  Victor | |
  Align2 | |
   AGPFunction | Implement AGP (Affine Gap Penalty) function |
| Align | Pairwise sequence and profile alignment |
| Alignment | Implement a simple alignment type |
| AlignmentBase | Abstract base class for all sorts of alignments |
| AlignmentData | Base class for printing alignments |
| 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 |
| EData | Class for structural alignments |
| EDistance | Calculate scores for profile to profile alignment using euclidean distance |
| FSAlign | Implement free-shift "glocal" alignment |
| GapFunction | Base class for gap functions |
| HenikoffProfile | Calculate a frequency profile or PSSM using Henikoff weighting scheme |
| 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 |
| NWAlign | Implement Needleman-Wunsch global alignment |
| NWAlignNoTermGaps | Implement Needleman-Wunsch global alignment with no penalty for the terminal hangouts of the sequence |
| Panchenko | Calculate scores for profile to profile alignment using Panchenko method |
| Pearson | Calculate scores for profile to profile alignment using Pearson's correlation coefficient |
| Prof | Calculate structural scores with info derived from PHD |
| Profile | Calculate a frequency profile or PSSM |
| ProfInput | Implement I/O objects for handling PHD files |
| PSICProfile | Calculate a frequency profile or PSSM using PSIC weighting scheme |
| PssmInput | Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix) |
| ScoringFunction | Base class for scoring functions |
| ScoringP2P | Calculate scores for profile to profile alignment |
| ScoringP2S | Calculate scores for profile to sequence alignment |
| ScoringS2S | Calculate scores for sequence to sequence alignment |
| ScoringScheme | Base class for scoring schemes |
| Sec | Calculate structural scores with info derived from secondary structure |
| SecSequenceData | Print alignment of two sequences considering also secondary structure |
| SeqDivergenceProfile | Calculate a frequency profile or PSSM using SeqDivergence weighting scheme |
| SequenceData | Print alignment of two sequences |
| Ss2 | Calculate structural scores with info derived from PSI-PRED |
| Ss2Input | Implement I/O objects for handling PSI-PRED files |
| Structure | Base class for structural scores |
| SubMatrix | Implement a standard substitution matrix |
| Substitution | Base class for deriving substitution matrices |
| SWAlign | Implement Smith-Waterman local alignment |
| Threading | Calculate structural scores with info derived from threading |
| ThreadingInput | Implement I/O objects for handling threading files |
| ThreadingProf | Calculate structural scores with info derived from threading and PHD |
| ThreadingSs2 | Calculate structural scores with info derived from threading and PSI-PRED |
| Traceback | Reconstruct the path in the alignment matrix |
| VGPFunction | Implement VGP (Variable Gap Penalty) function |
| VGPFunction2 | Implement VGP (Variable Gap Penalty) function |
 Zhou | Calculate scores for profile to profile alignment using Zhou-Zhou method |
| Biopool | |
| AminoAcid | It mplements a simple amino acid |
| AminoAcidHydrogen | Implements aminoacid hydrogens |
| 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 |
| EnergyVisitor | Base class implementing the visitor pattern |
| Group | This class implements a simple chemical group |
| Identity | Implements object id. With a "number" a "name" and a "counter" |
| IntCoordConverter | Implements methods to manage translation vector and angles between vectors |
| IntLoader | Loads components (Atoms, Groups, etc.) in internal format |
| IntSaver | Loads components (Atoms, Groups, etc.) in internal format |
| Ligand | Implements methods to verify the ligand properties |
| LigandSet | Class implements methods to manage the ligandSet |
| Loader | Base class for loading components (Atoms, Groups, etc.) |
| Monomer | Base class for components without elements |
| Nucleotide | Implements a simple nucleotide |
| OptimizationVisitor | Base class Optimizacion Patter |
| PdbLoader | Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format |
| PdbSaver | Saves components (Atoms, Groups, etc.) in standard PDB format |
| Polymer | Implements methods to manage a polymer created by components |
| 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) |
| RelLoader | Loads components (Atoms, Groups, etc.) in relative format |
| RelSaver | Save components (Atoms, Groups, etc.) in relative format |
| Saver | Base class for saving components (Atoms, Groups, etc.) |
| SeqConstructor | This class builds a spacer by concatenating the same aminoacid type for n times |
| SeqLoader | Loads components (Atoms, Groups, etc.) in SEQ format |
| SideChain | This class implements a side chain |
| 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 |
| Spacer | Implements a "Spacer" for a protein chain. Includes methods to obtain values from the atoms and its pdb information |
| XyzLoader | Loads components (Atoms, Groups, etc.) in XYZ (carthesian) format |
| XyzSaver | Saves components (Atoms, Groups, etc.) in carthesian format |
| Energy | |
| Chi1Chi2 | Class manages the angle qualities and the energy |
| EffectiveSolvationPotential | Implements a knowledge-based solvation with polar/hydrophobic information potential. A coefficient is used to normalize the propensity |
| EnergyFeatures | Interface/wrapper for energy and feature calculation for a protein chain |
| EnergyGreater | Energy operator. It compares enrgies of two Potential::ANGLES structures |
| 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 |
| PolarSolvationPotential | This class implements a knowledge-based solvation with polar/hydrophobic information potential |
| Potential | Abstract class for the energy 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 |
 Lobo | |
| CompressedLoopTableEntry | This structure allows to manage a compressed loop table information in vectors |
| globalStatistic | Methods to manages the global statistic data |
| 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 |
| 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 |
| solutionQueueElem | Struct that contains a queue element |
| VectorTransformation | This class allows to store transformation steps for transforming a vector v into v' according to the series of steps performed earlier |
1.8.6 
