Library Lib_General64

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Classes

AminoAcidAnyType

AminoAcidEqualType

AminoAcidType

AminoAcid_HHAG_Type

AminoAcid_HPMPAG_Type

AminoAcid_UserType

AtomGrid

AtomMolecule

AuxFunctions

BLOSUM62_only_positive_Selector

BLOSUM62positive_Selector

BMatch

Defines a match object used to build and refine matches between Molecule type objects. Matches are build by matching pairs of Particles from each Molecule.

BaseGrid

This class provides discrete representation of the molecule. The molecule is represented by a grid. Each voxel of the grid can be marked with DataT.

BestFit

BioCoreSelector

CompleteMolecule

DebOut

DistProbability

DistProbabilitySSE

DynProg

DynProg2D

DynProg2Dw

FMatch

Defines a match object used to build and refine matches between Molecule type objects. Matches are build by matching pairs of Particles from each Molecule.

FMolecule

Template defines a collection of Particles that make up a Molecule. Among others class hosts a PDB file readr and linear algebra operators.

FastClustering

Fast Clustering based on three points.

GeomAndMatrix_Selector

GeomPAndMatrix_Selector

GeomProfile

Structural profile.

GeomSelector

GeomSelectorChainEQ

HGeomHash

Helix

This class defines the information on the secondary structure alpha helix.

Log

Matrix_only_Selector

PAM250_only_positive_Selector

PAM250positive_Selector

PositionProfile

ProtSequence

Container for a protein sequence.

ProteinSequence

Holds a protein sequence.

SSEGeomPAndMatrix_Selector

SSgeomAndMatrix_Selector

SecondStruct

This class encapsulate all the reading of the secondary structure from the PDB file and gives various methods of verification on them

SequenceProfile

Sheet

This class defines a beta sheet that is constructed from beta strands

SimpleDynProg

Implements simplified version of 2D matrix dynamic programming algorithm. Matrix values are only 0 or 1.

Staccato

Strand

This class defines strand that is a part of the beta sheet.

StrandConnection

This class defines the connection between two strands in the same beta sheet.

StructureBasedMSA

TMolecule

Extension of the Molecule class. Holds 3 reference points, usually the most farthest points, that are used to answer the clustering question - the distance between two transformations.

hash_map2

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Data

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Global Functions

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template < class TMatch,class Mol, class PSelector> TMatch getCorrespondance(leda_GRAPH< int, float>& G, const leda_node* nodesModel, const leda_node* nodesTarget, const leda_list< leda_node>& listModelNodes, const leda_list< leda_node>& listTargetNodes, const Mol& molModel,const Mol& molTarget,float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol, class PSelector>
TMatch getCorrespondance(leda_GRAPH< int, float>& G,
			 const leda_node* nodesModel,
			 const leda_node* nodesTarget,
			 const leda_list< leda_node>& listModelNodes,
			 const leda_list< leda_node>& listTargetNodes,
			 const Mol& molModel,const Mol& molTarget,float fDistThr)  

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template < class TMatch,class Mol, class PSelector> TMatch getCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol, class PSelector>
TMatch getCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)  

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template < class TMatch,class Mol,class VecImpl> TMatch getCorrespondance(const Mol& molModel,const VecImpl& vecModel, const Mol& molTarget,const VecImpl& vecTarget, float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol,class VecImpl>
TMatch getCorrespondance(const Mol& molModel,const VecImpl& vecModel,
			 const Mol& molTarget,const VecImpl& vecTarget,
			 float fDistThr)  

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template < class TMatch,class Mol, class PSelector> TMatch getFastCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol, class PSelector>
TMatch getFastCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)  

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template < class TMatch,class Mol, class PSelector> TMatch getFastCorrespondanceScore(const Mol& molModel,const Mol& molTarget,float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol, class PSelector>
TMatch getFastCorrespondanceScore(const Mol& molModel,const Mol& molTarget,float fDistThr)  

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template < class TMatch,class Mol,class VecImpl> TMatch getFastCorrespondance(const Mol& molModel,const VecImpl& vecModel, const Mol& molTarget,const VecImpl& vecTarget, float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol,class VecImpl>
TMatch getFastCorrespondance(const Mol& molModel,const VecImpl& vecModel,
                        const Mol& molTarget,const VecImpl& vecTarget,
                        float fDistThr)  

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template < class TMatch,class Mol, class PSelector> TMatch getSeqOrderedCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol, class PSelector>
TMatch getSeqOrderedCorrespondance(const Mol& molModel,const Mol& molTarget,float fDistThr)  

