFilter, with guarantee of only returning single Isomer

Fixes

  • Moved OFE mapping section to after protein receive to avoid deadlocks
  • Removed Glide output atom renumbering to avoid incorrect isomer detection
  • Fixed score aggregation over isomers failing if some have NaN scores

Version 0.4.4

Features

  • Added GNINA node
  • Added simple switch to AL
  • Added generic tagging node
  • Added mapping-only option to OpenRFE
  • Added ChargeFilter
  • Improvements to Mol2MolStandalone
  • FEP subgraph improvements

Changes

  • Lots of extra logging
  • Changed IC smiles attribute to property with tag
  • Explicit casting to floats to avoid scorers sneaking in bad types
  • Removed deprecated super().prepare() calls
  • Removed references to old MultiParameter

Fixes

  • Fixed EpsilonGreedy not removing random component from surrogate
  • Fix semi-rare PDBQT conversion failures
  • Fixed OpenFE mapping failure recovery
  • Fix for EpsilonGreedy failing when n_mols < n_oracle
  • Fix for possible interference between RDKit and Qptuna

Version 0.4.3

Features

  • Added FEP subgraph
  • Added single-run AL progress node
  • Added docs for standalone REINVENT use

Fixes

  • Fixed some minor type errors in AL
  • Changed GlideDocking subgraph to use File2Molecule
  • Include package-based config by default

Version 0.4.2

Features

  • Added single-run active learning graph
  • Added custom tag option to ReinventExit
  • Added score_tag setter
  • Added alternative aggregation to mol scoring
  • Added timeout option to RMSD
  • Added file-based score caching

Changes

  • Skip licadmin on execution failure
  • Added retries to Schrodinger TokenGuard
  • Added explicit cast of tags to strings in save_sdf

Fixes

  • Added catch for semi-rare meeko PDBQT parsing issue

Version 0.4.1

Changes

  • Added File2Molecule to handle LoadMolecule with input

Fixes

  • Typing fixes
  • Fixed TagSorter not using correct test runner
  • Fixed first-conformer parsing problem in Glide

Version 0.4.0

Features

  • Added Gromacs module (Lily)
  • Added flexible docking with Vina
  • Added additional tag handling utilities
  • Added explicit prior and agent parameters to Reinvent
  • Added IsomerCollection tagging system
  • Added active learning module, subgraph, and example notebook

Changes

  • Reorganised cheminformatics

Fixes

  • Fixed relative-absolute conversion of BFEs not using reference correctly
  • Fixed MakeAbsolute not handling disconnected subgraphs
  • Fixed SaveLibrary not saving all conformers
  • Fixed AutoDockGPU not detecting tarred grids as inputs
  • Fixed OpenFE dumping failing on existing dump

Version 0.3.2

Features

  • Tests can now be skipped automatically based on available config options
  • Added absolute free energy conversion for OpenRFE

Changes

  • Updated REINVENT implementation
  • Updated bundled maize

Version 0.3.1

Changes

  • Updated bundled maize

Fixes

  • Fixed SaveCSV not using the correct tag order
  • Various type fixes

Version 0.3.0

Features

  • Several new filters
  • More subgraphs
  • OpenFE node
  • Constraints for AutoDockGPU and Glide
  • Nodes for reaction prediction
  • Batched CSV saving
  • Flexible docking with Vina

Changes

  • Various improvements to RMSD filtering
  • Performance improvements for Isomer tag handling
  • Allowed certain RDKit ops to timeout
  • More robust Schrodinger job handling
  • Integration tests
  • Maize core wheel for automated builds

Fixes

  • Fix for zombie threads when using REINVENT
  • Fix for installation only being possible using -e
  • Cleaned up typing

Version 0.2.3

Changes

  • Removed interface for REINVENT 3.2

Fixes

  • Cleanup of package structure
  • Updated dependencies
  • Added explicit check for Schrodinger license

Version 0.2.2

Features

  • Added Schrodinger grid preparation tools

Changes

  • Adjusted timeout for Gypsum-DL
  • Various enhancements for GLIDE

Fixes

  • Fixed Vina command validation for newer Vina versions
  • Fixed parsing issues for Vina

Version 0.2.1

Features

  • Improved REINVENT interface, using ReinventEntry and ReinventExit

Changes

  • Timeouts for conformer / isomer generation
  • Improved logging

Fixes

  • Check for zero bytes for Vina output

Version 0.2.0

Updated for public release.

Version 0.1

Initial release.