OpenStructure
contact_prediction_score.hh
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18 //------------------------------------------------------------------------------
19 #ifndef OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
20 #define OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
25 
26 /*
27  Authors: Niklaus Johner
28  Functions and objects used to calculate different scores for predicting contacts
29  from a multiple sequence alignment (MSA). Several scores are available:
30  1. Mutual information. The average product correction (apc_correction)
31  adds a correction term to account for common phylogenetic origin and inherent
32  entropy of each column. There is also a correction for small number of sequences
33  in the alignment and the possibility to use weighted mutual information.
34  2. ContactScore. For each residue pair, this score calculates the average interaction
35  energy for the amino-acid pairs in the corresponding columns of the MSA
36  3. ContactSubstitutionScore. For each residue pair, this score calculates
37  the average energy of the substitutions of amino-acid pairs in the corresponding
38  columns of the MSA.
39  */
40 namespace ost { namespace seq { namespace alg {
41 
43  std::vector <std::vector <Real> > matrix;
44  std::vector <std::pair <int,int> > sorted_indices;
45  void SetScore(int i, int j, Real score);
46  Real GetScore(int i, int j);
48  ContactPredictionScoreResult(std::vector <std::vector <Real> >);
49 };
50 
54  bool zpx_transformation=true,float small_number_correction=0.05);
55 
56 }}}
57 #endif
representation of a multiple sequence alignemnt consisting of two or more sequences
float Real
Definition: base.hh:44
ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultContactWeightMatrix()
statistical potential matrix containing interaction pseudo energies
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactSubstitutionScore(const AlignmentHandle &aln, int ref_seq_index=0, PairSubstWeightMatrix w=LoadDefaultPairSubstWeightMatrix())
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateMutualInformation(const AlignmentHandle &aln, ContactWeightMatrix w=LoadConstantContactWeightMatrix(), bool apc_correction=true, bool zpx_transformation=true, float small_number_correction=0.05)
ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadConstantContactWeightMatrix()
weight of 1 for all amino-acid pairs and 0 for gaps.
PairSubstWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultPairSubstWeightMatrix()
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactScore(const AlignmentHandle &aln, ContactWeightMatrix w=LoadDefaultContactWeightMatrix())
Definition: base.dox:1
#define DLLEXPORT_OST_SEQ_ALG
std::vector< std::pair< int, int > > sorted_indices
void SetScore(int i, int j, Real score)
ContactPredictionScoreResult(std::vector< std::vector< Real > >)
matrix to weight pairs of amino-acids.
position-independet pair substitution weight matrix