Shortcut: BRIDGE

Module adjmat
Description Usage
Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms used in 0 tutorialsused in 2 eggs
output value type
the number of bridging atoms between the two groups scalar

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
GROUP atoms the atoms for which you would like to calculate the adjacency matrix
GROUPA atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB atoms when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS atoms The list of atoms that can form the bridge between the two interesting parts of the structure

Further details and examples

Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms

\par Examples

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
GROUP input none the atoms for which you would like to calculate the adjacency matrix
GROUPA input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB input none when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS input none The list of atoms that can form the bridge between the two interesting parts of the structure
SWITCH optional not used The parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHA optional not used The switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHB optional not used The switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.