PROFASI  Version 1.5
Namespaces | Classes | Enumerations
prf Namespace Reference

The namespace containing the key classes of PROFASI. More...

Namespaces

namespace  prf_pdb_vars
 Constants describing the format of an atom record in PDB files.
 

Classes

class  Alanine
 Alanine. More...
 
class  AminoAcid
 Amino acid base class. More...
 
class  Arginine
 Arginine. More...
 
class  Asparagine
 asparagine More...
 
class  Aspartic_Acid
 Aspartic acid. More...
 
class  Cysteine
 Cystine. More...
 
class  Glutamic_Acid
 Glutamic acid. More...
 
class  Glutamine
 Glutamine. More...
 
class  Glycine
 Glycine. More...
 
class  Histidine
 Histidine. More...
 
class  Isoleucine
 Iso-leucine. More...
 
class  Leucine
 Leucine. More...
 
class  Ligand
 An abstract class providing a base for amino acids and capping groups. More...
 
class  Lysine
 Lysine. More...
 
class  Methionine
 Methionine. More...
 
class  Phenylalanine
 Phenyl-alanine. More...
 
class  Proline
 Proline. More...
 
class  Serine
 Serine. More...
 
class  Threonine
 Threonine. More...
 
class  Tryptophan
 Tryptophan. More...
 
class  Tyrosine
 Tyrosine. More...
 
class  Valine
 Valine. More...
 
class  MC
 MC class handles the Markov Chain Monte Carlo evolution. More...
 
class  ParTemp
 Parallel Tempering. More...
 
class  WangLandau
 Wang Landau iterations. More...
 
class  AtomLabelDictionary
 A translator for atom labels from other conventions. More...
 
class  AtomDescriptor
 Minimal information that identifies one atom in a PDB file. More...
 
class  AtomRecord
 Record corresponding to one atom in a PDB file. More...
 
class  SimplePredicate
 An extensible composite-capable simple predicate class. More...
 
class  CompositePredicate
 A composite predicate class. More...
 
class  FindCoord
 Simple but very useful class used widely in PROFASI to get coordinates. More...
 
class  MersenneTwister
 MersenneTwister is the default random number generator for profasi. More...
 
class  Named
 Anything that has a name. More...
 
class  PDB_model
 An abstraction of one model in a PDB file. More...
 
class  PDBReader
 A top level PDB file parser. More...
 
class  Ran3nEngine
 Ran3nEngine is the default random number generator class for profasi. More...
 
class  RandomNumberBase
 Base class for Random number generators for use in PROFASI. More...
 
class  RMSD
 Root Mean Square Deviation. More...
 
class  isAtom
 A trivial predicate to select all atoms. More...
 
class  isHeavyAtom
 A predicate that returns true if the atom is not Hydrogen. More...
 
class  isBackboneAtom
 A predicate that returns true if the atom is on the backbone. More...
 
class  AtomTypeSelector
 A predicate that returns true if the atom is of a certain species. More...
 
class  ResSelector
 A predicate that returns true if the atom is in one kind of residue. More...
 
class  LabelSelector
 A predicate that returns true if the atom has a certain label. More...
 
class  RMSD_Utils
 The RMSD_Utils handler class. More...
 
class  Shape
 Represents an abstract shape in space defined by a set of points. More...
 
class  Vector3
 A representation of three vectors. More...
 
class  ArginineTip
 Representation for the rigid tip of the Arginine side chain. More...
 
class  ATetGroup
 Asymmetric Tetrahedral Group. More...
 
class  Atom
 Representation of an atom in PROFASI. More...
 
class  AtomCoordinates
 A class to store the coordinates of an atom. More...
 
class  ATriGroup
 Assymetric Triangular group. More...
 
class  Backbone
 Representation for the protein backbone. More...
 
class  DihedralGroup
 The dihedral group or boomerang. More...
 
class  DOF_Index
 Helper class for population for DOF management. More...
 
class  DOF_Info
 A structure with 8 integers to characterize a degree of freedom. More...
 
class  HistidineTip
 Pentagon at the tip of the side chain of Histidine. More...
 
class  MPhenylGroup
 Modified Phenyl Group. More...
 
class  Node
 A Node is (like in graph theory) a meeting point of a few bonds. More...
 
class  PhenylGroup
 Represents the phenyl ring with attached hydrogens. More...
 
class  SelRes
 An abstraction for a residue selected for further processing. More...
 
class  PopBase
 Base class for a population of representations of proteins. More...
 
