Representation of a residue. More...
#include <OpenMS/CHEMISTRY/Residue.h>
| Public Types | |
| Enums | |
| enum | ResidueType { Full = 0, Internal, NTerminal, CTerminal, AIon, BIon, CIonMinusOne, CIon, CIonPlusOne, CIonPlusTwo, XIon, YIon, ZIonMinusOne, ZIon, ZIonPlusOne, ZIonPlusTwo, SizeOfResidueType } | 
| Public Member Functions | |
| Constructors | |
| Residue () | |
| default contructor  More... | |
| Residue (const Residue &residue) | |
| copy constructor  More... | |
| Residue (const String &name, const String &three_letter_code, const String &one_letter_code, const EmpiricalFormula &formula) | |
| detailed constructor  More... | |
| virtual | ~Residue () | 
| destructor  More... | |
| Assignment | |
| Residue & | operator= (const Residue &residue) | 
| assignment operator  More... | |
| void | setName (const String &name) | 
| sets the name of the residue  More... | |
| const String & | getName () const | 
| returns the name of the residue  More... | |
| void | setShortName (const String &short_name) | 
| sets the short name of the residue, this name is used in the PeptideSequence for output  More... | |
| const String & | getShortName () const | 
| returns the short name of the residue  More... | |
| void | setSynonyms (const std::set< String > &synonyms) | 
| sets the synonyms  More... | |
| void | addSynonym (const String &synonym) | 
| adds a synonym  More... | |
| const std::set< String > & | getSynonyms () const | 
| returns the sysnonyms  More... | |
| void | setThreeLetterCode (const String &three_letter_code) | 
| sets the name of the residue as three letter code  More... | |
| const String & | getThreeLetterCode () const | 
| returns the name of the residue as three letter code  More... | |
| void | setOneLetterCode (const String &one_letter_code) | 
| sets the name as one letter code  More... | |
| const String & | getOneLetterCode () const | 
| returns the name as one letter code  More... | |
| void | addLossFormula (const EmpiricalFormula &) | 
| adds a neutral loss formula  More... | |
| void | setLossFormulas (const std::vector< EmpiricalFormula > &) | 
| sets the neutral loss formulas  More... | |
| void | addNTermLossFormula (const EmpiricalFormula &) | 
| adds N-terminal losses  More... | |
| void | setNTermLossFormulas (const std::vector< EmpiricalFormula > &) | 
| sets the N-terminal losses  More... | |
| const std::vector < EmpiricalFormula > & | getLossFormulas () const | 
| returns the neutral loss formulas  More... | |
| const std::vector < EmpiricalFormula > & | getNTermLossFormulas () const | 
| returns N-terminal loss formulas  More... | |
| void | setLossNames (const std::vector< String > &name) | 
| set the neutral loss molecule name  More... | |
| void | setNTermLossNames (const std::vector< String > &name) | 
| sets the N-terminal loss names  More... | |
| void | addLossName (const String &name) | 
| add neutral loss molecule name  More... | |
| void | addNTermLossName (const String &name) | 
| adds a N-terminal loss name  More... | |
| const std::vector< String > & | getLossNames () const | 
| gets neutral loss name (if there is one, else returns an empty string)  More... | |
| const std::vector< String > & | getNTermLossNames () const | 
| returns the N-terminal loss names  More... | |
| void | setFormula (const EmpiricalFormula &formula) | 
| set empirical formula of the residue (must be full, with N and C-terminus)  More... | |
| EmpiricalFormula | getFormula (ResidueType res_type=Full) const | 
| returns the empirical formula of the residue  More... | |
| void | setAverageWeight (DoubleReal weight) | 
| sets average weight of the residue (must be full, with N and C-terminus)  More... | |
| DoubleReal | getAverageWeight (ResidueType res_type=Full) const | 
| returns average weight of the residue  More... | |
| void | setMonoWeight (DoubleReal weight) | 
| sets mono weight of the residue (must be full, with N and C-terminus)  More... | |
| DoubleReal | getMonoWeight (ResidueType res_type=Full) const | 
| returns mono weight of the residue  More... | |
