residue data base which holds residues More...
#include <OpenMS/CHEMISTRY/ResidueDB.h>
Public Types | |
Typedefs | |
| typedef std::set< Residue * > ::iterator | ResidueIterator |
| typedef std::set< const Residue * >::const_iterator | ResidueConstIterator |
Public Member Functions | |
Constructors and Destructors | |
| virtual | ~ResidueDB () |
| destructor More... | |
Accessors | |
| Size | getNumberOfResidues () const |
| returns the number of residues stored More... | |
| Size | getNumberOfModifiedResidues () const |
| const Residue * | getResidue (const String &name) const |
| returns a pointer to the residue with name, 3 letter code or 1 letter code name More... | |
| const Residue * | getModifiedResidue (const String &name) |
| const Residue * | getModifiedResidue (const Residue *residue, const String &name) |
| const std::set< const Residue * > | getResidues (const String &residue_set="All") const |
| returns a set of all residues stored in this residue db More... | |
| const std::set< String > & | getResidueSets () const |
| returns all residue sets that are registered which this instance More... | |
| void | setResidues (const String &filename) |
| sets the residues from given file More... | |
| void | addResidue (const Residue &residue) |
| adds a residue, i.e. a unkown residue, where only the weight is known More... | |
Predicates | |
| bool | hasResidue (const String &name) const |
| returns true if the db contains a residue with the given name More... | |
| bool | hasResidue (const Residue *residue) const |
| returns true if the db contains the residue of the given pointer More... | |
Iterators | |
| ResidueIterator | beginResidue () |
| ResidueIterator | endResidue () |
| ResidueConstIterator | beginResidue () const |
| ResidueConstIterator | endResidue () const |
Static Public Member Functions | |
| static ResidueDB * | getInstance () |
| this member function serves as a replacement of the constructor More... | |
Protected Member Functions | |
| void | readResiduesFromFile_ (const String &filename) |
| reads residues from the given file More... | |
| Residue * | parseResidue_ (Map< String, String > &values) |
| parses a residue, given the key/value pairs from i.e. an XML file More... | |
| void | clear_ () |
| deletes all sub-instances of the stored data like modifications and residues More... | |
| void | clearResidues_ () |
| clears the residues More... | |
| void | buildResidueNames_ () |
| builds an index of residue names for fast access, synonyms are also considered More... | |
| void | addResidue_ (Residue *residue) |
Private Constructors | |
| ResidueDB () | |
| default constructor More... | |
| ResidueDB (const ResidueDB &residue_db) | |
| copy constructor More... | |
Assignment | |
| ResidueDB & | operator= (const ResidueDB &aa) |
| assignment operator More... | |
Protected Attributes | |
| Map< String, Residue * > | residue_names_ |
| Map< String, Map< String, Residue * > > | residue_mod_names_ |
| std::set< Residue * > | residues_ |
| std::set< const Residue * > | const_residues_ |
| std::set< Residue * > | modified_residues_ |
| std::set< const Residue * > | const_modified_residues_ |
| Map< String, std::set< const Residue * > > | residues_by_set_ |
| std::set< String > | residue_sets_ |
residue data base which holds residues
The residues stored in this DB are defined in a XML file under data/CHEMISTRY/residues.xml
By default no modified residues are stored in an instance. However, if one queries the instance with getModifiedResidue, a new modified residue is added.
| typedef std::set<const Residue *>::const_iterator ResidueConstIterator |
| typedef std::set<Residue *>::iterator ResidueIterator |
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default constructor
| void addResidue | ( | const Residue & | residue | ) |
adds a residue, i.e. a unkown residue, where only the weight is known
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builds an index of residue names for fast access, synonyms are also considered
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deletes all sub-instances of the stored data like modifications and residues
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clears the residues
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this member function serves as a replacement of the constructor
| Size getNumberOfModifiedResidues | ( | ) | const |
| Size getNumberOfResidues | ( | ) | const |
returns the number of residues stored
returns a pointer to the residue with name, 3 letter code or 1 letter code name
returns a set of all residues stored in this residue db
The possible residues are defined in share/OpenMS/CHEMISTRY/Residues.xml. At the moment the following sets are available: All - all residues stored in the file Natural20 - default 20 naturally occuring residues Natural19WithoutI - default natural amino acids, excluding isoleucine (isobaric to leucine) Natural19WithoutL - default natural amino acids, excluding leucine (isobaric to isoleucine) Natural19J - default natural amino acids, (isobaric leucine/isoleucine are marked by 'J') AmbiguousWithoutX - all amino acids, including ambiguous ones B (asparagine or aspartate) Z (glutamine or glutamate) J (isoleucine or leucine) Ambiguous - all amino acids including all ambiguous ones (X can be every other amino acid) AllNatural - naturally occuring residues, including selenocysteine (U)
| const std::set<String>& getResidueSets | ( | ) | const |
returns all residue sets that are registered which this instance
| bool hasResidue | ( | const String & | name | ) | const |
returns true if the db contains a residue with the given name
| bool hasResidue | ( | const Residue * | residue | ) | const |
returns true if the db contains the residue of the given pointer
parses a residue, given the key/value pairs from i.e. an XML file
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reads residues from the given file
| void setResidues | ( | const String & | filename | ) |
sets the residues from given file
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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 |