This plugin calculates the native contacts in protein chains, returning a table of the contacts in each chain plus the contact order and a contact map. It can take pbds, adun systems and adun simulations as input.
It can also calculate the fraction of native contacts in a second structure relative to the first. Again the second structure can be a pdb, adun system or adun simulation. In the first two cases another data set detailing which of the native contacts are present in the second structure are returned, along with the fraction of native contacts. In the case of a simulation, the plugin calculates the fraction of native contacts for each frame in a range specified by the user. The plugin can perform this analysis if a single simulation is provided.
The linux source package and mac os x installer package (intel only) are available from the project download area.