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NCBI C++ ToolKit: src/algo/ms/omssa/msms.cpp Source File

(

=

;

< SeqLen;

++)

**PepStart,

*IntCalcMass,

*PrecursorIntCalcMass,

SeqChar(**PepStart);

(*PepStart == SeqStart ||

(*PepStart == SeqStart+1 &&

&& *SeqStart ==

))

NumMod, SeqChar, MaxNumMod, ModList,

(; *PepStart < SeqEnd; (*PepStart)++) {

SeqChar = **PepStart;

(

() && ( *PepStart - SeqStart < 2*Maxproductions ||

SeqEnd - *PepStart < 2*Maxproductions))) {

*PepStart,

, Modset);

(SeqChar, Masses, PrecursorIntCalcMass);

ModList, *PepStart, Modset);

(**PepStart, Masses, PrecursorIntCalcMass);

*PepStart,

, Modset);

=

;

=

;

(

<<

);

CMSMod::TModLists::const_iterator

;

const int kNumUniqueAA

@MSMod.hpp User-defined methods of the data storage class.

const char *const UniqueAA

eMSEnzymes_aspn_de Asp-N that cuts at D and E

eMSEnzymes_chymotrypsin_p chymotrypsin without proline rule

CChymoP(void)

Chymotrypsin without proline rule.

CChymotrypsin(void)

CChymotrypsin.

static CRef< CCleave > CleaveFactory(const EMSEnzymes enzyme)

Simple factory to return back object for enzyme.

const char * CleaveOffset

what is the cleavage offset

bool CheckProline

Should we apply the proline rule (no cleavage before proline)

bool CheckCleave(const char *iPepStart, const char *iSeqStart)

Check to see if we are at a cleavage point Used by CalcAndCut.

bool NMethionine

n-terminal methionine cleavage

void CalcMass(char SeqChar, int *Masses, const int *IntCalcMass)

bool CalcAndCut(const char *SeqStart, const char *SeqEnd, const char **PepStart, int *Masses, int &NumMod, int MaxNumMod, int *EndMasses, CMSMod &VariableMods, CMSMod &FixedMods, CMod ModList[], const int *IntCalcMass, const int *PrecursorIntCalcMass, CRef< CMSModSpecSet > &Modset, int Maxproductions)

cleaves the sequence.

void CheckMods(EMSModType NonSpecificIn, EMSModType Specific, CMSMod &VariableMods, CMSMod &FixedMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, CRef< CMSModSpecSet > &Modset)

checks all mods for a particular type

bool NonSpecific

Is this a non-specific search?

void EndMass(int *Masses)

int findfirst(char *Seq, int Pos, int SeqLen)

const char * CleaveAt

where to cleave.

bool GetTopDown(void) const

Is the enzyme really a top-down search?

bool TopDown

TopDown does this signify a top-down search.

int kCleave

How many cleavage characters.

void CheckAAMods(EMSModType ModType, CMSMod &VariableMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)

looks for amino acid specific ptms

CFormicAcid(void)

CFormicAcid.

CGluCAspN(void)

GluCAspN.

eMSEnzymes_gluc_de Glu-C that cuts at D and E

eMSEnzymes_lysn Cuts N term of lysine

bool IsArrayed(void)

Have the arrays been intialized?

int GetModNumChars(int Mod) const

get the number of modification AA's

char GetModChar(int Mod, int Number) const

get modification AA's

int GetModMass(int Mod) const

get modification mass

const TModLists & GetAAMods(EMSModType Type) const

void x_Init(const CMSSearchSettings::TProductsearchtype &SearchType)

double CalcMass[kNumUniqueAA]

int IntCalcMass[kNumUniqueAA]

void Init(const CMSSearchSettings::TProductsearchtype &SearchType)

initialize mass arrays with fixed mods

contains information for a post translational modification at a particular sequence site

eMSEnzymes_no_enzyme search without enzyme (precursor mass only)

CNoEnzyme(void)

NoEnzyme.

CPepsinA(void)

CCPepsinA.

Chymotrypsin, cuts N terminal at A,F,I,L,M or V.

eMSEnzymes_semi_tryptic semi tryptic search (one end of peptide has to be tryptic)

CSemiTryptic(void)

SemiTryptic.

eMSEnzymes_thermolysin_p cuts N terminal at A,F,I,L,M or V

eMSEnzymes_top_down top-down search of ETD spectra

CTopDown(void)

Top-down, whole protein search.

CTrypCNBr(void)

CTrypCNBr.

CTrypChymo(void)

CTrypChymo.

CTrypsinP(void)

CTrypsinP.

whole protein (no cleavage)

CWholeProtein(void)

Whole Protein.

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

EMSEnzymes

enumerate enzymes

@ eMSSearchType_multiisotope

@ eMSSearchType_monoisotopic

@ eMSModType_modn

at the N terminus of a protein

@ eMSModType_modc

at the C terminus of a protein

@ eMSModType_modnpaa

at the N terminus of a peptide at particular amino acids

@ eMSModType_modcpaa

at the C terminus of a peptide at particular amino acids

@ eMSModType_modnp

at the N terminus of a peptide

@ eMSModType_modaa

at particular amino acids

@ eMSModType_modcaa

at the C terminus of a protein at particular amino acids

@ eMSModType_modcp

at the C terminus of a peptide

@ eMSModType_modnaa

at the N terminus of a protein at particular amino acids

@ eMSEnzymes_whole_protein

@ eMSEnzymes_chymotrypsin

@ eMSEnzymes_semi_chymotrypsin

@ eMSEnzymes_semi_tryptic

@ eMSEnzymes_chymotrypsin_p

@ eMSEnzymes_thermolysin_p

const double AverageMass[]

const double MonoN15Mass[]

const double kWater

mass of water

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