Proximity Shells

Get steric hindrance of an atom depending on its environment.

Introduction

Proximity shells (P) are calculated by increasing the covalent atomic radii within the definition of coordination number. Here, the user is able to define the outer and inner limit by the size flag that is used as a scaling parameter in the calculation of proximity shells

$$P_{i}^{(k,l)} = CN_{i}\left(R^{cov'}_{AB} = k\times R^{cov}_{AB}\right) - CN_{i}\left(R^{cov'}_{AB} = l\times R^{cov}_{AB}\right) \text{with} \quad k>l$$

This atomic feature is useful to determine the steric hindrance that occurs due to neighbouring groups. The depiction below exemplifies this for the toluene molecule with k=3 and l=2 (see Applications part), where larger P-values show a higher steric hindrance in the near neighbourhood.

Define the Subcommands

prox

> kallisto prox options arguments

options

  # note that the inner (smaller) border is given first
 --size <int> <int>
 (optional, default: 2 3)
 description:
  defines inner and outer border for proximity shells
  
--out <string> 
(optional)
description: 
 write output to file

arguments

input file is given as (positional) argument

Application

Let's calculate proximity shells for the toluene molecule by calling the subcommand prox

> cat toluene.xyz
15
Toluene
  C      1.2264      0.0427      0.0670
  C      1.0031     -1.3293      0.0600
  C     -0.2945     -1.8256     -0.0060
  C     -1.3704     -0.9461     -0.0646
  C     -1.1511      0.4266     -0.0578
  C      0.1497      0.9292      0.0066
  C      0.3871      2.3956     -0.0022
  H      2.2495      0.4310      0.1211
  H      1.8510     -2.0202      0.1071
  H     -0.4688     -2.9062     -0.0109
  H     -2.3926     -1.3347     -0.1157
  H     -2.0006      1.1172     -0.1021
  H      0.5024      2.7582     -1.0330
  H      1.2994      2.6647      0.5466
  H     -0.4475      2.9470      0.4506
# Note that the default sizes are l, k = 2, 3
> kallisto prox toluene.xyz
4.381228500236796
3.3677521535602004
2.8495247846705114
3.366999124462712
4.382826391660659
2.5949138877345828
2.1800188277556742
4.125179817959886
3.9722691198666404
3.801239033949839
3.972333555437317
4.128082932610809
3.7384516775418555
4.073729305140565
4.075067940009211
# Save output to file 'prox'
> kallisto prox --out prox toluene.xyz
> cat prox
4.381228500236796
3.3677521535602004
2.8495247846705114
3.366999124462712
4.382826391660659
2.5949138877345828
2.1800188277556742
4.125179817959886
3.9722691198666404
3.801239033949839
3.972333555437317
4.128082932610809
3.7384516775418555
4.073729305140565
4.075067940009211