Commandline Usage

The kallisto program is intended to be applied via the commandline. We use click to build kallisto, which enables us to define subcommands in a clear and structured way.

Subcommands

The most basic properties in kallisto are obtained by sub-commands: coordination numbers (cns), electronegativity equilibration atomic partial charges (eeq), atomic static polarizabilities (alp), and charge dependent atomic van der Waals radii (vdw).

Coordination number
command:cns
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
cntype:--cntype {exp, cov, erf} (optional)
default:cov
description:choose between different damping functions (string)
output:standard output (or to file with name <output>) 
> kallisto cns --inp <str> --cntype <str> <output>
Electronegativity equilibration atomic partial charges
command:eeq
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
charge:--chrg <int> (optional)
default:0
description:absolute charge of the molecule (integer)
output:standard output (or to file with name <output>) 
> kallisto eeq --inp <str> --chrg <int> <output>
Static atomic polarizabilities
command:alp
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
charge:--chrg <int> (optional)
default:0
description:absolute charge of the molecule (integer)
output:standard output (or to file with name <output>) 
> kallisto alp --inp <str> --chrg <int> <output>
Charge dependent van der Waals radii
command:vdw
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
input:--vdwtype <str> (optional)
default:rahm
description:
reference atomic van der Waals radii
rahm (DOI: 10.1002/chem.201700610)
truhlar (DOI: 10.1021/jp8111556)
charge:--chrg <int> (optional)
default:0
description:absolute charge of the molecule (integer)
charge:--angstrom (optional)
default:radii in Bohr
description:print out van der Waals radii in Angstrom instead of Bohr.
output:standard output (or to file with name <output>) 
> kallisto vdw --inp <str> --chrg <int> <output>
Write out connectivity of underlying structure
command:bonds
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
input:--partner <int> (optional)
description:write out partner for atom (indexing starts with 0 for the first atom)
input:--constrain (optional)
default:False
description:write out constrain.inp file in xtb format. Constrains all bonds in structure.
output:standard output (or to file with name <output>) 
> kallisto bonds --inp <str> --partner <str> --constrain <output>
Sort underlying structure according to a breadth first search (BFS) algorithm with respect to connectivity
command:sort
input:--inp <str> (optional)
default:coord (Turbomole)
description:input file in xyz or Turbomole format (string)
input:--start <int> (optional)
default:0
description:define the start of the BFS sorting.
output:standard output (or to file with name <output>) 
> kallisto sort --inp <str> --start <int> <output>