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.gitignore

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__pycache__
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*.pyc
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package.json
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.vscode
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tags
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.idea
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tests/junk
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!tests/junk/desc.txt
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dockstream/config/tests_config/config.json
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dockstream.log
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dockstream.err
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.directory

ChangeLog.md

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# Changelog of `DockStream`
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## 1.0.0 - 2021-08-02 (RC)
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### Added
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- Minimal environment definitions.
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### Fixed
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- Fixed bug in `Schrodinger`/`LigPrep` sublist generation ('0' was interpreted as '1').
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### Internal
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- Added additional unit test for `Schrodinger`/`LigPrep` CLI application.
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## 0.2.2 - 2020-04-30
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### Added
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- Extended input overwrite capabilities for `docker.py` (CSV specification).
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- New parsing capability to load SDF input with `DockStream` nomenclature to ensure enumerations are properly assigned.
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- Exposed additional command-line parameters for `Schrodinger`/`LigPrep`.
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- Added execution of `Schrodinger`/LigPrep` on AWS ("relative paths" bug on Schrodinger's side - workaround).
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### Fixed
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- Hotfix to improve `Corina` result parsing.
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### Internal
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- Show-case of how to execute `Schrodinger`/`LigPrep` on AWS including a token guard.
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- Show-case of how to execute `Schrodinger`/`Glide` on AWS including a token guard.
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## 0.2.1 - 2021-04-16
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### Added
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- Additional measures to protect agains failing ligands at the embedding stage.
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- Added `OpenEye`/`OMEGA` embedder.
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### Fixed
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- Hotfix to increase stability of `RDkit` ligand preparator.
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### Internal
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- Added unit test to cover changes in parameters for `LigPrep` when using `EPIK`.
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- Improved logging for embedding stage.
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- Reverted file system handling for `Glide`.
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## 0.2.0 - 2021-03-31
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### Added
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- New backend `Hybrid` (`OpenEye`) added (will replace the API version shortly).
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- Added stereo-isomer support using `RDkit`.
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- Added stereo-isomer support using `Corina`.
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- Exposed `Corina`'s "-d" options.
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- Added support for `Ligprep`'s filtering capabilities.
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- Enhanced stability for parallel execution mode for `Hybrid`, `Gold` and `Glide`.
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- Benchmarking script added.
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- Analysis script added.
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### Fixed
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- Fixed instability with protonations when using `RDkit` ligand embedding.
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- Fixed logging bug within `Ligprep`/`Schrodinger`.
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- Hot-fix for problem with CSV write-out when no pose was accepted.
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- Improved logging for `Ligprep`/`Schrodinger`.
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### Internal
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- Introduced stereo-enumeration factory class.
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- Adde `pydantic`-based parsing.
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- Optimized log messages.
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- Removed most versions from environment specifications.
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## 0.1.4 - 2020-11-03
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### Added
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- Added support for parallelization for `Ligprep`/`Schrodinger` embedding.
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- Added `best_per_ligand` write-out mode for conformers.
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- Added CSV-option for entry point `sdf2smiles.py`.
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### Fixed
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- Fixed bug for `OpenEye` backend, when `max_compounds_per_subjob` was set to 0.
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- Fixed bug in `best_per_enumeration` write-out mode for CSV results.
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- Fixed irregularity with `Gold` conformer ordering (fitness versus score).
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- Fixed naming bug in `OpenEye` backend.
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### Internal
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- Extended `AutoDock Vina` unit tests for tautomer compounds.
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- Small update of `Ligprep`/`Schrodinger` unit tests.
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- Updated docking backend unit tests to fully cover enumerations.
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- Added unit test for `Glide`/`Schrodinger` constraints.
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## 0.1.3 - 2020-09-29
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### Added
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- Added `OpenBabel`/`AutoDock Vina` target preparation (generating `PDBQT` files).
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- Added `OpenBabel`/`AutoDock Vina` box extraction (based on XYZ coordinate ranges of template ligand).
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- Added `AutoDock Vina` backend and result parser.
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- Added possibility to specify binary path for external binary executions.
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### Fixed
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- Fixed issue with logfile logging for `Glide` when time was exceeded.
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- Fixed issue with `OpenBabel` binary call when environment was not loaded.
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### Internal
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- Implemented hard over-write of `POSE_OUTTYPE` to be the only supported type.
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- Redesign of internal dictionary usage.
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- Addition of unit tests.
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- Added logging the version number (and started tagging versions).
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- Changed internal structure to be "package ready".
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- Improved the tag adding (and extended it for the ligand preparation step).
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## 0.1.2 - 2020-09-09
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### Added
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- Integration of a "progress bar" to docking jobs.
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- Added support for parameter `max_compounds_per_subjob` to reign in (sub-)lists too long (especially with `Glide`).
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- Added option to only output the best scores per enumeration.
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- Added `ligprep` to available ligand embedding techniques.
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### Fixed
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- Fixed issues with "internal alignment" and integrated a fail-safe version.
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- Made all receptor paths `lists` rather than simple strings to streamline the interface prior to the implementation of `ensemble docking`.
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### Internal
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- Clean-up of "OpenEye" result parser.
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- Refactored result parsers.
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- Improved `Gold` feedback for docking.
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- Restructuring of internal "Ligand" handling.
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- Refactored "docker.py" entry point.
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- Added result parser output checks to respective unit tests.
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- Refactored some methods of the ligand preparation tools.
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- Updated example configuration files.
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## 0.1.1 - 2020-08-17
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### Added
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- Added possibility to change the logfile path.
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- Added parameter to change the time limit per compound for `Glide` docking.
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- Added support to set a prefix for the output files.
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- Refactored and extended tagging system for all backends (adds "smiles" and "original_smiles" now).
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- Added option to only output the best poses per enumeration.
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- Added transformation support (using SMIRKS and `OpenEye`) for ligand preparation.
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- Added `Glide`/`Schrodinger` token guard.
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- Added support of "SDF" files as input.
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- Added support of arbitrary names to the parsing of CSV files as input.
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- Added "-debug" parameter to entry points.
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### Fixed
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- Critical fix for score aggregation if enumerations were used.
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- Made "Corina" embedding much more stable.
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- Several minor bug fixes in the logging write-out.
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### Internal
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- Added "ChangeLog.md".
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- Changed entry point structure (refactored and harmonized).
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- Fixed issue with "min"/"max" docking scoring directions (Gold/CCDC backend).

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