OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called.
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#include <OpenMS/CHEMISTRY/ResidueDB.h>
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| bool | hasResidue (const std::string &name) const |
| | returns true if the db contains a residue with the given name
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| bool | hasResidue (const Residue *residue) const |
| | returns true if the db contains the residue of the given pointer
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| void | initResidues_ () |
| | initializes all residues by building
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OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called.
- Note
- The database is immutable from a caller's perspective:
getInstance() returns a const pointer and every public accessor is const. getModifiedResidue() does lazily create and cache modified residues, but this is a transparent memoization (the same inputs always yield the same result); the cache members are therefore declared mutable and the mutation is internally synchronized (see the ResidueDB OpenMP critical section). No public method changes the observable state of the singleton.
◆ ~ResidueDB()
◆ ResidueDB() [1/2]
◆ ResidueDB() [2/2]
◆ addModifiedResidue_()
| void addModifiedResidue_ |
( |
Residue * |
residue | ) |
const |
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protected |
lazily register a freshly created modified residue and its names in the cache (logically const memoization; only the mutable cache members are touched)
◆ addModifiedResidueNames_()
| void addModifiedResidueNames_ |
( |
const Residue * |
| ) |
const |
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protected |
adds names of single modified residue to the index
◆ addResidueNames_()
| void addResidueNames_ |
( |
const Residue * |
| ) |
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protected |
adds names of single residue to the index
◆ buildResidues_()
◆ getInstance()
◆ getModifiedResidue() [1/3]
Returns a pointer to a modified residue given a residue and a pointer to a modification from the ModificationsDB.
The modified residue is added to the database if it doesn't exist yet. The origin of the modification has to match the residue and the term has to be ResidueModification::Anywhere.
- Exceptions
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◆ getModifiedResidue() [2/3]
| const Residue * getModifiedResidue |
( |
const Residue * |
residue, |
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const std::string & |
name |
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) |
| const |
Returns a pointer to a modified residue given a residue and a modification name.
The modified residue is added to the database if it doesn't exist yet.
- Exceptions
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◆ getModifiedResidue() [3/3]
| const Residue * getModifiedResidue |
( |
const std::string & |
name | ) |
const |
Returns a pointer to a modified residue given a modification name.
The "base" residue is looked up in ModificationsDB using the modification name. The modified residue is added to the database if it doesn't exist yet.
- Note
- Logically
const: the lazily created modified residue is memoized in the (mutable) cache; repeated calls return the same pointer.
◆ getNumberOfModifiedResidues()
| Size getNumberOfModifiedResidues |
( |
| ) |
const |
returns the number of modified residues stored
◆ getNumberOfResidues()
| Size getNumberOfResidues |
( |
| ) |
const |
returns the number of residues stored
◆ getResidue() [1/2]
| const Residue * getResidue |
( |
const std::string & |
name | ) |
const |
returns a pointer to the residue with name, 3 letter code or 1 letter code name
◆ getResidue() [2/2]
| const Residue * getResidue |
( |
const unsigned char & |
one_letter_code | ) |
const |
returns a pointer to the residue with 1 letter code name
◆ getResidues()
| const std::set< const Residue * > getResidues |
( |
const std::string & |
residue_set = "All" | ) |
const |
returns a set of all residues stored in this residue db
Following sets are available: All - all residues Natural20 - default 20 naturally occurring 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 occurring residues, including selenocysteine (U)
returns an empty set if the specified residue set is not defined
◆ getResidueSets()
| const std::set< std::string > getResidueSets |
( |
| ) |
const |
returns all residue sets that are registered which this instance
◆ hasResidue() [1/2]
| bool hasResidue |
( |
const Residue * |
residue | ) |
const |
returns true if the db contains the residue of the given pointer
◆ hasResidue() [2/2]
| bool hasResidue |
( |
const std::string & |
name | ) |
const |
returns true if the db contains a residue with the given name
◆ initResidues_()
initializes all residues by building
◆ insertResidueAndAssociateWithResidueSet_()
| void insertResidueAndAssociateWithResidueSet_ |
( |
Residue * |
residue, |
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const std::vector< std::string > & |
residue_sets |
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) |
| |
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protected |
creates and adds residues to a lookup table including the residue set
◆ operator=()
◆ const_modified_residues_
| std::set<const Residue*> const_modified_residues_ |
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mutableprotected |
all modified residues (lazily filled by getModifiedResidue)
◆ const_residues_
| std::set<const Residue*> const_residues_ |
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protected |
all (unmodified) residues
◆ residue_by_one_letter_code_
| std::array<const Residue*, 256> residue_by_one_letter_code_ = {{nullptr}} |
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protected |
fast lookup table for residues
◆ residue_mod_names_
| std::map<std::string, std::map<std::string, const Residue*> > residue_mod_names_ |
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mutableprotected |
cache of name -> modification-name -> modified residue (lazily filled by getModifiedResidue)
◆ residue_names_
| std::unordered_map<std::string, const Residue*> residue_names_ |
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protected |
lookup from name to residue
◆ residue_sets_
| std::set<std::string> residue_sets_ |
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protected |
◆ residues_by_set_
| std::map<std::string, std::set<const Residue*> > residues_by_set_ |
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protected |
1.9.8