Source code for qcelemental.vanderwaals_radii

Contains van der Waals radii

import collections
from decimal import Decimal
from typing import Dict, Union

from .datum import Datum, print_variables
from .exceptions import DataUnavailableError
from .periodic_table import periodictable

[docs]class VanderWaalsRadii: r"""Van der Waals radii sets. Parameters ---------- context : str {'MANTINA2009'} Origin of loaded data. Attributes ---------- vdwr : Dict[str, Datum] Each van der Waals radius is an entry in `vdwr`, where key is the "Fe"-cased element symbol if generic or symbol-prefixed label if specialized within element. The value is a Datum object with `lbl` the same as key, `units` and `data` value as Decimal object. doi : str The DOI of the current context. name : str The name of the context ('MANTINA2009') native_units : str The units the original data was provided in. year : int The year the context was created. """ def __init__(self, context: str = "MANTINA2009"): self.vdwr: Dict[str, Datum] = collections.OrderedDict() from .data import mantina_2009_vanderwaals_radii if context == "MANTINA2009": self.doi = mantina_2009_vanderwaals_radii["doi"] self.native_units = mantina_2009_vanderwaals_radii["units"] # TypedDict wont be in until 3.8, have to ignore heterogeneous dicts for now for vdwr in mantina_2009_vanderwaals_radii["vanderwaals_radii"]: # type: ignore self.vdwr[vdwr[0]] = Datum(vdwr[0], self.native_units, Decimal(vdwr[1]), doi=self.doi) else: raise KeyError("Context set as '{}', only contexts {'MANTINA2009', } are currently supported") = context self.year = int(mantina_2009_vanderwaals_radii["date"][:4]) # type: ignore def __str__(self) -> str: return "VanderWaalsRadii(context='{}')".format(
[docs] def get( self, atom: Union[int, str], *, return_tuple: bool = False, units: str = "bohr", missing: float = None ) -> Union[float, "Datum"]: r""" Access a van der Waals radius for species ``atom``. Parameters ---------- atom Identifier for element or nuclide, e.g., ``H``, ``C``, ``Al``. units 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 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 .. code-block:: python try: rad = qcel.vdwradii.get(atom) except qcel.DataUnavailableError: rad = 4.0 Only relevant for ``return_tuple=False``. return_tuple 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`. """ if atom in self.vdwr.keys(): # catch extra labels like 'C_sp3' identifier = atom else: identifier = periodictable.to_E(atom) try: assert isinstance(identifier, str) # Should be string by now qca = self.vdwr[identifier] except KeyError as e: if missing is not None and return_tuple is False: return missing else: raise DataUnavailableError("vanderwaals radius", identifier) from e if return_tuple: return qca else: return qca.to_units(units)
[docs] def string_representation(self) -> str: """Print name, value, and units of all van der Waals radii.""" return print_variables(self.vdwr)
[docs] def write_c_header(self, filename: str = "vdwrad.h", missing: float = 2.0) -> None: r"""Write C header file defining Van der Waals radii array. Parameters ---------- filename File name for header. Note that changing this won't change the header guard. missing In order that the C array be atomic-number indexable and that it span the periodic table, this value is used anywhere data is missing. """ text = [ "#ifndef _qcelemental_vdwrad_h_", "#define _qcelemental_vdwrad_h_", "", "/* This file is autogenerated from the QCElemental python module */", "", "const double vanderwaals_radii[] = {", ] for el in periodictable.E: try: qca = self.vdwr[el] text.append("{}, /*- [{}] {} {} -*/".format(, qca.units, qca.label, qca.comment)) except KeyError: text.append( "{:.2f}, /*- [{}] {} {} -*/".format( missing, self.native_units, el, "Default value for missing data" ) ) text.append("};") text.append("#endif /* header guard */") text.append("") with open(filename, "w") as handle: handle.write("\n".join(text)) print("File written ({}). Remember to add license and clang-format it.".format(filename))
# singleton vdwradii = VanderWaalsRadii("MANTINA2009")