py2sambvca v1.4.2

py2sambvca Patch Release 1.4.2

This patch release adds official support for Python 3.12!

What's Changed

• add python 3.12 by @JacksonBurns in #35

Full Changelog: v1.4.1...v1.4.2

py2sambvca v1.4.1

py2sambvca Patch Release 1.4.1

This patch release fixes a packaging bug in v1.4.0 (see #34). Thanks to @GwydionJon for catching the error!

What's Changed

• setup.py - add radii_tables to include by @JacksonBurns in #34

Full Changelog: v1.4.0...v1.4.1

py2sambvca v1.4.0

py2sambvca Minor Release v1.4.0

Release Highlights

This minor release of py2sambvca adds a new optional parameter to the py2sambvca constructor: radii_table. By passing in a dictionary of atomic symbol abbreviations mapped to atomic radii, you can customize the behavior of Sambvca21. For convenience, the default behavior of py2sambvca is to use the modified bondii radii from the original publication (default), though the original van der walls radii are now also available with the option vdw.

This minor release maintains complete backwards compatibility with all releases of py2sambvca v1.0+

What's Changed

• Make Radii Table Modular via Argument by @JacksonBurns in #27

Full Changelog: v1.3.4...v1.4.0

py2sambvca v1.3.4

py2sambvca Patch Release v1.3.4

Thanks to @andre-cloud a bug was found and fixed in which molecules of a sufficient size (total free volume greater than or equal to 1,000 cubic angstroms) could not be read!

py2sambvca v1.3.4 maintains complete backwards compatibility with all v1.x releases.

Some minor formatting changes were also introduced in the source code.

What's Changed

• Fix bug in retrieving results for molecules with V_free >=1000 by @JacksonBurns in #32
• bump version for patch release by @JacksonBurns in #33

Full Changelog: v1.3.3...v1.3.4

py2sambvca v1.3.3

This patch release officially adds support for Python 3.11 🎉

There has also been a small update in the README, as well as some QOL changes in the constant integration and automatic reviews GitHub actions.

What's Changed

• Combine all CI into one Workflow & Change Coverage Reviewer to wait until Ready for Review by @JacksonBurns in #30

Full Changelog: v1.3.2...v1.3.3

py2sambvca v1.3.2

In addition to some quality of life improvements for the GitHub repository, this release also includes one small update to py2sambvca: calc() will now provide a more helpful error if the sambvca executable cannot be found.

What's Changed

• Update README.md by @JacksonBurns in #21
• improved executable-related error handling by @JacksonBurns in #25
• add enhanced CI for python versions by @JacksonBurns in #26

Full Changelog: v1.3.1...v1.3.2

py2sambvca v1.3.1

This release contains only small internal fixes and quality of life updates - no new functions are introduced or removed (though get_buried_vol now has a deprecation warning that points users toward get_buried_volume).

py2sambvca v1.3.1 changes:

• citation updated
• added type hints to constructor
• small python style/security changes
• 100% (!!) code coverage and a pull request coverage verification action/branch protection

What's Changed

• py2sambvca v1.3.1 by @JacksonBurns in #18

Full Changelog: v1.3.0...v1.3.1

py2sambvca v1.3.0

This release to py2sambvca adds a new optional argument to specify a 'working directory', in which all input and output files will be placed. Thanks to @GwydionJon for opening the PR!

v1.3.0 maintains backwards compatibility with all v1.* releases of py2sambvca.

What's Changed

• Added ability to set working directory by @GwydionJon in #7

New Contributors

• @GwydionJon made their first contribution in #7

Full Changelog: v1.2.0...v1.3.0

py2sambvca v1.2.0

What's Changed

This update to py2sambvca includes significant quality of life improvements for the codebase, as well as a complete backend re-write to enable the addition of a multitude of useful functions:

• README now contains better examples
• All functions interfacing with the output of py2sambvca now use a single internal get_regex function
• Tests now cover 96% of the codebase
• import has been dramatically simplified
• All results from SambVca are readily accessible through getters and class attributes.

This minor version maintains complete backwards compatibility with previous versions of py2sambvca.

New Functions

Running is now simple with the single line run() function.

All values for the total complex, quadrants, and octants are available through getters:

Total Values:

• get_free_volume()
• get_buried_volume()
• get_exact_volume()
• get_total_volume()
• get_percent_buried_volume()
• get_percent_free_volume()
• get_percent_total_volume()

Quadrant Values:

• get_quadrant_free_volume()
• get_quadrant_buried_volume()
• get_quadrant_total_volume()
• get_quadrant_percent_buried_volume()
• get_quadrant_percent_free_volume()

Octant Values:

• get_octant_free_volume()
• get_octant_buried_volume()
• get_octant_total_volume()
• get_octant_percent_buried_volume()
• get_octant_percent_free_volume()

Results can also be accessed through a general getter method: get(), get_quadrant_result(), and get_octant_result().

All results can also be directly accessed through dictionaries, returned from a call to run() or parse_output() and available through p2s.total_results, p2s.quadrant_results, and p2s.octant_results.

In case there is something else you are looking for, you can use a general purpose get_regex() function to return the line containing a pattern.

PR's and Changelog

• Quality of Life Improvements for py2sambvca by @JacksonBurns in #2
• get version from init by @JacksonBurns in #3

Full Changelog: v1.1.0...v1.2.0

py2sambvca v1.1.0

py2sambvca

Simple thin client to interface python scripts with SambVca catalytic pocket Fortran calculator.

Installation

py2sambvca is available on PyPi and can be installed like so:

pip install py2sambvca

Usage

After installation, py2sambvca can be added to a Python script via import and instantiated:

# import the class and give it a simpler alias
from py2sambvca.py2sambvca import py2sambvca as p2s

buried_vol = p2s(r'myxyzfiles\ligand_4.xyz',...)
buried_vol.write_input()
buried_vol.calc()

# retrieve the buried volume and assign it
ligand_4_buried_volume = buried_vol.get_buried_vol()
...
# clean up input and output files
buried_vol.clean_files()

License

py2sambvca is available under the GNU GPLv3 in accordance with the base Fortran code which is available under the same license and can be retreieved here: https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html

Updates

Version 1.1.0 is the first API upgrade for py2sambvca, all thanks to @kjelljorner!

Added method 'parse_output()' to retrieve more values from the output file.

v1.1.0 also contains some general repository cleanup -- removal of .pyc, dist files, etc.