Secondary Structure Classes Documentation


Documentation for the following classes is available:


Class CompSubStruc

/*********************************************************************
Class: CompSubStruc

Method: IntrCompSubStruc();
Description: Creates a Compound SubStructure, empty shell
This class serves as an ancestor base for sec struc classes
such as Helix,Strand,Turn...
Usage:
Caution: This class is an Abstract Base Class. Do not instantiate it.
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: IntrCompSubStruc(const IntrCompSubStruc& );
Description: COPY CTOR for CompSubStruc.
Usage:
Caution: This class is an Abstract Base Class. Do not instantiate it.
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: virtual void AddAfter(void*)
Description: This funct is a pure virtual
Usage:
Caution: If U use OBJECTSTORE, it is not pure, since OS cannot handle it
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: virtual void InsertBefore(void*)
Description: This funct is a pure virtual
Usage:
Caution: If U use OBJECTSTORE, it is not pure, since OS cannot handle it
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: void * Next() const
Description: returns its next member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: void * Previous() const
Description: returns its previous member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: SSTRUCTYPE MyType() const
Description: returns its type which is one of these :
enum SSTRUCTYPE {SHEET, SITE, HELIX, STRAND, TURN};
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: char * MyName() const
Description: returns its name member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: void SetName(char *name)
Description: sets its name member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: void DeleteMySubEntityList()
Description: deletes its SubEntity List
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: virtual const Compound * MyCompound() const
Description: This funct is a pure virtual
Usage:
Caution: If U use OBJECTSTORE, it is not pure, since OS cannot handle it
/*********************************************************************
/*********************************************************************
Class: CompSubStruc

Method: virtual CompSubStruc* MyCompSubStruc() const
Description: This funct is a pure virtual
Usage:
Caution: If U use OBJECTSTORE, it is not pure, since OS cannot handle it
/*********************************************************************


Class MultiEntitySubStruc

/*********************************************************************
Class: MultiEntitySubStruc

Method: IntrMultiEntitySubStruc()
Description: Def CTOR for MultiEntitySubStruc. This class has a
virtual base class, CompSubStruc, cause, class Sheet, which
inherits from it, already inherits a CompSubStruc through
the other part of its inheritance hierarchy
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: IntrMultiEntitySubStruc(const IntrMultiEntitySubStruc& m)
Description: Copy CTOR for MultiEntitySubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: const Compound * MyCompound() const
Description: returns the compound that it belongs to
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: MultiEntitySubStruc *NextMultiEntitySubStruc() const
Description: returns its next member inherited from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: MultiEntitySubStruc *PreviousMultiEntitySubStruc() const
Description: returns its next member inherited from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: void AssignCompound(Compound& c)
Description: Assigns its compound member to c
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: MultiEntitySubStruc

Method: CompSubStruc * MyCompSubStruc() const
Description: returns its real CompSubStruc part of the object. This
is needed, because of virtual inheritance of CompSubStruc
Usage:
Caution:
/*********************************************************************


Class Helix

/*********************************************************************
Class: Helix

Method: IntrHelix();
Description: Default Helix CTOR
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Helix

Method: IntrHelix(const IntrHelix&);
Description: Copy Ctor for Helix
Usage:
Caution:
/*********************************************************************


Class IntrTurn

/*********************************************************************
Class: IntrTurn

Method: IntrTurn()
Description: Default Turn CTOR
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: IntrTurn

Method: IntrTurn(const IntrTurn& t)
Description: Copy CTOR for Turn
Usage:
Caution:
/*********************************************************************


Class Strand

/*********************************************************************
Class: Strand

Method: IntrStrand();
Description: Default CTOR for Strand
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Strand

Method: IntrStrand(const IntrStrand&);
Description: Copy CTOR for Strand
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Strand

Method: Sheet *MySheet() const
Description: returns the sheet that it belongs to
Usage:
Caution:
/*********************************************************************


Class SStrucSE

/*********************************************************************
Class: SStrucSE

Method: IntrSStrucSE();
Description: Default CTOR for SStrucSE, inherits from SStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: IntrSStrucSE(const IntrSStrucSE&);
Description: Copy CTOR for SStrucSE
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: void AddAfter(void *sp);
Description: this is added after sp in the SStruc list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: void InsertBefore(void *sp);
Description: this is added before sp in the SStruc list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: Entity *MyEntity() const
Description: returns the Entity that it belongs to
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: char *MyComment() const
Description: returns its comment member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: int MySerialNumber() const
Description: returns its serial number member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: SubEntity * MyBeginSubEntity() const
Description: returns its begin_SubEntity member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: SubEntity * MyEndSubEntity() const
Description: returns its end_SubEntity member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: const Compound *MyCompound() const;
Description: returns its entity members compound
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: int AssignSubEntities(SubEntity& subentity1, SubEntity& subentity2);
Description: assigns its begin and end subentity members to subentity1, and
subentity2 respectively.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: void AddSStrucSEAfter(SStrucSE* s)
Description: calls AddAfter(s)...refer to AddAfter(void *)
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: void InsertSStrucSEBefore(SStrucSE* s)
Description: calls InsertBefore(s)...refer to InsertBefore(void *)
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStrucSE

