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CChymoP Class Reference

Search Toolkit Book for CChymoP

eMSEnzymes_chymotrypsin_p chymotrypsin without proline rule More...

#include "msms.hpp"
(Private to src/algo/ms/omssa.)

+ Inheritance diagram for CChymoP:
+ Collaboration diagram for CChymoP:

Public Member Functions

 CChymoP (void)
 Chymotrypsin without proline rule. More...
 
- Public Member Functions inherited from CCleave
 CCleave (void)
 
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. More...
 
bool CheckCleave (const char *iPepStart, const char *iSeqStart)
 Check to see if we are at a cleavage point Used by CalcAndCut. More...
 
bool CheckCleaveChar (const char *iPepStart) const
 is the character given one of the cleavage chars? More...
 
void CalcMass (char SeqChar, int *Masses, const int *IntCalcMass)
 
void EndMass (int *Masses)
 
int findfirst (char *Seq, int Pos, int SeqLen)
 
void CheckNonSpecificMods (EMSModType ModType, CMSMod &VariableMods, int &NumMod, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset)
 looks for non-specific ptms More...
 
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 More...
 
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 More...
 
bool GetTopDown (void) const
 Is the enzyme really a top-down search? More...
 
const char * GetStop (void) const
 Get the enzyme stop value. More...
 
const char *& SetStop (void)
 Set the enzyme stop value. More...
 
bool GetNonSpecific (void) const
 Is this a non-specific search? More...
 
int GetCleaveNum (void) const
 Get the number of cleavage chars. More...
 
const char * GetCleaveOffset (void) const
 Get the the cleave offset, 0 = cterm, 1 = nterm. More...
 
bool GetNMethionine (void) const
 Is there n-term methionine cleavage? More...
 
boolSetNMethionine (void)
 Set n-term methionine cleavage. More...
 
const string GetCleaveAt (void) const
 What are the cleavage chars? More...
 
bool GetCheckProline (void) const
 Should we check for proline? More...
 
const char * GetCleaveSense (void) const
 Should we check for proline? More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CCleave
int ProtonMass
 
int TermMass
 
CAA ReverseAA
 
const char * CleaveAt
 where to cleave. More...
 
const char * CleaveOffset
 what is the cleavage offset More...
 
int kCleave
 How many cleavage characters. More...
 
bool TopDown
 TopDown does this signify a top-down search. More...
 
const char * Stop
 Stop Stop position for no-enzyme and semi-tryptic searches. More...
 
bool NonSpecific
 Is this a non-specific search? More...
 
bool CheckProline
 Should we apply the proline rule (no cleavage before proline) More...
 
bool NMethionine
 n-terminal methionine cleavage More...
 

Detailed Description

eMSEnzymes_chymotrypsin_p chymotrypsin without proline rule

Definition at line 1042 of file msms.hpp.

Constructor & Destructor Documentation

◆ CChymoP()

CChymoP::CChymoP ( void  )

Chymotrypsin without proline rule.

Definition at line 462 of file msms.cpp.

References CCleave::CheckProline, CCleave::CleaveAt, CCleave::CleaveOffset, CCleave::kCleave, CCleave::NonSpecific, and CCleave::TopDown.


The documentation for this class was generated from the following files:
Modified on Thu Feb 29 12:23:16 2024 by modify_doxy.py rev. 669887