py2sambvca 1.2.0

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

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

py2sambvca has zero external depdencies.

Usage

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

from py2sambvca import p2s

nhc_p2s = p2s(
    "test/data/nhc.xyz",
    [22],
    [5],
    [1],
    path_to_sambvcax="sambvca21.exe",
)

From here, running can be done stepwise or with a single function:

nhc_p2s.run()
# equivalent to
nhc_p2s.write_input()
nhc_p2s.calc()
nhc_p2s.parse_output()
nhc_p2s.clean_files()

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 availabel 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.

Examples

Here are a couple repositories using py2sambvca as a Python package or extending its source code, check them out:

• Metal-organic framework stability analysis by Hiu Ki
• Phosphine ligand parameterization for Machine Learning by Kjell Jorner

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