Method: SStrucSE *NextSStrucSE()
Description: returns its next member through the inherited NextSStruc() member
Usage:
Caution:
/*********************************************************************


Class SStruc

/*********************************************************************
Class: SStruc

Method: IntrSStruc()
Description: Defaults CTOR for SStruc, which represents a Secondary
Structure. It inherits virtually from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStruc

Method: IntrSStruc(const IntrSStruc& s)
Description: Copy CTOR from SStruc. It inherits virtually from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStruc

Method: SStruc * NextSStruc() const
Description: returns the next member inherited from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStruc

Method: SStruc * PreviousSStruc() const
Description: returns the previous member inherited from CompSubStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: SStruc

Method: CompSubStruc * MyCompSubStruc() const
Description: returns its real CompSubStruc part of the object. This
is needed, because of virtual inheritance of CompSubStruc
Usage:
Caution:
/*********************************************************************


Class Site

/*********************************************************************
Class: Site

Method: void AddAfter(void *sp);
Description: this is added after sp in the SStruc Site list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: void InsertBefore(void *sp);
Description: this is added before sp in the SStruc Site list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: IntrSite()
Description: Default CTOR for Site
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: IntrSite(const IntrSite& s)
Description: Copy CTOR for Site
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: Site* NextSite() const
Description: returns its inherited next member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: Site* PreviousSite() const
Description: returns its inherited previous member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: void AddSiteAfter(Site* s)
Description: calls AddAfter(void *)... refer to it.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: void InsertSiteBefore(Site* s)
Description: calls InsertBefore(void *)... refer to it.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Site

Method: void AddSubEntity(SubEntity*);
Description: Adds an SE to its NonLinear list mgr of SubEntity
Usage:
Caution:
/*********************************************************************


Class Sheet

/*********************************************************************
Class: Sheet

Method: void AddAfter(void *sp);
Description: this is added after sp in the SStruc Sheet list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void InsertBefore(void *sp);
Description: this is added before sp, in the SStruc Sheet list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: IntrSheet()
Description: Default CTOR for Sheet, which multiply inherits from
MultiEntitySubStruc and SStruc
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: IntrSheet(const IntrSheet & s)
Description: Copy CTOR for Sheet
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void AddStrand(Strand *sp);
Description: The Sheet maintains a LListOfSSConn, thus it adds the
strand to this list.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void AddConnection(SStrucSE* current,
SStrucSE* previous,
HydroBond* hb, PARALLELISM parallel){
Description: calls its LListOfSSConn's AddConnection, refer to it.
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: HydroBond * NewHydroBond(SubEntity*, SubEntity*, char*, char*);
Description: returns a new HydroBond, between SE's N_atom() and O_atom()
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: SSConnectivity * SSConnectivityOf(Strand* s);
Description: calls its LListOfSSConn's FindSSConnectivity, refer to it
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: HydroBond * HydroBondBetween(Strand*, Strand*) const;
Description: checks its LListOfSSConn member, if they are connected
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: PARALLELISM ParallelismOf(Strand*, Strand*) const;
Description: gets its LListOfSSConn members, ConnectionElement and gets
their PARALLELISM
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: Sheet * NextSheet() const
Description: returns its inherited next member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: Sheet * PreviousSheet() const
Description: returns its inherited previous member
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: Strand * FindStrand(Strand*) const;
Description: Looks up its LListOfSSConn member, for the strand
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: Strand * FindStrand(char*) const;
Description: Looks up its LListOfSSConn member, for the strand
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void Merge(Sheet *sp);
Description: merges this and sp
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void RemoveSelfFromList();
Description: removes this from the list
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void AddSheetAfter(Sheet* s)
Description: calls AddAfter, refer to it
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: void InsertSheetBefore(Sheet* s)
Description: calls InsertBefore, refer to it
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: const Compound * MyCompound() const
Description: returns its Compound
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: const SSList * MySSList() const
Description: returns its LinearSSList
Usage:
Caution:
/*********************************************************************
/*********************************************************************
Class: Sheet

Method: CompSubStruc * MyCompSubStruc() const
Description: returns its CompSubStruc Part
Usage:
Caution:
/*********************************************************************

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Currently under Heavy Construction, please excuse the mess


jcooper@cuhhca.hhmi.columbia.edu