| void | setModification (const String &name) | 
| sets by the name, this mod should be present in ModificationsDB  More... | |
| const String & | getModification () const | 
| returns the name of the modification to the modification  More... | |
| void | setLowMassIons (const std::vector< EmpiricalFormula > &low_mass_ions) | 
| sets the low mass marker ions as a vector of formulas  More... | |
| const std::vector < EmpiricalFormula > & | getLowMassIons () const | 
| returns a vector of formulas with the low mass markers of the residue  More... | |
| void | setResidueSets (const std::set< String > &residues_sets) | 
| sets the residue sets the amino acid is contained in  More... | |
| void | addResidueSet (const String &residue_sets) | 
| adds a residue set to the residue sets  More... | |
| const std::set< String > & | getResidueSets () const | 
| returns the residue sets this residue is contained in  More... | |
| Predicates | |
| bool | hasNeutralLoss () const | 
| true if the residue has neutral loss  More... | |
| bool | hasNTermNeutralLosses () const | 
| true if N-terminal neutral losses are set  More... | |
| bool | operator== (const Residue &residue) const | 
| equality operator  More... | |
| bool | operator!= (const Residue &residue) const | 
| inequality operator  More... | |
| bool | operator== (char one_letter_code) const | 
| equality operator for one letter code  More... | |
| bool | operator!= (char one_letter_code) const | 
| equality operator for one letter code  More... | |
| DoubleReal | getPka () const | 
| returns the pka of the residue  More... | |
| DoubleReal | getPkb () const | 
| returns the pkb of the residue  More... | |
| DoubleReal | getPkc () const | 
| returns the pkc of the residue if it exists otherwise -1  More... | |
| DoubleReal | getPiValue () const | 
| calculates the isoelectric point using the pk* values  More... | |
| void | setPka (DoubleReal value) | 
| sets the pka of the residue  More... | |
| void | setPkb (DoubleReal value) | 
| sets the pkb of the residue  More... | |
| void | setPkc (DoubleReal value) | 
| sets the pkc of the residue  More... | |
| DoubleReal | getSideChainBasicity () const | 
| returns the side chain basicity  More... | |
| void | setSideChainBasicity (DoubleReal gb_sc) | 
| sets the side chain basicity  More... | |
| DoubleReal | getBackboneBasicityLeft () const | 
| returns the backbone basicitiy if located in N-terminal direction  More... | |
| void | setBackboneBasicityLeft (DoubleReal gb_bb_l) | 
| sets the N-terminal direction backbone basicitiy  More... | |
| DoubleReal | getBackboneBasicityRight () const | 
| returns the C-terminal direction backbone basicitiy  More... | |
| void | setBackboneBasicityRight (DoubleReal gb_bb_r) | 
| sets the C-terminal direction backbone basicity  More... | |
| bool | isModified () const | 
| true if the residue is a modified one  More... | |
| bool | isInResidueSet (const String &residue_set) | 
| true if the residue is contained in the set  More... | |
| Protected Attributes | |
| String | name_ | 
| String | short_name_ | 
| std::set< String > | synonyms_ | 
| String | three_letter_code_ | 
| String | one_letter_code_ | 
| EmpiricalFormula | formula_ | 
| EmpiricalFormula | internal_formula_ | 
| DoubleReal | average_weight_ | 
| DoubleReal | mono_weight_ | 
| bool | is_modified_ | 
| String | pre_mod_name_ | 
| String | modification_ | 
| std::vector< String > | loss_names_ | 
| std::vector< EmpiricalFormula > | loss_formulas_ | 
| std::vector< String > | NTerm_loss_names_ | 
| std::vector< EmpiricalFormula > | NTerm_loss_formulas_ | 
| DoubleReal | loss_average_weight_ | 
| DoubleReal | loss_mono_weight_ | 
| std::vector< EmpiricalFormula > | low_mass_ions_ | 
| DoubleReal | pka_ | 
| DoubleReal | pkb_ | 
| DoubleReal | pkc_ | 
| DoubleReal | gb_sc_ | 
| DoubleReal | gb_bb_l_ | 
| DoubleReal | gb_bb_r_ | 
| std::set< String > | residue_sets_ | 
| Friends | |
| std::ostream & | operator<< (std::ostream &os, const Residue &residue) | 
| ostream iterator to write the residue to a stream  More... | |
Representation of a residue.
