#include <OpenMS/CHEMISTRY/Residue.h>
Typedefs and Constants | |
typedef std::vector < EmpiricalFormula > ::const_iterator | LowMassConstIterator |
typedef std::vector < EmpiricalFormula >::iterator | LowMassIterator |
static const EmpiricalFormula & | getInternalToFull () |
static DoubleReal | getInternalToFullAverageWeight () |
static DoubleReal | getInternalToFullMonoWeight () |
static const EmpiricalFormula & | getNTerminalToFull () |
static DoubleReal | getNTerminalToFullAverageWeight () |
static DoubleReal | getNTerminalToFullMonoWeight () |
static const EmpiricalFormula & | getCTerminalToFull () |
static DoubleReal | getCTerminalToFullAverageWeight () |
static DoubleReal | getCTerminalToFullMonoWeight () |
static const EmpiricalFormula & | getBIonToFull () |
static DoubleReal | getBIonToFullAverageWeight () |
static DoubleReal | getBIonToFullMonoWeight () |
static const EmpiricalFormula & | getAIonToFull () |
static DoubleReal | getAIonToFullAverageWeight () |
static DoubleReal | getAIonToFullMonoWeight () |
static const EmpiricalFormula & | getYIonToFull () |
static DoubleReal | getYIonToFullAverageWeight () |
static DoubleReal | getYIonToFullMonoWeight () |
static const EmpiricalFormula & | getCIonToFull () |
static DoubleReal | getCIonToFullAverageWeight () |
static DoubleReal | getCIonToFullMonoWeight () |
static const EmpiricalFormula & | getXIonToFull () |
static DoubleReal | getXIonToFullAverageWeight () |
static DoubleReal | getXIonToFullMonoWeight () |
static const EmpiricalFormula & | getZIonToFull () |
static DoubleReal | getZIonToFullAverageWeight () |
static DoubleReal | getZIonToFullMonoWeight () |
Public Types | |
Enums | |
enum | ResidueType { Full = 0, Internal, NTerminal, CTerminal, AIon, BIon, CIon, XIon, YIon, ZIon } |
Public Member Functions | |
Constructors | |
Residue () | |
default contructor | |
Residue (const Residue &residue) | |
copy constructor | |
Residue (const String &name, const String &three_letter_code, const String &one_letter_code, const EmpiricalFormula &formula, const EmpiricalFormula &neutral_loss) | |
detailed constructor | |
virtual | ~Residue () |
destructor | |
Assignment | |
Residue & | operator= (const Residue &residue) |
assignment operator | |
void | setName (const String &name) |
sets the name of the residue | |
const String & | getName () const |
returns the name of the residue | |
void | setShortName (const String &short_name) |
sets the short name of the residue, this name is used in the PeptideSequence for output | |
const String & | getShortName () const |
returns the short name of the residue | |
void | setSynonyms (const std::set< String > &synonyms) |
sets the synonyms | |
void | addSynonym (const String &synonym) |
adds a synonym | |
const std::set< String > & | getSynonyms () const |
returns the sysnonyms | |
void | setThreeLetterCode (const String &three_letter_code) |
sets the name of the residue as three letter code | |
const String & | getThreeLetterCode () const |
returns the name of the residue as three letter code | |
void | setOneLetterCode (const String &one_letter_code) |
sets the name as one letter code | |
const String & | getOneLetterCode () const |
returns the name as one letter code | |
void | setLossFormula (const EmpiricalFormula &) |
sets the neutral loss formula (if there is one) | |
const EmpiricalFormula & | getLossFormula () const |
returns the neutral loss formula (or just an empty string if there is none) | |
void | setLossAverageWeight (DoubleReal weight) |
sets the average weight of the neutral loss molecule | |
DoubleReal | getLossAverageWeight () const |
return the average weight of the neutral loss molecule | |
void | setLossMonoWeight (DoubleReal weight) |
sets the mono isotopic weight of the neutral loss molecule | |
DoubleReal | getLossMonoWeight () const |
returns the mono isotopic weight of the neutral loss molecule | |
void | setLossName (const String &name) |
set the neutral loss molecule weight (if there is one) | |
const String & | getLossName () const |
gets neutral loss name (if there is one, else returns an empty string) | |
void | setFormula (const EmpiricalFormula &formula, ResidueType res_type=Full) |
set empirical formula of the residue | |
EmpiricalFormula | getFormula (ResidueType res_type=Full) const |
returns the empirical formula of thre residue | |
void | setAverageWeight (DoubleReal weight, ResidueType res_type=Full) |
sets average weight of the residue | |
DoubleReal | getAverageWeight (ResidueType res_type=Full) const |
returns average weight of the residue | |
void | setMonoWeight (DoubleReal weight, ResidueType res_type=Full) |
sets mono weight of the residue | |
DoubleReal | getMonoWeight (ResidueType res_type=Full) const |
returns mono weight of the residue | |
void | setModification (ResidueModification *modification) |
sets the modification pointer | |
const ResidueModification * | getModification () const |
returns a pointer to the modification, if the residue is unmodified, 0 is returned | |