class  Population
 A population of proteins. More...
 
class  Protein
 Representation for a poly peptide chain. More...
 
class  TetrahedralGroup
 The Tetrahedral group. More...
 
class  TrigonalGroup
 A Node with two out-going bonds. More...
 
class  TryptophanTip
 Tip of the side chain of Tryptophan. More...
 
class  Bias
 Bias or E_{loc}. More...
 
class  ChargedSCInteraction
 Effective hydrophobic attraction between non-polar side chains. More...
 
class  Energy
 Energy base class. More...
 
class  DihedralRestraints
 A restraint energy term based on dihedral angles. More...
 
class  DistanceRestraint
 A single distance restraint. More...
 
class  DistanceRestraints
 Distance restraints. More...
 
class  ObsEnergy
 This class provides an energy term based on an arbritrary Observable. More...
 
class  RestraintFunction
 Simple harmonic potential well for arbitrary variable. More...
 
class  PowerLawRestraint
 Generic power law potential. More...
 
class  FlattenedPL
 Power law with a small distance cut. More...
 
class  GaussianRestraint
 Restraint of the form of a Gaussian. More...
 
class  CircularNormal
 Circular normal potential well. More...
 
class  ExVol
 The excluded volume term. More...
 
class  ExVolBase
 Helper class for both ExVol and LocExVol classes. More...
 
class  HydrogenBond
 HydrogenBond base class from which the HBMM and HBMS classes are derived. More...
 
class  HBMM
 The Backbone-Backbone hydrogen bond term. More...
 
class  HBMS
 The Backbone-Sidechain hydrogen bond term. More...
 
class  Hydrophobicity
 Effective hydrophobic attraction between non-polar side chains. More...
 
class  LocExVol
 Third-neighbour excluded volume contribution. More...
 
class  TorsionTerm
 Torsion angle potential. More...
 
class  AtomDistance
 Distance between two designated atoms. More...
 
class  Contact
 An abstraction of a contact. More...
 
class  ContactFunction
 A boolean function object class on Contacts. More...
 
class  CaContact
 A simple contact function based on Calpha separation. More...
 
class  Proximity
 A ContactFunction based on spatial proximity. More...
 
class  HBContact
 A ContactFunction based on hydrogen bonds. More...
 
class  HPContact
 A Contact function for Hydrophobic contacts. More...
 
class  ContactMap
 Utility to help keep track of a set of contacts. More...
 
class  NativenessQ
 A measure of nativeness based on local environment of residues. More...
 
class  Observable
 An observable is in principle anything that is named and has a value. More...
 
class  ObsHandler
 A handler class for Observables. More...
 
class  OligoOrient
 Number of pairs of parallelly oriented peptides in oligomers. More...
 
class  PeriodicObs
 Minimize another Observable with respect to the periodoc box. More...
 
class  RC_phi
 A single Ramachandran Phi angle as an observable. More...
 
class  RC_psi
 A single Ramachandran Psi angle as an observable. More...
 
class  Chi
 A single side chain Chi angle as an observable. More...
 
class  ProteinRMSD
 RMSD evaluator between a file and a collection of atoms in the program. More...
 
class  RCAngleRMSD
 Root mean square deviation of Ramachandran angles. More...
 
class  Rg
 Radius of gyration of a section of a protein chain. More...
 
class  RCBin
 Secondary structure analyzer. More...
 
class  BGS
 Biased Gaussian Steps. More...
 
class  Pivot
 Pivot move twists the protein about one backbone degree of freedom. More...
 
class  Rot
 Rotation of a single side chain torsional degree of freedom. More...
 
class  Rotation
 Rigid body rotation of a whole chain. More...
 
class  Translation
 Rigid body translation of a whole chain. More...
 
struct  dof_change_type
 A structure to hold the most basic information about one change. More...
 
class  Update
 The base class for all conformational updates. More...
 

Enumerations

enum  AtomKind
 An enumerated representation for relevant kinds of atoms.
 

Detailed Description

The prf namespace contains classes representing the main concepts behind PROFASI, for instance: the building blocks like Atom, AtomCoordinates, AminoAcid, Protein, Population; the energy terms like Bias or Hydrophobicity; the conformational updates like BGS or Rotation; the Monte Carlo methods, like SimTemp (simulated tempering)... These classes together (roughly) define this model. In principle, energy terms are a different kind of classes than updates, and they could be organized in separate namespaces inside the prf namespace. This may be done in the future.


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