Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12]

prf	The namespace containing the key classes of PROFASI
prf_pdb_vars	Constants describing the format of an atom record in PDB files
Alanine	Alanine
AminoAcid	Amino acid base class
Arginine	Arginine
Asparagine	Asparagine
Aspartic_Acid	Aspartic acid
Cysteine	Cystine
Glutamic_Acid	Glutamic acid
Glutamine	Glutamine
Glycine	Glycine
Histidine	Histidine
Isoleucine	Iso-leucine
Leucine	Leucine
Ligand	An abstract class providing a base for amino acids and capping groups
Lysine	Lysine
Methionine	Methionine
Phenylalanine	Phenyl-alanine
Proline	Proline
Serine	Serine
Threonine	Threonine
Tryptophan	Tryptophan
Tyrosine	Tyrosine
Valine	Valine
MC	MC class handles the Markov Chain Monte Carlo evolution
ParTemp	Parallel Tempering
WangLandau	Wang Landau iterations
AtomLabelDictionary	A translator for atom labels from other conventions
AtomDescriptor	Minimal information that identifies one atom in a PDB file
AtomRecord	Record corresponding to one atom in a PDB file
SimplePredicate	An extensible composite-capable simple predicate class
CompositePredicate	A composite predicate class
FindCoord	Simple but very useful class used widely in PROFASI to get coordinates
MersenneTwister	MersenneTwister is the default random number generator for profasi
Named	Anything that has a name
PDB_model	An abstraction of one model in a PDB file
PDBReader	A top level PDB file parser
Ran3nEngine	Ran3nEngine is the default random number generator class for profasi
RandomNumberBase	Base class for Random number generators for use in PROFASI
RMSD	Root Mean Square Deviation
isAtom	A trivial predicate to select all atoms
isHeavyAtom	A predicate that returns true if the atom is not Hydrogen
isBackboneAtom	A predicate that returns true if the atom is on the backbone
AtomTypeSelector	A predicate that returns true if the atom is of a certain species
ResSelector	A predicate that returns true if the atom is in one kind of residue
LabelSelector	A predicate that returns true if the atom has a certain label
RMSD_Utils	The RMSD_Utils handler class
Shape	Represents an abstract shape in space defined by a set of points
Vector3	A representation of three vectors
ArginineTip	Representation for the rigid tip of the Arginine side chain
ATetGroup	Asymmetric Tetrahedral Group
Atom	Representation of an atom in PROFASI
AtomCoordinates	A class to store the coordinates of an atom
ATriGroup	Assymetric Triangular group
Backbone	Representation for the protein backbone
DihedralGroup	The dihedral group or boomerang
DOF_Index	Helper class for population for DOF management
DOF_Info	A structure with 8 integers to characterize a degree of freedom
HistidineTip	Pentagon at the tip of the side chain of Histidine
MPhenylGroup	Modified Phenyl Group
Node	A Node is (like in graph theory) a meeting point of a few bonds
PhenylGroup	Represents the phenyl ring with attached hydrogens
SelRes	An abstraction for a residue selected for further processing
PopBase	Base class for a population of representations of proteins
Population	A population of proteins
Protein	Representation for a poly peptide chain
TetrahedralGroup	The Tetrahedral group
TrigonalGroup	A Node with two out-going bonds
TryptophanTip	Tip of the side chain of Tryptophan
Bias	Bias or E_{loc}
ChargedSCInteraction	Effective hydrophobic attraction between non-polar side chains
Energy	Energy base class
DihedralRestraints	A restraint energy term based on dihedral angles
DistanceRestraint	A single distance restraint
DistanceRestraints	Distance restraints
ObsEnergy	This class provides an energy term based on an arbritrary Observable
RestraintFunction	Simple harmonic potential well for arbitrary variable
PowerLawRestraint	Generic power law potential
FlattenedPL	Power law with a small distance cut
GaussianRestraint	Restraint of the form of a Gaussian
CircularNormal	Circular normal potential well
ExVol	The excluded volume term
ExVolBase	Helper class for both ExVol and LocExVol classes
