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CHANGELOG.rst

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

0.7.3

  • placeholder.

0.7.2

  • Apply qmflows templates when using the dissociation workflow.
  • Fixed an issue wherein the core_index option was not properly respected.
  • Add the option to optimize QDs and XYn-dissociated QDs in the dissociation workflow.
  • Fix the frequency analysis component of the BDE workflow being incompatible with custom CP2K settings.
  • Allow computing the bulkiness for multiple lattice spacing values.
  • Add a new workflow for computing ligand cone angles.

0.7.1

  • Deprecate usage of Molecule.get_formula in favor of a PLAMS <=1.5.1-based backport.
  • Fix a failure in the documentation generation

0.7.0

  • Added a new fast-bulkiness workflow.
  • Added a new COSMO-RS recipe.
  • Various fixes.

0.6.1

  • Added a new conceptual DFT (CDFT) workflow.

0.6.0

  • Moved a number of functions to the nanoutils package.

0.5.4

  • Add the nth_shell argument to the replace_surface() recipe. Used for applying the workflow to surfaces of one or more sub-surface shells.

0.5.3

  • Added a new recipe for running conceptual DFT calculations with ADF.

0.5.2

  • Added on option for setting diameter to None.
  • Added recipes for filtering molecules based on properties.
  • Add an option to filter molecules based on the number of functional groups in the bulk_workflow() recipe.

0.5.1

  • Added a recipe for multi-ligand optimizations.
  • Officially dropped Nano-CAT support for Python 3.6.
  • Marked Nano-CAT as a typed package.
  • Added recipe for extracting coordination numbers from Molecules; courtesy of https://github.com/juliette1996 (#45).
  • Added a short recipe for calculating and rescaling ligand charges (#44).

0.5.0

  • Moved the CAT.recipes module to Nano-CAT.
  • Moved the CAT.attachment.qd_opt_ff module to Nano-CAT.
  • Improved handling of Exceptions.
  • Updated tests.

0.4.5

  • Created a separate module for the identify_surface() function, the latter being used for identifying which atoms are located on the surface, rather than in the bulk.

0.4.4

  • Added the EnenergyGatherer() class, a Mapping for managing all forcefield potential energies.
  • Changed the minimum Pandas version to >= 0.24.0.
  • Updated the keyword arguments of get_asa_md().
  • Fixed an issue were the charge was not properly set to an integer value when optimizing individual ligands.

0.4.3

  • Changed the a number of function signatures in md_asa.py to ensure signature compatiblity with Auto-FOX 0.7.2: nlesc-nano/auto-FOX#79.

0.4.2

  • Import the now fixed add_Hs() function from PLAMS.
  • Cleaned up the md_asa module.
  • Following the convention of CP2K, 1,4-electrostatic interactions are now ignored during the MD-ASA workflow.

0.4.1

  • Updated the MD-ASA workflow: The ligand interaction is now calculated using neutral parameters; the strain using ionic parameters.

0.4.0

  • Made Auto-FOX a hard dependency; removed a number of (now-duplicate) functions and modules.
  • Added a workflow for perfoming activation strain analyses on entire MD trajectories.

0.3.2

  • Reworked the ligand dissociation procedure.

0.3.1

  • Finalized the implementation an acitvation strain workflow with custom MATCH-based forcefields.

0.3.0

  • Finalize the introduction of a new CAT template system (WorkFlow()).
  • WiP: Implement an acitvation strain workflow with custom MATCH-based forcefields.

0.2.4

  • Custom Job types and Job Settings can now be specified for the ligand Activation Strain workflow.
  • Removed CRSJob() and CRSResults(); import them from PLAMS instead.
  • Import assertions from AssertionLib rather than CAT.
  • WiP: Introduction of a new CAT template system (WorkFlow()).

0.2.3

  • Moved the ligand bulkiness workflow from the ligand to the qd block in the CAT input.
  • Updated the formula for the ligand bulkiness calculation.

0.2.2

  • Updated the ligand bulkiness workflow.

0.2.1

  • Added a workflow for calculating ligand bulkiness.

0.2.0

  • Implemented an interface to MATCH: Multipurpose Atom-Typer for CHARMM.
  • Added the PSFContainer() and PRMContainer() classes handling .psf and .prm files, respectively.
  • Updated the handling of assertions, see CAT.assertions.assertion_manager.
  • A couple of bug fixes to the ligand dissociation module(s).
  • Added tests.

0.1.4

  • Bug fix: polyatomic ions are now properly dissociated in the ligand dissociation module(s).

0.1.3

  • Lowered Python version requirement from >=3.7 to >=3.6.

0.1.2

0.1.1

  • Added now features to the ligand dissociation module (see #1).

[Unreleased]

  • Empty Python project directory structure.