A molecule modification specification. More...
#include <TraData.hpp>
Public Member Functions | |
| Modification () | |
| bool | empty () const |
| returns true iff all members are zero and contain no params | |
 Public Member Functions inherited from pwiz::data::ParamContainer | |
| CVParam | cvParam (CVID cvid) const |
| finds cvid in the container: | |
| CVParam | cvParamChild (CVID cvid) const |
| finds child of cvid in the container: | |
| std::vector< CVParam > | cvParamChildren (CVID cvid) const |
| finds all children of cvid in the container: | |
| bool | hasCVParam (CVID cvid) const |
| returns true iff cvParams contains exact cvid (recursive) | |
| bool | hasCVParamChild (CVID cvid) const |
| returns true iff cvParams contains a child (is_a) of cvid (recursive) | |
| UserParam | userParam (const std::string &) const |
| finds UserParam with specified name | |
| void | set (CVID cvid, const std::string &value="", CVID units=CVID_Unknown) |
| set/add a CVParam (not recursive) | |
| void | set (CVID cvid, double value, CVID units=CVID_Unknown) |
| set/add a CVParam (not recursive) | |
| void | set (CVID cvid, int value, CVID units=CVID_Unknown) |
| set/add a CVParam (not recursive) | |
| template<typename value_type > | |
| void | set (CVID cvid, value_type value, CVID units=CVID_Unknown) |
| set/add a CVParam (not recursive) | |
| void | clear () |
| clears the collections | |
| bool | operator== (const ParamContainer &that) const |
| returns true iff this and that have the exact same cvParams and userParams | |
| bool | operator!= (const ParamContainer &that) const |
| returns !(this==that) | |
| template<> | |
| void | set (CVID cvid, bool value, CVID units) |
| special case for bool (outside the class for gcc 3.4, and inline for msvc) | |
Public Attributes | |
| int | location |
| Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1. | |
| double | monoisotopicMassDelta |
| Atomic mass delta when assuming only the most common isotope of elements in Daltons. | |
| double | averageMassDelta |
| Atomic mass delta when considering the natural distribution of isotopes in Daltons. | |
| Public Attributes inherited from pwiz::data::ParamContainer | |
| std::vector< ParamGroupPtr > | paramGroupPtrs |
| a collection of references to ParamGroups | |
| std::vector< CVParam > | cvParams |
| a collection of controlled vocabulary terms | |
| std::vector< UserParam > | userParams |
| a collection of uncontrolled user terms | |
Detailed Description
A molecule modification specification.
If n modifications are present on the peptide, there should be n instances of the modification element. If multiple modifications are provided as cvParams, it is assumed the modification is ambiguous, i.e. one modification or the other. If no cvParams are provided it is assumed that the delta has not been matched to a known modification.
Definition at line 192 of file TraData.hpp.
Constructor & Destructor Documentation
| pwiz::tradata::Modification::Modification | ( | ) |
Member Function Documentation
| bool pwiz::tradata::Modification::empty | ( | ) | const |
returns true iff all members are zero and contain no params
Reimplemented from pwiz::data::ParamContainer.
Member Data Documentation
| int pwiz::tradata::Modification::location |
Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.
Definition at line 197 of file TraData.hpp.
| double pwiz::tradata::Modification::monoisotopicMassDelta |
Atomic mass delta when assuming only the most common isotope of elements in Daltons.
Definition at line 200 of file TraData.hpp.
| double pwiz::tradata::Modification::averageMassDelta |
Atomic mass delta when considering the natural distribution of isotopes in Daltons.
Definition at line 203 of file TraData.hpp.
The documentation for this struct was generated from the following file:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/tradata/TraData.hpp
