19 #ifndef OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
20 #define OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
40 namespace ost {
namespace seq {
namespace alg {
43 std::vector <std::vector <Real> >
matrix;
45 void SetScore(
int i,
int j,
Real score);
46 Real GetScore(
int i,
int j);
47 void RefreshSortedIndices();
54 bool zpx_transformation=
true,
float small_number_correction=0.05);
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)
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactScore(const AlignmentHandle &aln, ContactWeightMatrix w=LoadDefaultContactWeightMatrix())
#define DLLEXPORT_OST_SEQ_ALG
PairSubstWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultPairSubstWeightMatrix()
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactSubstitutionScore(const AlignmentHandle &aln, int ref_seq_index=0, PairSubstWeightMatrix w=LoadDefaultPairSubstWeightMatrix())
position-independet pair substitution weight matrix
ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultContactWeightMatrix()
statistical potential matrix containing interaction pseudo energies
representation of a multiple sequence alignemnt consisting of two or more sequences ...
ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadConstantContactWeightMatrix()
weight of 1 for all amino-acid pairs and 0 for gaps.