HydrogenBond	HydrogenBond base class from which the HBMM and HBMS classes are derived
HBMM	The Backbone-Backbone hydrogen bond term
HBMS	The Backbone-Sidechain hydrogen bond term
Hydrophobicity	Effective hydrophobic attraction between non-polar side chains
LocExVol	Third-neighbour excluded volume contribution
TorsionTerm	Torsion angle potential
AtomDistance	Distance between two designated atoms
Contact	An abstraction of a contact
ContactFunction	A boolean function object class on Contacts
CaContact	A simple contact function based on Calpha separation
Proximity	A ContactFunction based on spatial proximity
HBContact	A ContactFunction based on hydrogen bonds
HPContact	A Contact function for Hydrophobic contacts
ContactMap	Utility to help keep track of a set of contacts
NativenessQ	A measure of nativeness based on local environment of residues
Observable	An observable is in principle anything that is named and has a value
ObsHandler	A handler class for Observables
OligoOrient	Number of pairs of parallelly oriented peptides in oligomers
PeriodicObs	Minimize another Observable with respect to the periodoc box
RC_phi	A single Ramachandran Phi angle as an observable
RC_psi	A single Ramachandran Psi angle as an observable
Chi	A single side chain Chi angle as an observable
ProteinRMSD	RMSD evaluator between a file and a collection of atoms in the program
RCAngleRMSD	Root mean square deviation of Ramachandran angles
Rg	Radius of gyration of a section of a protein chain
RCBin	Secondary structure analyzer
BGS	Biased Gaussian Steps
Pivot	Pivot move twists the protein about one backbone degree of freedom
Rot	Rotation of a single side chain torsional degree of freedom
Rotation	Rigid body rotation of a whole chain
Translation	Rigid body translation of a whole chain
dof_change_type	A structure to hold the most basic information about one change
Update	The base class for all conformational updates
prf_app	Application side classes expected to be used frequently
prf_traj
prf_raw_conf	Reader for PROFASI's raw binary data format
TrajIterator	Iterator to browse trajectories
Trajectory	PROFASI (multi-segment) trajectories
TrajSeg	A segment of a trajectory
TrajSnapshot	Snapshot of program state
prf_utils	The namespace containing auxiliary useful classes used inside PROFASI
AdaptiveHis	A histogram that can adjust its own range according to the data
His1D	The default histogram utility in ProFASi is based on His1D
His2D	A histogram with 2 independent variables
Permutation	Permutation class originally developed by SM for ALFS
prf_time	Abstraction for some system time function
OptBase	Base class for program switches and options
ProgSwitch	A program switch
ProgOpt	One option that a program may handle
ProgArgs	A utility to help manage program parameters
CorrelationEvaluator
MeanFinder	Simple utility to find the mean of a vector
StatBox
RangeBox	Small utility class RangeBox
CorrelationBox	CorrelationBox finds the correlation coefficient between two data streams
Timer	ProFASi's own timer for managing time limited runs
prf_xml
XML_Node	A class to represent an XML node
Chunk	A "chunk" of data in an XML file
XML_Mini	A small class to do the book keeping for XML parsing
UnivConstants	Set of frequently used constants
BasicMCRun	Constant temperature Monte Carlo simulations
ContactOrder	Relative contact order
extract_props	Calculating run-time properties from traj files
extract_snapshot	Extracting a snapshot configuration
minimize	Minimize an expression over degrees of freedom of a protein molecule
ParTempRun	Parallel tempering class
PopulationHandler	Helper class for configuring the protein population
regularizer	A program to regularize PDB structures
Retrace	A program to retrace the path of an individual replica of parallel tempering
SimAnnealRun	Simulated annealing
SimTempRun	Simulated tempering with profasi
UpdatesHandler	A manager for MC updates
WLRun	Monte Carlo simulations with the Wang Landau method