graphdot.graph.adjacency.atomic module¶
-
class
graphdot.graph.adjacency.atomic.
AtomicAdjacency
(shape='tent1', length_scale='vdw_radius', zoom=1.0)[source]¶ Bases:
object
Converts interatomic distances into edge weights using the equation \(a(i, j) = w(\frac{\lVert\mathbf{r}_{ij}\rVert}{\sigma_{ij}})\), where \(w\) is a weight function that generally decays with distance, and \(\sigma_{ij}\) is a length scale parameter betweens atom \(i\) and \(j\) and loosely corresponds to the typically distance of interatomic interactions between the atoms.
Parameters: - shape (str or callable) –
If string, must match one of the following patterns:
tent[n]
: e.g.tent1
,teng2
, etc.Tent
.gaussian
:Gaussian
.compactbell[a,b]
: e.g.compactbell4,2
,CompactBell
.
- length_scale (str) –
The atomic property to be used to determine the range and strength of edges to be constructed between pairs of atoms. The strength will generally fall to zero at roughly a distance 3 times the length scale. Possible values are:
- atomic_radius
- atomic_radius_rahm
- vdw_radius (default)
- vdw_radius_bondi
- vdw_radius_truhlar
- vdw_radius_rt
- vdw_radius_batsanov
- vdw_radius_dreiding
- vdw_radius_uff
- vdw_radius_mm3
- vdw_radius_alvarez
- covalent_radius_cordero
- covalent_radius_pyykko
- covalent_radius_bragg
- covalent_radius_pyykko_double
- covalent_radius_pyykko_triple
- metallic_radius
- metallic_radius_c12
- zoom (float) – A zooming factor to be multiplied with the length scales to extend the range of interactions.
- shape (str or callable) –