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template < class TMatch,class Mol> TMatch getSeqOrderedGlobalCorrespondance(const Mol& mol1,const Mol& mol2)

/* Mol should implemet [] access operator and size() function */
/* works faster if the first molecule is smaller */ 
template < class TMatch,class Mol>
TMatch getSeqOrderedGlobalCorrespondance(const Mol& mol1,const Mol& mol2)  

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template < class TMatch,class Mol> float getSeqOrderedGlobalCorrespondanceWithScaling(const Mol& mol1,const Mol& mol2)

taken from gi/RMSDhits. No prior transformation or correspondence is required if one curve is shorter than it is upscaled to the longer curve and rmsd between all points is computed. Should be somewhat similar to area between two curves.

template < class TMatch,class Mol>
float getSeqOrderedGlobalCorrespondanceWithScaling(const Mol& mol1,const Mol& mol2)  

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template< class T_Molecule, class T_PSelector> vector< vector< int> > multCorrespondence(const T_Molecule& i_refMol, vector< T_Molecule* >& i_vMols, vector< RigidTrans3 >& i_vRigidTrans, float i_fDistThr)

template< class T_Molecule, class T_PSelector>
vector< vector< int> > multCorrespondence(const T_Molecule& i_refMol,
					vector< T_Molecule* >& i_vMols,
					vector< RigidTrans3 >& i_vRigidTrans,
					float i_fDistThr)  

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/*Alex 05/10 - 
1. To save all the molecule in grid and access with the pivot.
2. To save according to the order of the first molecule
Goal: to go over the pseudocenetrs of the first molecule and check that there is a 
matching pseudcenter in the rest */

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template < class TMatch,class Mol, class PSelector> TMatch getCorrespondanceHash(const GeomHash < Vector3,int>& gHash, const Mol& molTarget, const Mol& molModel, float fDistThr)

/*
 match is redundant
*/
template < class TMatch,class Mol, class PSelector>
TMatch getCorrespondanceHash(const GeomHash < Vector3,int>& gHash,	
			     const Mol&  molTarget,
			     const Mol&  molModel, float fDistThr)                  

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ifdef PHARMA template< class TMatch,class T_Molecule, class T_PSelector> TMatch getPhaCorrespondance(const T_Molecule& molModel,const T_Molecule& molTarget,float fDistThr)

#ifdef PHARMA
template< class TMatch,class T_Molecule, class T_PSelector>
TMatch getPhaCorrespondance(const T_Molecule& molModel,const T_Molecule& molTarget,float fDistThr)  

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template < class TMol, class PSelector> vector< vector< int> > multPhaCorrespondence(const TMol& i_refMol, vector< TMol* >& i_vMols, vector< RigidTrans3 >& o_vRigidTrans, float i_fDistThr)

template < class TMol, class PSelector>
vector< vector< int> > multPhaCorrespondence(const TMol& i_refMol,
					vector< TMol* >& i_vMols,
					vector< RigidTrans3 >& o_vRigidTrans,
					float i_fDistThr)  

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template< class T> T max4(const T x, const T y, const T z,const T t) ;

template< class T>
inline T max4(const T x, const T y, const T z,const T t)                                                          ;

Function is currently defined inline.

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template< class TSequence> ostream& operator<<(ostream& s, const MSA< TSequence>& sp)

template< class TSequence>
ostream& operator<<(ostream& s, const MSA< TSequence>& sp)                        

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template< class T> bool IF_SSE(const T& x) ;

Template function

template< class T>
inline bool IF_SSE(const T& x)                                                                                                       
;

Function is currently defined inline.

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typedef GeomAndMatrix_Selector< AminoAcidScore::PAM250> PAM250_Selector;

typedef GeomAndMatrix_Selector< AminoAcidScore::PAM250> PAM250_Selector;

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typedef GeomAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_Selector;

typedef GeomAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_Selector;

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typedef SSgeomAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_SSE_Selector;

typedef SSgeomAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_SSE_Selector;

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typedef GeomPAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_DistProbability_Selector;

typedef GeomPAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_DistProbability_Selector;

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typedef SSEGeomPAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_SSE_DistProbability_Selector;

typedef SSEGeomPAndMatrix_Selector< AminoAcidScore::BLOSUM62> BLOSUM62_SSE_DistProbability_Selector;

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typedef hash_map< unsigned int, pair< char,short> >::iterator HashIter;

Maps a residue index to its SSE number

  typedef hash_map< unsigned int, pair< char,short> >::iterator HashIter;

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void staccato_init()

void staccato_init()                                                                                                                                   

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