PROFASI  Version 1.5
Classes
Measurements

Classes

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::PeriodicObs
 Minimize another Observable with respect to the periodoc box. 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...
 

Detailed Description

Measurement of different properties of the protein chain or more general properties of the system are performed through "Observable" classes. An Observable typically calculates one specific property of the system, and returns a double precision value when asked.

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.


PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2