void | setUnmodifiedName (const String &name) |
sets the name of the unmodified residue | |
const String & | getUnmodifiedName () const |
returns the name of the unmodified residue | |
void | setLowMassIons (const std::vector< EmpiricalFormula > &low_mass_ions) |
sets the low mass marker ions as a vector of formulas | |
const std::vector < EmpiricalFormula > & | getLowMassIons () const |
returns a vector of formulas with the low mass markers of the residue | |
Predicates | |
bool | hasNeutralLoss () const |
true if the residue has neutral loss | |
bool | operator== (const Residue &residue) const |
equality operator | |
bool | operator!= (const Residue &residue) const |
inequality operator | |
bool | operator== (char one_letter_code) const |
equality operator for one letter code | |
bool | operator!= (char one_letter_code) const |
equality operator for one letter code | |
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 | |
DoubleReal | getPiValue () const |
calculates the isoelectric point using the pk* values | |
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 | |
DoubleReal | getSideChainBasicity () const |
returns the side chain basicity | |
void | setSideChainBasicity (DoubleReal gb_sc) |
sets the side chain basicity | |
DoubleReal | getBackboneBasicityLeft () const |
returns the backbone basicitiy if located in N-terminal direction | |
void | setBackboneBasicityLeft (DoubleReal gb_bb_l) |
sets the N-terminal direction backbone basicitiy | |
DoubleReal | getBackboneBasicityRight () const |
returns the C-terminal direction backbone basicitiy | |
void | setBackboneBasicityRight (DoubleReal gb_bb_r) |
sets the C-terminal direction backbone basicity | |
bool | isModified () const |
true if the residue is a modified one | |
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_ |
ResidueModification * | modification_ |
String | loss_name_ |
EmpiricalFormula | loss_formula_ |
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_ |
Friends | |
std::ostream & | operator<< (std::ostream &os, const Residue &residue) |
ostream iterator to write the residue to a stream |
typedef std::vector<EmpiricalFormula>::const_iterator LowMassConstIterator |
typedef std::vector<EmpiricalFormula>::iterator LowMassIterator |
enum ResidueType |
Residue | ( | ) |
default contructor
Residue | ( | const String & | name, | |
const String & | three_letter_code, | |||
const String & | one_letter_code, | |||
const EmpiricalFormula & | formula, | |||
const EmpiricalFormula & | neutral_loss | |||
) |
detailed constructor
virtual ~Residue | ( | ) | [virtual] |
destructor
static const EmpiricalFormula& getInternalToFull | ( | ) | [inline, static] |
static DoubleReal getInternalToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getInternalToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getNTerminalToFull | ( | ) | [inline, static] |
static DoubleReal getNTerminalToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getNTerminalToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getCTerminalToFull | ( | ) | [inline, static] |
static DoubleReal getCTerminalToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getCTerminalToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getBIonToFull | ( | ) | [inline, static] |
static DoubleReal getBIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getBIonToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getAIonToFull | ( | ) | [inline, static] |
static DoubleReal getAIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getAIonToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getYIonToFull | ( | ) | [inline, static] |
static DoubleReal getYIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getYIonToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getCIonToFull | ( | ) | [inline, static] |
static DoubleReal getCIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getCIonToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getXIonToFull | ( | ) | [inline, static] |
static DoubleReal getXIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getXIonToFullMonoWeight | ( | ) | [inline, static] |
static const EmpiricalFormula& getZIonToFull | ( | ) | [inline, static] |
static DoubleReal getZIonToFullAverageWeight | ( | ) | [inline, static] |
static DoubleReal getZIonToFullMonoWeight | ( | ) | [inline, static] |
void setName | ( | const String & | name | ) |
sets the name of the residue
Accessors
const String& getName | ( | ) | const |
returns the name of the residue
void setShortName | ( | const String & | short_name | ) |
sets the short name of the residue, this name is used in the PeptideSequence for output
const String& getShortName | ( | ) | const |
returns the short name of the residue
void setSynonyms | ( | const std::set< String > & | synonyms | ) |
sets the synonyms
void addSynonym | ( | const String & | synonym | ) |
adds a synonym
const std::set<String>& getSynonyms | ( | ) | const |
returns the sysnonyms
void setThreeLetterCode | ( | const String & | three_letter_code | ) |
