van der Waals Radii

Access van der Waals Radii information within QCElemental.

>>> qcel.vdwradii.get(6)
3.212534413278308
>>> qcel.vdwradii.get("C")
3.212534413278308
>>> qcel.vdwradii.get("C12")
3.212534413278308
>>> qcel.vdwradii.get("Carbon")
3.212534413278308

Contexts

To prepare for future changes, van der waals radii are contained in contexts. The qcel.vdwradii context will be updated over time to the latest data. To “pin” a context version, a specific context can be created like so:

>>> context = qcel.VanderWaalsRadii("MANTINA2009")
>>> qcel.vdwradii.get(6)
3.212534413278308

Currently only MANTINA2009 is available.

API

Top level user functions:

get(atom, *[, return_tuple, units, missing])

Access a van der Waals radius for species atom.

string_representation()

Print name, value, and units of all van der Waals radii.

Function Definitions

qcelemental.vdwradii.get(atom: Union[int, str], *, return_tuple: bool = False, units: str = 'bohr', missing: float = None) → Union[float, qcelemental.datum.Datum]

Access a van der Waals radius for species atom.

Parameters
  • atom (int or str) – Identifier for element or nuclide, e.g., H, C, Al.

  • units (str, optional) – Units of returned value. To return in native unit (MANTINA2009: angstrom), pass it explicitly. Only relevant for return_tuple=False since True returns underlying data structure with native units.

  • missing (float or None, optional) –

    How to handle when atom is valid but outside the available data range. When None, raises DataUnavailableError. When a float, returns that float, so supply in units units. Supplying a float is a more compact assurance that a call will work over all the periodic table than the equivalent

    try:
        rad = qcel.vdwradii.get(atom)
    except qcel.DataUnavailableError:
        rad = 4.0
    

    Only relevant for return_tuple=False.

  • return_tuple (bool, optional) – See below.

Returns

  • float – When return_tuple=False, value of Van der Waals radius. If multiple defined for element, returns largest.

  • qcelemental.Datum – When return_tuple=True, Datum with units, description, uncertainty, and value of van der Waals radius as Decimal (preserving significant figures). If multiple defined for element, returns largest.

Raises
  • NotAnElementError – If atom cannot be resolved into an element or nuclide or label.

  • DataUnavailableError – If atom is a valid element or nuclide but not one for which a van der Waals radius is available and missing=None.

qcelemental.vdwradii.string_representation() → str

Print name, value, and units of all van der Waals radii.