This script calculates residue contact maps and compares them between different structures. Residues are considered in contact when the minimum inter-residue distance of all pairs of heavy atoms is less than 4.2A.
In the default mode with two structures as arguments the fraction of contacts present in the second structure with respect to the first is determined. Also calculated is the continuous quantity rho that uses a sigmoidal function for the minimum inter-residue distance around 4.2 A to effectively include residue pairs that are slightly further apart with a reduced weight. An extended output is available with -list to get a list of all residue contacts in the reference structure with the minimum distances in the reference as well as the test structures.
If only one structure is given as an argument no comparison is done. A residue contact list is printed out instead. This list can be used in later comparisons with -read to save time if multiple structures are compared to the same reference. The more costly calculation of the reference residue map then has to be done only once.
The option -l is available to limit the residue map to contacts with a subset of residues as might be useful for loop modeling.