35 #ifndef OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
36 #define OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
75 static const std::string NamesOfEnzymes[SIZE_OF_ENZYMES];
86 static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
103 void setMissedCleavages(
SignedSize missed_cleavages);
109 void setEnzyme(
Enzyme enzyme);
126 void digest(
const AASequence & protein, std::vector<AASequence> & output)
const;
132 bool isLogModelEnabled()
const;
135 void setLogModelEnabled(
bool enabled);
138 double getLogThreshold()
const;
142 void setLogThreshold(
double threshold);
155 position(), AAname() {}
158 position(p), AAname(name) {}
179 p_cleave(0), p_miss(0) {}
181 p_cleave(p_c), p_miss(p_m) {}
207 #endif // OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
Definition: EnzymaticDigestion.h:81
A more convenient string class.
Definition: String.h:57
bool use_log_model_
Use the log model (only supported for 'Trypsin' with zero missed cleavages) or naive digestion (with ...
Definition: EnzymaticDigestion.h:198
BindingSite(const Size &p, const String &name)
Definition: EnzymaticDigestion.h:157
Map< BindingSite, CleavageModel > model_data_
Holds the cleavage model.
Definition: EnzymaticDigestion.h:202
Definition: EnzymaticDigestion.h:80
CleavageModel()
Definition: EnzymaticDigestion.h:178
Definition: EnzymaticDigestion.h:149
Definition: EnzymaticDigestion.h:70
Definition: EnzymaticDigestion.h:173
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
Class for the enzymatic digestion of proteins.
Definition: EnzymaticDigestion.h:64
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
bool operator<(const BindingSite &rhs) const
Definition: EnzymaticDigestion.h:160
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
BindingSite()
Definition: EnzymaticDigestion.h:154
bool operator==(const BindingSite &rhs) const
Definition: EnzymaticDigestion.h:165
double p_cleave
Definition: EnzymaticDigestion.h:175
Definition: EnzymaticDigestion.h:82
Enzyme
Possible enzymes for the digestion (adapt NamesOfEnzymes & nextCleavageSite_() if you add more enzyme...
Definition: EnzymaticDigestion.h:68
Enzyme enzyme_
Used enzyme.
Definition: EnzymaticDigestion.h:193
ConstIterator for AASequence.
Definition: AASequence.h:80
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:78
CleavageModel(const double &p_c, const double &p_m)
Definition: EnzymaticDigestion.h:180
Specificity specificity_
specificity of enzyme
Definition: EnzymaticDigestion.h:195
String AAname
Definition: EnzymaticDigestion.h:152
Definition: EnzymaticDigestion.h:71
double p_miss
Definition: EnzymaticDigestion.h:176
Size position
Definition: EnzymaticDigestion.h:151
double log_model_threshold_
Threshold to decide if position is cleaved or missed (only for the model)
Definition: EnzymaticDigestion.h:200
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
SignedSize missed_cleavages_
Number of missed cleavages.
Definition: EnzymaticDigestion.h:191