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