sets the name of the residue as three letter code
const String& getThreeLetterCode | ( | ) | const |
returns the name of the residue as three letter code
void setOneLetterCode | ( | const String & | one_letter_code | ) |
sets the name as one letter code
const String& getOneLetterCode | ( | ) | const |
returns the name as one letter code
void setLossFormula | ( | const EmpiricalFormula & | ) |
sets the neutral loss formula (if there is one)
const EmpiricalFormula& getLossFormula | ( | ) | const |
returns the neutral loss formula (or just an empty string if there is none)
void setLossAverageWeight | ( | DoubleReal | weight | ) |
sets the average weight of the neutral loss molecule
DoubleReal getLossAverageWeight | ( | ) | const |
return the average weight of the neutral loss molecule
void setLossMonoWeight | ( | DoubleReal | weight | ) |
sets the mono isotopic weight of the neutral loss molecule
DoubleReal getLossMonoWeight | ( | ) | const |
returns the mono isotopic weight of the neutral loss molecule
void setLossName | ( | const String & | name | ) |
set the neutral loss molecule weight (if there is one)
const String& getLossName | ( | ) | const |
gets neutral loss name (if there is one, else returns an empty string)
void setFormula | ( | const EmpiricalFormula & | formula, | |
ResidueType | res_type = Full | |||
) |
set empirical formula of the residue
EmpiricalFormula getFormula | ( | ResidueType | res_type = Full |
) | const |
returns the empirical formula of thre residue
void setAverageWeight | ( | DoubleReal | weight, | |
ResidueType | res_type = Full | |||
) |
sets average weight of the residue
DoubleReal getAverageWeight | ( | ResidueType | res_type = Full |
) | const |
returns average weight of the residue
void setMonoWeight | ( | DoubleReal | weight, | |
ResidueType | res_type = Full | |||
) |
sets mono weight of the residue
DoubleReal getMonoWeight | ( | ResidueType | res_type = Full |
) | const |
returns mono weight of the residue
void setModification | ( | ResidueModification * | modification | ) |
sets the modification pointer
const ResidueModification* getModification | ( | ) | const |
returns a pointer to the modification, if the residue is unmodified, 0 is returned
void setUnmodifiedName | ( | const String & | name | ) |
sets the name of the unmodified residue
const String& getUnmodifiedName | ( | ) | const |
returns the name of the unmodified residue
void setLowMassIons | ( | const std::vector< EmpiricalFormula > & | low_mass_ions | ) |
sets the low mass marker ions as a vector of formulas
const std::vector<EmpiricalFormula>& getLowMassIons | ( | ) | const |
returns a vector of formulas with the low mass markers of the residue
bool hasNeutralLoss | ( | ) | const |
true if the residue has neutral loss
bool operator== | ( | const Residue & | residue | ) | const |
equality operator
bool operator!= | ( | const Residue & | residue | ) | const |
inequality operator
bool operator== | ( | char | one_letter_code | ) | const |
equality operator for one letter code
bool operator!= | ( | char | one_letter_code | ) | const |
equality operator for one letter code
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
DoubleReal getPiValue | ( | ) | const |
calculates the isoelectric point using the pk* values
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
DoubleReal getSideChainBasicity | ( | ) | const |
returns the side chain basicity
void setSideChainBasicity | ( | DoubleReal | gb_sc | ) |
sets the side chain basicity
DoubleReal getBackboneBasicityLeft | ( | ) | const |
returns the backbone basicitiy if located in N-terminal direction
void setBackboneBasicityLeft | ( | DoubleReal | gb_bb_l | ) |
sets the N-terminal direction backbone basicitiy
DoubleReal getBackboneBasicityRight | ( | ) | const |
returns the C-terminal direction backbone basicitiy
void setBackboneBasicityRight | ( | DoubleReal | gb_bb_r | ) |
sets the C-terminal direction backbone basicity
bool isModified | ( | ) | const |
true if the residue is a modified one
std::ostream& operator<< | ( | std::ostream & | os, | |
const Residue & | residue | |||
) | [friend] |
ostream iterator to write the residue to a stream
String short_name_ [protected] |
String three_letter_code_ [protected] |
String one_letter_code_ [protected] |
EmpiricalFormula formula_ [protected] |
EmpiricalFormula internal_formula_ [protected] |
DoubleReal average_weight_ [protected] |
DoubleReal mono_weight_ [protected] |
bool is_modified_ [protected] |
String pre_mod_name_ [protected] |
ResidueModification* modification_ [protected] |
String loss_name_ [protected] |
EmpiricalFormula loss_formula_ [protected] |
DoubleReal loss_average_weight_ [protected] |
DoubleReal loss_mono_weight_ [protected] |
std::vector<EmpiricalFormula> low_mass_ions_ [protected] |
DoubleReal pka_ [protected] |
DoubleReal pkb_ [protected] |
DoubleReal pkc_ [protected] |
DoubleReal gb_sc_ [protected] |
DoubleReal gb_bb_l_ [protected] |
DoubleReal gb_bb_r_ [protected] |
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |