The Secondary Structure List Classes Documentation


Documentation for the following classes is available:


Class LListOfSS

/*********************************************************************
Class: LListOfSS

Method: LListOfSS()
Description: Def. CTOR for basic container for Singly Linked List of
SStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: LListOfSS

Method: LListOfSS *NextLListOfSS()
Description: returns its next member
Usage:
Caution:
/*********************************************************************


Class DLlistOfSS

/*********************************************************************
Class: DLlistOfSS

Method: DLlistOfSS *NextDLlistOfSS()
Description: returns the next member inherited from LListOfSS
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: DLlistOfSS

Method: DLlistOfSS *PreviousDLlistOfSS()
Description: returns its previous member
Usage:
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/*********************************************************************
/*********************************************************************
Class: DLlistOfSS

Method: void InsertBefore(DLlistOfSS *sp);
Description: Inserts sp before the (*this) object
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: DLlistOfSS

Method: void AddAfter(DLlistOfSS *sp);
Description: Adds sp after the (*this) object
Usage:
Caution:
/*********************************************************************


Class SSConnectionElement

/*********************************************************************
Class: SSConnectionElement

Method: SSConnectionElement()
Description: This class inherits from LListOfSS, and adds in some of
its members. This default CTOR
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SSConnectionElement

Method: SSConnectionElement *NextSSConnectionElement()
Description: returns the next member it inherits from LListOfSS
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectionElement

Method: HydroBond * MyHydroBond()
Description: returns its HydroBond member
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectionElement

Method: PARALLELISM MyParallelism()
Description: returns its PARALLELISM member
Usage:
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/*********************************************************************


Class SSConnectivity

/*********************************************************************
Class: SSConnectivity

Method: SSConnectivity()
Description: SSConnectivity inherits from DLlistOfSS. Thus it is a doubly
Linked list of SSConnectionElement, which itself is a singly linked
list. This is the DEF CTOR for it
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: LListOfSS * ConnectedSecondarystrucs()
Description: returns its member SSConnectionElement, linked list
as a generic list, LListOfSS
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: SSConnectionElement* ConnectedSSConnectionElement()
Description: returns its member SSConnectionElement, linked list
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: SSConnectivity *NextSSConnectivity()
Description: returns its inherited next member
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: SSConnectivity * PreviousSSConnectivity()
Description: returns its previous member
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: SSConnectionElement* FindSSConnectionElement(SStruc *sp);
Description: Finds sp in its SSConnectionElement list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SSConnectivity

Method: void AddConnection(SSConnectivity *sp,HydroBond hb*,PARALLELISM p);
Description: Adds a new SSConnectionElement, with its SSConnectivity,
set to sp and its _sstruc, set to sp's _sstruc
Usage:
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/*********************************************************************


Class SSList

/*********************************************************************
Class: SSList

Method: operator const void * () const
Description: retunrs 0 if its _sstruc is 0
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: SStruc & operator()()
Description: returns a ref to its SStruc
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual void operator++()=0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual void operator--()=0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual void ResetToTop()=0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual void ResetToEnd()=0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual SSList *CopyOfSelf() const =0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************
/*********************************************************************
Class: SSList

Method: virtual void AddSStruc(SStruc*)=0;
Description: pure virtual, will be defined later
Usage:
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/*********************************************************************


Class LinearSSList

/*********************************************************************
Class: LinearSSList

Method: void operator++();
Description: sets its _sstruc member to its _sstruc->NextSStruc();
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: void operator--();
Description: sets its _sstruc member to its _sstruc->PreviousSStruc()
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: void ResetToTop()
Description: goes to the top of the list
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: void ResetToEnd();
Description: goes to the tail of the list
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: SSList *CopyOfSelf() const
Description: returns a copy of itself
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: LinearSSList()
Description: Default CTOR for LinearSSList
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: LinearSSList(SStruc *s1, SStruc *s2 =NULL)
Description: sets its head to s1 and tail to s2
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: LinearSSList(const LinearSSList * lst)
Description: sets its head and tail to lst's head and tail.
Shallow COPY CTOR
Usage:
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/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: void AddSStruc(SStruc *sp);
Description: Adds sp in order of its begin and end SubEntity's.
Usage:
Caution: This member funct. uses the overloaded op <,==
/*********************************************************************
/*********************************************************************
Class: LinearSSList

Method: void AddSStrucSE(SStrucSE *sp);
Description: Adds the sp into its list in order
Usage:
Caution:
/*********************************************************************


Class NonLinearSSList

/*********************************************************************
Class: NonLinearSSList

Method: void operator++();
Description: Sets _current to the next DListOfSS structure in its list
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: void operator--();
Description: Sets _current to the previous DListOfSS structure in its list
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: void ResetToTop();
Description: Sets _current to the top of its list
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: void ResetToEnd();
Description: Sets _current to the end of its list
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: SSList * CopyOfSelf() const
Description: returns a Copy of Its self
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: NonLinearSSList()
Description: Def CTOR, creates an empty list and
sets _head and _current to 0.
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: NonLinearSSList( const NonLinearSSList *list)
Description: Copy CTOR of NonLinearSSList, This is a shallow copy
Usage:
Caution: Deleting the new list that this CTOR returns will not
/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: void AddSStruc(SStruc*);
Description: Adds the secStruc in order
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: virtual DLlistOfSS *new_DLlistOfSS()
Description: returns a new DLlistOfSS container
Usage:
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/*********************************************************************
/*********************************************************************
Class: NonLinearSSList

Method: LListOfSS * ListOfSStrucs()
Description: returns its head
Usage:
Caution:
/*********************************************************************


Class LListOfSSConn

/*********************************************************************
Class: LListOfSSConn

Method: LListOfSSConn()
Description: This is a specialization of the NonLinearSSList.
It maintains a NonLinearSSList of SSConnectivity.
This is its DEF CTOR.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: LListOfSSConn(const LListOfSSConn * lst)
Description: Copy CTOR of LListOfSSConn, This is a shallow copy
This just calls the NonLinearSSList COPY CTOR.
Usage:
Caution: Deleting the new list that this CTOR returns will not
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: void AddConnection(SStrucSE *current, SStrucSE *prev,
HydroBond *hb, PARALLELISM p);
Description: It first looks up its list to find prev in its List, and
finds its corresponding SSConnectivity. Then it checks if
current is not in that SSConnectivity's SSConnectionElement list.
If these 2 conditions are satisfied, we add current's SSConnectivity
to prev's SSConnectivity's SSConnectionElement list.


Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: DLlistOfSS *new_DLlistOfSS()
Description: returns a new SSConnectivity
Usage:
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/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: SSConnectivity * FindSSConnectivity(SStrucSE *sse);
Description: Checks if sse is in its SSConnectivity list
Usage:
Caution: returns 0 if not found
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: SSConnectivity * FindSSConnectivity(char *sse);
Description: Checks if sse is in its SSConnectivity list
Usage:
Caution: returns 0 if not found
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: SSConnectivity * MyLListOfSSConnectivity();
Description: returns its head
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: LListOfSSConn

Method: void Merge(LListOfSSConn *lp);
Description: Merges lp with its list
Usage:
Caution:
/*********************************************************************

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jcooper@cuhhca.hhmi.columbia.edu