| prf_utils::AdaptiveHis | A histogram that can adjust its own range according to the data |
| prf::Alanine | Alanine |
| prf::AminoAcid | Amino acid base class |
| prf::Arginine | Arginine |
| prf::ArginineTip | Representation for the rigid tip of the Arginine side chain |
| prf::Asparagine | Asparagine |
| prf::Aspartic_Acid | Aspartic acid |
| prf::ATetGroup | Asymmetric Tetrahedral Group |
| prf::Atom | Representation of an atom in PROFASI |
| prf::AtomCoordinates | A class to store the coordinates of an atom |
| prf::AtomDescriptor | Minimal information that identifies one atom in a PDB file |
| prf::AtomDistance | Distance between two designated atoms |
| prf::AtomRecord | Record corresponding to one atom in a PDB file |
| prf::AtomTypeSelector | A predicate that returns true if the atom is of a certain species |
| prf::ATriGroup | Assymetric Triangular group |
| prf::Backbone | Representation for the protein backbone |
| BasicMCRun | Constant temperature Monte Carlo simulations |
| prf::BGS | Biased Gaussian Steps |
| prf::Bias | Bias is a local interaction term acting along the protein backbone |
| prf::CaContact | A simple contact function based on Calpha separation |
| prf::Chi | A single side chain Chi angle as an observable |
| prf::CompositePredicate< T > | A composite predicate class |
| prf::Contact | An abstraction of a contact |
| prf::ContactFunction | A boolean function object class on Contacts |
| prf::ContactMap | Utility to help keep track of a set of contacts |
| ContactOrder | Relative contact order |
| prf_utils::CorrelationBox | CorrelationBox finds the correlation coefficient between two data streams |
| prf_utils::CorrelationEvaluator | |
| prf::Cysteine | Cystine |
| prf::DihedralGroup | The dihedral group or boomerang |
| prf::Energy | Energy base class |
| extract_props | Calculating run-time properties from conf files |
| extract_snapshot | Extracting a snapshot configuration |
| prf::ExVol | The excluded volume term |
| prf::ExVolBase | Helper class for both ExVol and LocExVol classes |
| prf::FindCoord | Simple but very useful class used widely in PROFASI to get coordinates |
| prf::Glutamic_Acid | Glutamic acid |
| prf::Glutamine | Glutamine |
| prf::Glycine | Glycine |
| prf::HBContact | A ContactFunction based on hydrogen bonds |
| prf::HBMM | The Backbone-Backbone hydrogen bond term |
| prf::HBMS | The Backbone-Sidechain hydrogen bond term |
| prf_utils::His1D | |
| prf_utils::His2D | A histogram with 2 independent variables |
| prf::Histidine | Histidine |
| prf::HistidineTip | Pentagon at the tip of the side chain of Histidine |
| prf::HPContact | A Contact function for Hydrophobic contacts |
| prf::HydrogenBond | HydrogenBond base class from which the HBMM and HBMS classes are derived |
| prf::Hydrophobicity | Effective hydrophobic attraction between non-polar side chains |
| prf_app::InterfaceBase | A representation of a "pure" and default Monte Carlo engine |
| prf::isBackboneAtom | A predicate that returns true if the atom is on the backbone |
| prf::isHeavyAtom | A predicate that returns true if the atom is not Hydrogen |
| prf::Isoleucine | Iso-leucine |
| prf::LabelSelector | A predicate that returns true if the atom has a certain label |
| prf::Leucine | Leucine |
| prf::Ligand | An abstract class providing a base for amino acids and capping groups |
| prf::LocExVol | Third-neighbour excluded volume contribution |
| prf::Lysine | Lysine |
| prf::MC | MC class handles the Markov Chain Monte Carlo evolution |
| prf::MCTotEnergy | A simple class to retrieve the total energy as an Observable |
| prf_utils::MeanFinder | Simple utility to find the mean of a vector |
| prf::MersenneTwister | MersenneTwister is the default random number generator for profasi |
| prf::Methionine | Methionine |
| prf::MPhenylGroup | Modified Phenyl Group |
| prf::Named | Anything that has a name |
| prf::NativenessQ | A measure of nativeness based on local environment of residues |
| prf::Node | A Node is (like in graph theory) a meeting point of a few bonds |
| prf::Observable | An observable is in principle anything that is named and has a value |
| prf_app::ObsHandler | A handler class for Observables |
| prf::OligoOrient | Number of pairs of parallelly oriented peptides in oligomers |
| prf::ParTemp | Parallel Tempering |
| ParTempRun | Parallel tempering with PROFASI |
| prf::PDB_model | An abstraction of one model in a PDB file |
| prf::PDBReader | A top level PDB file parser |
| prf_utils::Permutation | Permutation class originally developed by SM for ALFS |
| prf::Phenylalanine | Phenyl-alanine |
| prf::PhenylGroup | Represents the phenyl ring with attached hydrogens |
| prf::Pivot | Pivot move twists the protein about one backbone degree of freedom |
| prf::PopBase | Base class for a population of representations of proteins |
| prf::Population | A population of proteins |
| prf_utils::ProgArgs | A utility to help parse command line arguments |
| prf_utils::ProgOpt | One option that a program may handle |
| prf::Proline | Proline |
| prf::Protein | Representation for a poly peptide chain |
| prf::ProteinRMSD | RMSD evaluator between a file and a collection of atoms in the program |
| prf::Proximity | A ContactFunction based on spatial proximity |
| prf::Ran3nEngine | Ran3nEngine is the default random number generator class for profasi |
| prf::RandomNumberBase | Base class for Random number generators for use in PROFASI |
| prf_utils::RangeBox | Small utility class RangeBox |
| prf::RC_phi | A single Ramachandran Phi angle as an observable |
| prf::RC_psi | A single Ramachandran Psi angle as an observable |
| prf::RCAngleRMSD | Root mean square deviation of Ramachandran angles |
| prf::RCBin | Secondary structure analyzer |
| prf::ResSelector | A predicate that returns true if the atom is in one kind of residue |
| prf::Rg | Radius of gyration of a section of a protein chain |
| prf::RMSD | Root Mean Square Deviation |
| prf::RMSD_Utils | The RMSD_Utils handler class |
| prf::Rot | Rotation of a single side chain torsional degree of freedom |
| prf::Rotation | Rigid body rotation of a whole chain |
| prf::SelRes | An abstraction for a residue selected for further processing |
| prf::Serine | Serine |
| prf::Shape | Represents an abstract shape in space defined by a set of points |
| SimAnnealRun | Simulated annealing |
| prf::SimplePredicate< T > | An extensible composite-capable simple predicate class |
| SimTempRun | Simulated tempering with profasi |
| prf_utils::StatBox | |
| prf::TetrahedralGroup | The Tetrahedral group |
| prf::Threonine | Threonine |
| prf::Translation | Rigid body translation of a whole chain |
| prf::TrigonalGroup | A Node with two out-going bonds |
| prf::Tryptophan | Tryptophan |
| prf::TryptophanTip | Tip of the side chain of Tryptophan |
| prf::Tyrosine | Tyrosine |
| prf::Update | The base class for all conformational updates |
| UpdateProbs | A helper class to handle assignment of probabilities to updates |
| prf::Valine | Valine |
| prf::Vector3 | A representation of three vectors |