This class represents residues. Residues can have many different attributes, like the formula physico-chemical values of properties and so on.
A very important property of residues are their modifications. By default no modification is present. Any modification which is present in the ModificationsDB can be applied, if appropriate.
| enum ResidueType | 
| Enumerator | |
|---|---|
| Full | |
| Internal | |
| NTerminal | |
| CTerminal | |
| AIon | |
| BIon | |
| CIonMinusOne | |
| CIon | |
| CIonPlusOne | |
| CIonPlusTwo | |
| XIon | |
| YIon | |
| ZIonMinusOne | |
| ZIon | |
| ZIonPlusOne | |
| ZIonPlusTwo | |
| SizeOfResidueType | 
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| Residue | ( | ) | 
default contructor
| Residue | ( | const String & | name, | 
| const String & | three_letter_code, | ||
| const String & | one_letter_code, | ||
| const EmpiricalFormula & | formula | ||
| ) | 
detailed constructor
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destructor
| void addLossFormula | ( | const EmpiricalFormula & | ) | 
adds a neutral loss formula
| void addLossName | ( | const String & | name | ) | 
add neutral loss molecule name
| void addNTermLossFormula | ( | const EmpiricalFormula & | ) | 
adds N-terminal losses
| void addNTermLossName | ( | const String & | name | ) | 
adds a N-terminal loss name
| void addResidueSet | ( | const String & | residue_sets | ) | 
adds a residue set to the residue sets
| void addSynonym | ( | const String & | synonym | ) | 
adds a synonym
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| DoubleReal getAverageWeight | ( | ResidueType | res_type = Full | ) | const | 
returns average weight of the residue
| DoubleReal getBackboneBasicityLeft | ( | ) | const | 
returns the backbone basicitiy if located in N-terminal direction
| DoubleReal getBackboneBasicityRight | ( | ) | const | 
returns the C-terminal direction backbone basicitiy
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| EmpiricalFormula getFormula | ( | ResidueType | res_type = Full | ) | const | 
returns the empirical formula of the residue
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| const std::vector<EmpiricalFormula>& getLossFormulas | ( | ) | const | 
returns the neutral loss formulas
| const std::vector<String>& getLossNames | ( | ) | const | 
gets neutral loss name (if there is one, else returns an empty string)
| const std::vector<EmpiricalFormula>& getLowMassIons | ( | ) | const | 
returns a vector of formulas with the low mass markers of the residue
| const String& getModification | ( | ) | const | 
returns the name of the modification to the modification
| DoubleReal getMonoWeight | ( | ResidueType | res_type = Full | ) | const | 
returns mono weight of the residue
| const String& getName | ( | ) | const | 
returns the name of the residue
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| const std::vector<EmpiricalFormula>& getNTermLossFormulas | ( | ) | const | 
returns N-terminal loss formulas
| const std::vector<String>& getNTermLossNames | ( | ) | const | 
returns the N-terminal loss names
| const String& getOneLetterCode | ( | ) | const | 
returns the name as one letter code
Referenced by AAIndex::calculateGB().
