soprano.data.vdw

soprano.data.vdw#

Van der Waals radii

Available sets:

  • csd: extrapolated from the Cambridge Structural Database by Santiago

Alvarez, as seen in S. Alvarez, “A cartography of the van der Waals territories”, Dalton Trans. 42, 8617 (2013) - jmol: extracted from the source code of JMol - ase: default set for the Atomic Simulation Environment

Functions

build_custom_vdw(vdw_set[, vdw_scale, ...])

Build a custom VdW set

vdw_radius(el[, vdwset])

Return Van der Waals radius for a certain element
soprano.data.vdw.build_custom_vdw(vdw_set, vdw_scale=1.0, default_vdw=2.0, vdw_custom={})[source]#

Build a custom VdW set

soprano.data.vdw.vdw_radius(el, vdwset='csd')[source]#

Return Van der Waals radius for a certain element

Return a Van der Waals radius for a given element, as taken from one of three available databases:

  • csd: extrapolated from the Cambridge Structural Database by Santiago

Alvarez, as seen in S. Alvarez, “A cartography of the van der Waals territories”, Dalton Trans. 42, 8617 (2013) [default] - jmol: extracted from the source code of JMol - ase: default set for the Atomic Simulation Environment

Args:
el (str): element symbol
vdwset (str): VdW set to use. Default is ‘csd’.
Returns:
vdw_radius (float): the Van der Waals radius