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 |