| DoubleReal getPiValue | ( | ) | const | 
calculates the isoelectric point using the pk* values
| DoubleReal getPka | ( | ) | const | 
returns the pka of the residue
| DoubleReal getPkb | ( | ) | const | 
returns the pkb of the residue
| DoubleReal getPkc | ( | ) | const | 
returns the pkc of the residue if it exists otherwise -1
| const std::set<String>& getResidueSets | ( | ) | const | 
returns the residue sets this residue is contained in
| 
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returns the ion name given as a residue type
| const String& getShortName | ( | ) | const | 
returns the short name of the residue
| DoubleReal getSideChainBasicity | ( | ) | const | 
returns the side chain basicity
| const std::set<String>& getSynonyms | ( | ) | const | 
returns the sysnonyms
| const String& getThreeLetterCode | ( | ) | const | 
returns the name of the residue as three letter code
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| bool hasNeutralLoss | ( | ) | const | 
true if the residue has neutral loss
| bool hasNTermNeutralLosses | ( | ) | const | 
true if N-terminal neutral losses are set
| bool isInResidueSet | ( | const String & | residue_set | ) | 
true if the residue is contained in the set
| bool isModified | ( | ) | const | 
true if the residue is a modified one
| bool operator!= | ( | const Residue & | residue | ) | const | 
inequality operator
| bool operator!= | ( | char | one_letter_code | ) | const | 
equality operator for one letter code
| bool operator== | ( | const Residue & | residue | ) | const | 
equality operator
| bool operator== | ( | char | one_letter_code | ) | const | 
equality operator for one letter code
| void setAverageWeight | ( | DoubleReal | weight | ) | 
sets average weight of the residue (must be full, with N and C-terminus)
| void setBackboneBasicityLeft | ( | DoubleReal | gb_bb_l | ) | 
sets the N-terminal direction backbone basicitiy
| void setBackboneBasicityRight | ( | DoubleReal | gb_bb_r | ) | 
sets the C-terminal direction backbone basicity
| void setFormula | ( | const EmpiricalFormula & | formula | ) | 
set empirical formula of the residue (must be full, with N and C-terminus)
| void setLossFormulas | ( | const std::vector< EmpiricalFormula > & | ) | 
sets the neutral loss formulas
| void setLossNames | ( | const std::vector< String > & | name | ) | 
set the neutral loss molecule name
| void setLowMassIons | ( | const std::vector< EmpiricalFormula > & | low_mass_ions | ) | 
sets the low mass marker ions as a vector of formulas
| void setModification | ( | const String & | name | ) | 
sets by the name, this mod should be present in ModificationsDB
| void setMonoWeight | ( | DoubleReal | weight | ) | 
sets mono weight of the residue (must be full, with N and C-terminus)
| void setName | ( | const String & | name | ) | 
sets the name of the residue
Accessors
| void setNTermLossFormulas | ( | const std::vector< EmpiricalFormula > & | ) | 
sets the N-terminal losses
| void setNTermLossNames | ( | const std::vector< String > & | name | ) | 
sets the N-terminal loss names
| void setOneLetterCode | ( | const String & | one_letter_code | ) | 
sets the name as one letter code
| void setPka | ( | DoubleReal | value | ) | 
sets the pka of the residue
| void setPkb | ( | DoubleReal | value | ) | 
sets the pkb of the residue
| void setPkc | ( | DoubleReal | value | ) | 
sets the pkc of the residue
| void setResidueSets | ( | const std::set< String > & | residues_sets | ) | 
sets the residue sets the amino acid is contained in
| void setShortName | ( | const String & | short_name | ) | 
sets the short name of the residue, this name is used in the PeptideSequence for output
| void setSideChainBasicity | ( | DoubleReal | gb_sc | ) | 
sets the side chain basicity
| void setSynonyms | ( | const std::set< String > & | synonyms | ) | 
sets the synonyms
| void setThreeLetterCode | ( | const String & | three_letter_code | ) | 
sets the name of the residue as three letter code
| 
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ostream iterator to write the residue to a stream
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |