35 #ifndef OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
36 #define OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
74 static const std::string NamesOfEnzymes[SIZE_OF_ENZYMES];
85 static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];
102 void setMissedCleavages(
SignedSize missed_cleavages);
108 void setEnzyme(
Enzyme enzyme);
125 void digest(
const AASequence & protein, std::vector<AASequence> & output)
const;
131 bool isLogModelEnabled()
const;
134 void setLogModelEnabled(
bool enabled);
154 position(), AAname() {}
157 position(p), AAname(name) {}
178 p_cleave(0), p_miss(0) {}
180 p_cleave(p_c), p_miss(p_m) {}
206 #endif // OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
A more convenient string class.
Definition: String.h:56
bool use_log_model_
use the log model or naive digestion (with missed cleavages)
Definition: EnzymaticDigestion.h:197
BindingSite(const Size &p, const String &name)
Definition: EnzymaticDigestion.h:156
Map< BindingSite, CleavageModel > model_data_
Holds the cleavage model.
Definition: EnzymaticDigestion.h:201
CleavageModel()
Definition: EnzymaticDigestion.h:177
Definition: EnzymaticDigestion.h:148
Definition: EnzymaticDigestion.h:172
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:151
Definition: EnzymaticDigestion.h:81
Class for the enzymatic digestion of proteins.
Definition: EnzymaticDigestion.h:64
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
bool operator<(const BindingSite &rhs) const
Definition: EnzymaticDigestion.h:159
DoubleReal p_miss
Definition: EnzymaticDigestion.h:175
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:77
Definition: EnzymaticDigestion.h:79
Definition: EnzymaticDigestion.h:70
BindingSite()
Definition: EnzymaticDigestion.h:153
bool operator==(const BindingSite &rhs) const
Definition: EnzymaticDigestion.h:164
Definition: EnzymaticDigestion.h:80
Enzyme enzyme_
Used enzyme.
Definition: EnzymaticDigestion.h:192
DoubleReal log_model_threshold_
Threshold to decide if position is cleaved or missed (only for the model)
Definition: EnzymaticDigestion.h:199
ConstIterator for AASequence.
Definition: AASequence.h:94
Enzyme
Possible enzymes for the digestion (adapt NamesOfEnzymes & nextCleavageSite_() if you add more enzyme...
Definition: EnzymaticDigestion.h:68
Specificity specificity_
specificity of enzyme
Definition: EnzymaticDigestion.h:194
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
String AAname
Definition: EnzymaticDigestion.h:151
CleavageModel(const DoubleReal &p_c, const DoubleReal &p_m)
Definition: EnzymaticDigestion.h:179
Size position
Definition: EnzymaticDigestion.h:150
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
SignedSize missed_cleavages_
Number of missed cleavages.
Definition: EnzymaticDigestion.h:190
DoubleReal p_cleave
Definition: EnzymaticDigestion.h:174