database which holds all residue modifications from UniMod More...
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
| Public Member Functions | |
| Size | getNumberOfModifications () const | 
| returns the number of modifications read from the unimod.xml file  More... | |
| const ResidueModification & | getModification (Size index) const | 
| returns the modification with the given index  More... | |
| void | searchTerminalModifications (std::set< const ResidueModification * > &mods, const String &name, ResidueModification::Term_Specificity term_spec) const | 
| returns all modifications which have the given name as synonym  More... | |
| void | searchModifications (std::set< const ResidueModification * > &mods, const String &orgin, const String &mod_name, ResidueModification::Term_Specificity term_spec) const | 
| returns all modification which have the given name as synonym and the given origin  More... | |
| void | searchModifications (std::set< const ResidueModification * > &mods, const String &mod_name, ResidueModification::Term_Specificity term_spec) const | 
| returns all modification which have the given name as synonym  More... | |
| const ResidueModification & | getTerminalModification (const String &name, ResidueModification::Term_Specificity term_spec) const | 
| returns the modifications of the given name  More... | |
| const ResidueModification & | getModification (const String &residue_name, const String &mod_name, ResidueModification::Term_Specificity term_spec) const | 
| returns the modification with the given name and given residue  More... | |
| const ResidueModification & | getModification (const String &modification) const | 
| Size | findModificationIndex (const String &mod_name) const | 
| returns the index of the modification in the mods_ vector; a unique name must be given  More... | |
| void | getTerminalModificationsByDiffMonoMass (std::vector< String > &mods, DoubleReal mass, DoubleReal error, ResidueModification::Term_Specificity term_spec) | 
| query the modifications DB to get the terminal modifications with mass  More... | |
| void | getModificationsByDiffMonoMass (std::vector< String > &mods, DoubleReal mass, DoubleReal error=0.0) | 
| query the modifications DB to get the modifications with mass, without any specific origin  More... | |
| void | getModificationsByDiffMonoMass (std::vector< String > &mods, const String &residue, DoubleReal mass, DoubleReal error=0.0) | 
| query the modifications DB to get modifications with the given mass at the given residue  More... | |
| void | readFromOBOFile (const String &filename) | 
| adds modifications from a given file in OBO format  More... | |
| void | readFromUnimodXMLFile (const String &filename) | 
| adds modifications from a given file in Unimod XML format  More... | |
| void | getAllSearchModifications (std::vector< String > &modifications) | 
| get all modifications that can be used for identification searches  More... | |
| Static Public Member Functions | |
| static ModificationsDB * | getInstance () | 
| Protected Attributes | |
| std::vector < ResidueModification * > | mods_ | 
| stores the modifications  More... | |
| Map< String, std::set< const ResidueModification * > > | modification_names_ | 
| stores the mappings of (unique) names to the modifications  More... | |
| Private Member Functions | |
| Constructors and Destructors | |
| ModificationsDB () | |
| default constructor  More... | |
| ModificationsDB (const ModificationsDB &residue_db) | |
| copy constructor  More... | |
| virtual | ~ModificationsDB () | 
| destructor  More... | |
| Assignment | |
| ModificationsDB & | operator= (const ModificationsDB &aa) | 
| assignment operator  More... | |
database which holds all residue modifications from UniMod
This singleton class serves as a storage of the available modifications represented by UniMod (www.unimod.org). The modifications are identified by there name and possibly other ids from UniMod or the PSI-MOD ontology. Modifications can have different specificities, e.g. they can occur only at the termini, anywhere or only at specific amino acids.
The modifications are defined in share/OpenMS/CHEMISTRY/unimod.xml and in share/OpenMS/CHEMISTRY/PSI-MOD.obo. The unimod file can be directly downloaded from unimod.org and replaced if the modifications change.
To add a new modification, not contained in UniMod, one should follow the way described at the unimod.org website and download the file then from unimod.org. The same can be done to add support for the modifications to search engines, e.g. Mascot.
| 
 | private | 
default constructor
| 
 | private | 
copy constructor
| 
 | privatevirtual | 
destructor
returns the index of the modification in the mods_ vector; a unique name must be given
| void getAllSearchModifications | ( | std::vector< String > & | modifications | ) | 
get all modifications that can be used for identification searches
| 
 | inlinestatic | 
| const ResidueModification& getModification | ( | Size | index | ) | const | 
returns the modification with the given index
| const ResidueModification& getModification | ( | const String & | residue_name, | 
| const String & | mod_name, | ||
| ResidueModification::Term_Specificity | term_spec | ||
| ) | const | 
returns the modification with the given name and given residue
| const ResidueModification& getModification | ( | const String & | modification | ) | const | 
| void getModificationsByDiffMonoMass | ( | std::vector< String > & | mods, | 
| DoubleReal | mass, | ||
| DoubleReal | error = 0.0 | ||
| ) | 
query the modifications DB to get the modifications with mass, without any specific origin
| void getModificationsByDiffMonoMass | ( | std::vector< String > & | mods, | 
| const String & | residue, | ||
| DoubleReal | mass, | ||
| DoubleReal | error = 0.0 | ||
| ) | 
query the modifications DB to get modifications with the given mass at the given residue
| Size getNumberOfModifications | ( | ) | const | 
returns the number of modifications read from the unimod.xml file
| const ResidueModification& getTerminalModification | ( | const String & | name, | 
| ResidueModification::Term_Specificity | term_spec | ||
| ) | const | 
returns the modifications of the given name
This can either be the PSI-MOD identifier or every other unique identifier which can be found in the PSI-MOD definitions file.
To search for more than one modification searchModifications() can be used!
| ElementNotFound | is thrown if no or more than one element is found | 
| void getTerminalModificationsByDiffMonoMass | ( | std::vector< String > & | mods, | 
| DoubleReal | mass, | ||
| DoubleReal | error, | ||
| ResidueModification::Term_Specificity | term_spec | ||
| ) | 
query the modifications DB to get the terminal modifications with mass
| 
 | private | 
assignment operator
| void readFromOBOFile | ( | const String & | filename | ) | 
adds modifications from a given file in OBO format
| void readFromUnimodXMLFile | ( | const String & | filename | ) | 
adds modifications from a given file in Unimod XML format
| void searchModifications | ( | std::set< const ResidueModification * > & | mods, | 
| const String & | orgin, | ||
| const String & | mod_name, | ||
| ResidueModification::Term_Specificity | term_spec | ||
| ) | const | 
returns all modification which have the given name as synonym and the given origin
| void searchModifications | ( | std::set< const ResidueModification * > & | mods, | 
| const String & | mod_name, | ||
| ResidueModification::Term_Specificity | term_spec | ||
| ) | const | 
returns all modification which have the given name as synonym
| void searchTerminalModifications | ( | std::set< const ResidueModification * > & | mods, | 
| const String & | name, | ||
| ResidueModification::Term_Specificity | term_spec | ||
| ) | const | 
returns all modifications which have the given name as synonym
| 
 | protected | 
stores the mappings of (unique) names to the modifications
| 
 | protected | 
stores the modifications
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |