Biobb Structure Utils changelog

What’s new in version 5.0.0?

Changes

  • FIX: Accept lists in different formats on input properties.

  • CI/CD: Update set-up micromamba.

  • CI/CD: Update GA test workflow to Python >3.9

  • DOCS: Updating to Python 3.9

  • CI/CD: Update .gitignore to include the new file extensions to ignore

  • FEATURE: Importing submodules when a module is loaded

  • CI/CD: Change test conf.yml to adapt to new settings configuration

  • [FEATURE] New sandbox_path property

What’s new in version 4.2.0?

In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.

New features

  • Update to biobb_common 4.2.0 (general)

What’s new in version 4.1.0?

In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version. Also biobb_structure_checking has been updated from 3.12.1 to 3.13.4.

New features

  • Update to biobb_common 4.1.0 (general)

  • Update to biobb_structure_checking 3.13.4 (utils module)

What’s new in version 4.0.0?

In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.

New features

  • Update to biobb_common 4.0.0 (general)

What’s new in version 3.9.0?

In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.

New features

  • Update to biobb_common 3.9.0 (general)

  • All inputs/outputs are checked for correct file format, extension and type (general)

What’s new in version 3.8.0?

In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version. Also biobb_structure_checking has been updated from 3.9.11 to 3.10.1.

New features

  • Update to biobb_common 3.8.1 (general)

  • Update to biobb_structure_checking 3.10.1 (utils module)

What’s new in version 3.7.6?

In version 3.7.6 compatibility PDBQT

What’s new in version 3.7.4?

In version 3.7.4 ExtractResidues block has been added.

Other changes

  • Add keep_canonical_resnames option added to StrCheckAddHydrogens

What’s new in version 3.7.3?

In version 3.7.3 some minor bugs have been fixed.

Other changes

  • Minor bug fixes in StrCheckAddHydrogens

What’s new in version 3.7.1?

In version 3.7.1 some minor bugs have been fixed.

Other changes

  • Minor bug fixes in CatPDB

  • Minor bug fixes in ExtractChain

  • Minor bug fixes in ExtractHeteroAtoms

  • Minor bug fixes in ExtractModel

  • Minor bug fixes in ExtractMolecule

  • Minor bug fixes in StrCheckAddHydrogens

  • Minor bug fixes in StructureCheck

What’s new in version 3.7.0?

In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.

New features

  • Update to biobb_common 3.7.0 (general)

What’s new in version 3.6.1?

In version 3.6.1 the dependency biobb_structure_checking has been updated to 3.8.5 version.

New features

  • Update to biobb_structure_checking 3.8.5

What’s new in version 3.6.0?

In version 3.6.0 the dependency biobb_common has been updated to 3.6.0 version

New features

  • Update to biobb_common 3.6.0 (general)

  • Update to Biopython 1.79 (general)

What’s new in version 3.5.3?

In version 3.5.3 the tool extract_protein has been renamed to extract_molecule.

New features

  • Tool extract_protein renamed to extract_molecule

What’s new in version 3.5.2?

In version 3.5.2 the dependency biobb_structure_checking has been updated to 3.7.3 version. New tool for checking structures.

New features

  • Update to biobb_structure_checking 3.7.3

  • New StructureCheck tool

What’s new in version 3.5.1?

In version 3.5.1 the dependency biobb_structure_checking has been updated to 3.5.3 version.

New features

  • Update to biobb_structure_checking 3.5.3

What’s new in version 3.5.0?

In version 3.5.0 the dependency biobb_common has been updated to 3.5.1 version. Also, there has been implemented the new version of docstrings, therefore the JSON Schemas have been modified.

New features

  • Update to biobb_common 3.5.1 (general)

  • Update to Biopython 1.78 (general)

  • New extended and improved JSON schemas (Galaxy and CWL-compliant) (general)

Other changes

  • New docstrings

What’s new in version 3.0.1?

In version 3.0.1 the dependency biobb_common has been updated to 3.0.1 version. New tool for adding hydrogens to a 3D structure.

New features

  • Update to biobb_common 3.0.1

  • New StrCheckAddHydrogens tool

Other changes

  • Bug fixes in CatPDB

  • Bug fixes in ExtractChain

  • Bug fixes in ExtractHeteroAtoms

  • Bug fixes in ExtractModel

  • Bug fixes in ExtractProtein

  • Bug fixes in RemovePdbWater

What’s new in version 3.0.0?

In version 3.0.0 Python has been updated to version 3.7 and Biopython to version 1.76. Big changes in the documentation style and content. Finally a new conda installation recipe has been introduced.

New features

  • Update to Python 3.7 (general)

  • Update to Biopython 1.76 (general)

  • New conda installer (installation)

  • Adding type hinting for easier usage (API)

  • Deprecating os.path in favour of pathlib.path (modules)

  • New command line documentation (documentation)

Other changes

  • New documentation styles (documentation)