Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123456]

Align	Pairwise sequence and profile alignment
FSAlign	Implement free-shift "glocal" alignment
NWAlign	Implement Needleman-Wunsch global alignment
NWAlignNoTermGaps	Implement Needleman-Wunsch global alignment with no penalty for the terminal hangouts of the sequence
SWAlign	Implement Smith-Waterman local alignment
AlignmentBase	Abstract base class for all sorts of alignments
Alignment	Implement a simple alignment type
AlignmentData	Base class for printing alignments
SecSequenceData	Print alignment of two sequences considering also secondary structure
SequenceData	Print alignment of two sequences
AminoAcidHydrogen	Implements aminoacid hydrogens
CompressedLoopTableEntry	This structure allows to manage a compressed loop table information in vectors
EData	Class for structural alignments
EnergyFeatures	Interface/wrapper for energy and feature calculation for a protein chain
EnergyGreater	Energy operator. It compares enrgies of two Potential::ANGLES structures
EnergyVisitor	Base class implementing the visitor pattern
GapFunction	Base class for gap functions
AGPFunction	Implement AGP (Affine Gap Penalty) function
VGPFunction	Implement VGP (Variable Gap Penalty) function
VGPFunction2	Implement VGP (Variable Gap Penalty) function
globalStatistic	Methods to manages the global statistic data
Identity	Implements object id. With a "number" a "name" and a "counter"
IntCoordConverter	Implements methods to manage translation vector and angles between vectors
Loader	Base class for loading components (Atoms, Groups, etc.)
IntLoader	Loads components (Atoms, Groups, etc.) in internal format
PdbLoader	Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format
RelLoader	Loads components (Atoms, Groups, etc.) in relative format
SeqLoader	Loads components (Atoms, Groups, etc.) in SEQ format
XyzLoader	Loads components (Atoms, Groups, etc.) in XYZ (carthesian) format
LoopExtractor	Extracts all the loop regions (by numbers) from a given spacer
LoopTable	Defines a table of possible amino chain end points and end directions after k amino acids have been concatenated
LoopTableEntry	Implements an entry for the loop table (equivalent to the old "ProteinTableEntry" from the previous version
OptimizationVisitor	Base class Optimizacion Patter
Potential	Abstract class for the energy potential
EffectiveSolvationPotential	Implements a knowledge-based solvation with polar/hydrophobic information potential. A coefficient is used to normalize the propensity
PolarSolvationPotential	This class implements a knowledge-based solvation with polar/hydrophobic information potential
RapdfPotential	Distance-dependent residue-specific all-atom probability discriminatory function
SolvationPotential	Includes methods that allow to calculate solvation, energy and propensity
TorsionPotential	This class implements a simple torsion potential based on the statistical preference of aminoacid types for certain angles
Chi1Chi2	Class manages the angle qualities and the energy
Omega	Class manages the angle qualities and the energy
PhiPsi	Class manages the angle qualities and the energy
PhiPsiOmega	Class manages the angle qualities and the energy
PhiPsiOmegaChi1	Class manages the angle qualities and the energy
PhiPsiOmegaChi1Chi2	Class manages the angle qualities and the energy
PhiPsiOmegaChi1Chi2PreAngle	Class manages the angle qualities and the energy
PhiPsiOmegaChi1PreAngle	Class manages the angle qualities and the energy, tortion potential
PhiPsiOmegaPreAngle	Class manages the angle qualities and the energy
PhiPsiPreAngle	Class manages the angle qualities and the energy, torsion potential
Profile	Calculate a frequency profile or PSSM
HenikoffProfile	Calculate a frequency profile or PSSM using Henikoff weighting scheme
PSICProfile	Calculate a frequency profile or PSSM using PSIC weighting scheme
SeqDivergenceProfile	Calculate a frequency profile or PSSM using SeqDivergence weighting scheme
ProfInput	Implement I/O objects for handling PHD files
PssmInput	Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix)
RamachandranData	This struct implements the container for ramachandran plot-like phi/psi angle combinations for the LoopTable class(es)
RankAnalyzer	This class implements functions to analyze the ranking output of lobo
ranking_helper	Contains methods to manage the ranking
ranking_helper2	Class contains methods to manage the ranking
Saver	Base class for saving components (Atoms, Groups, etc.)
IntSaver	Loads components (Atoms, Groups, etc.) in internal format
PdbSaver	Saves components (Atoms, Groups, etc.) in standard PDB format
RelSaver	Save components (Atoms, Groups, etc.) in relative format
XyzSaver	Saves components (Atoms, Groups, etc.) in carthesian format
ScoringFunction	Base class for scoring functions
AtchleyCorrelation	Calculate scores for profile to profile alignment using sequence metric factor
AtchleyDistance	Calculate scores for profile to profile alignment using sequence metric factor
CrossProduct	Calculate scores for profile to profile alignment using sum of pairs method
DotPFreq	Calculate scores for profile to profile alignment using dot product method
DotPOdds	Calculate scores for profile to profile alignment using dot product method
EDistance	Calculate scores for profile to profile alignment using euclidean distance
JensenShannon	Calculate scores for profile to profile alignment using Jensen-Shannon method
LogAverage	Calculate scores for profile to profile alignment using sum of pairs method
Panchenko	Calculate scores for profile to profile alignment using Panchenko method
Pearson	Calculate scores for profile to profile alignment using Pearson's correlation coefficient
Zhou	Calculate scores for profile to profile alignment using Zhou-Zhou method
ScoringScheme	Base class for scoring schemes
ScoringP2P	Calculate scores for profile to profile alignment
ScoringP2S	Calculate scores for profile to sequence alignment
ScoringS2S	Calculate scores for sequence to sequence alignment
SeqConstructor	This class builds a spacer by concatenating the same aminoacid type for n times
SimpleBond	Defines chemical and abstract bonds between objects. eg.: covalent bonds. Attention: copy() strips orig from its SimpleBonds and attaches them to the new SimpleBond
Atom	Implements a simple atom type
Bond	Defines chemical and abstract bonds between objects which are compositions of atoms
Component	Base class for composite structures
Monomer	Base class for components without elements
Group	This class implements a simple chemical group
AminoAcid	It mplements a simple amino acid
Ligand	Implements methods to verify the ligand properties
Nucleotide	Implements a simple nucleotide
SideChain	This class implements a side chain
Polymer	Implements methods to manage a polymer created by components
LigandSet	Class implements methods to manage the ligandSet
Protein	Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present)
Spacer	Implements a "Spacer" for a protein chain. Includes methods to obtain values from the atoms and its pdb information
solutionQueueElem	Struct that contains a queue element
Ss2Input	Implement I/O objects for handling PSI-PRED files
Structure	Base class for structural scores
Prof	Calculate structural scores with info derived from PHD
Sec	Calculate structural scores with info derived from secondary structure
Ss2	Calculate structural scores with info derived from PSI-PRED
Threading	Calculate structural scores with info derived from threading
ThreadingProf	Calculate structural scores with info derived from threading and PHD
ThreadingSs2	Calculate structural scores with info derived from threading and PSI-PRED
Substitution	Base class for deriving substitution matrices
SubMatrix	Implement a standard substitution matrix
ThreadingInput	Implement I/O objects for handling threading files
Traceback	Reconstruct the path in the alignment matrix
VectorTransformation	This class allows to store transformation steps for transforming a vector v into v' according to the series of steps performed earlier