Classes | |
| class | prf::MCTotEnergy |
| A simple class to retrieve the total energy as an Observable. More... | |
| class | prf::AtomDistance |
| Distance between two designated atoms. More... | |
| class | prf::ContactMap |
| Utility to help keep track of a set of contacts. More... | |
| class | ContactOrder |
| Relative contact order. More... | |
| class | prf::NativenessQ |
| A measure of nativeness based on local environment of residues. More... | |
| class | prf::Observable |
| An observable is in principle anything that is named and has a value. More... | |
| class | prf::OligoOrient |
| Number of pairs of parallelly oriented peptides in oligomers. More... | |
| class | prf::RC_phi |
| A single Ramachandran Phi angle as an observable. More... | |
| class | prf::RC_psi |
| A single Ramachandran Psi angle as an observable. More... | |
| class | prf::Chi |
| A single side chain Chi angle as an observable. More... | |
| class | prf::ProteinRMSD |
| RMSD evaluator between a file and a collection of atoms in the program. More... | |
| class | prf::RCAngleRMSD |
| Root mean square deviation of Ramachandran angles. More... | |
| class | prf::Rg |
| Radius of gyration of a section of a protein chain. More... | |
All Observables in PROFASI (version 1.1 and later) can be initialized and customized through a string based interface. They can receive "commands" for specific settings as strings, and store them. At the time of initialisation, they make use of the commands they have received to customize their properties. Of course, the commands have to make sense for an Observable to implement them. If you send and arbitrary command, such as "set cutoff -56.7" to an observable that calculates the radius of gyration, it will simply be ignored. But something like "histogram -10.0 10.0 100" might potentially make sense for most measurements.