Implements a "Spacer" for a protein chain. Includes methods to obtain values from the atoms and its pdb information. More...

Inheritance diagram for Spacer:

Collaboration diagram for Spacer:

Public Member Functions
	Spacer ()

	Spacer (const Spacer &orig)

virtual	~Spacer ()

virtual void	acceptCalculator (EnergyVisitor *v)

virtual void	acceptOptimizer (OptimizationVisitor *v)

void	addGap (int index)

void	addRot (vgMatrix3< double > r)

void	addTrans (vgVector3< double > t)

virtual void	bindIn (Atom &_this, Bond &c, Atom &_other)

virtual void	bindIn (SimpleBond &c)

virtual void	bindOut (Atom &_this, Bond &c, Atom &_other)

virtual void	bindOut (SimpleBond &c)

virtual Component *	clone ()

bool	collides (Component &other, double dist=0.0)

void	copy (const Bond &orig)

void	copy (const Polymer &orig)

virtual void	copy (const SimpleBond &orig)

void	copy (const Component &orig)

void	copy (const Spacer &orig)

void	deleteComponent (Component *c)

AminoAcid &	getAmino (unsigned int n)

const AminoAcid &	getAmino (unsigned int n) const

vector< pair< unsigned int, unsigned int > >	getHelixData ()

vector< pair< int, int > >	getHoles ()

const Spacer &	getInBond (unsigned int n) const

Spacer &	getInBond (unsigned int n)

virtual Atom &	getInBondRef (unsigned int n)

int	getIndexFromPdbNumber (int index)

virtual vgVector3< double >	getLowerBound (double dist=0.0)

unsigned int	getMaxInBonds () const

unsigned int	getMaxOutBonds () const

virtual const Atom &	getOpenInBondRef (unsigned int n=0) const

virtual Atom &	getOpenInBondRef (unsigned int n=0)

virtual const Atom &	getOpenOutBondRef (unsigned int n=0) const

virtual Atom &	getOpenOutBondRef (unsigned int n=0)

const Spacer &	getOutBond (unsigned int n) const

Spacer &	getOutBond (unsigned int n)

virtual Atom &	getOutBondRef (unsigned int n)

int	getPdbNumberFromIndex (int index)

Spacer &	getSpacer (unsigned int n)

const Spacer &	getSpacer (unsigned int n) const

vector< pair< unsigned int, unsigned int > >	getStrandData ()

virtual string	getType () const

virtual vgVector3< double >	getUpperBound (double dist=0.0)

void	groupLikeStateCode ()

void	insertAminoAfter (string code, unsigned int n=9999, double phi=-62, double psi=-41, double omega=180, double NToCaLen=1.458, double CaToCLen=1.52, double CToOLen=1.231, double atCaToCAng=111.6, double CaToOAng=120.80, double CtoNLen=1.33, double atCToNAng=116.4, double OToNAng=123.2, double atNToCaAng=121.9)

void	insertAminoAfterWithGaps (string code, unsigned int n=9999, double phi=-62, double psi=-41, double omega=180, int beginHole=0, int endHole=0, vgVector3< double > ca1=vgVector3< double >(), vgVector3< double > ca2=vgVector3< double >(), string target="", Spacer refSpacer=0, Spacer pOriginalSpacer=0, double NToCaLen=1.458, double CaToCLen=1.52, double CToOLen=1.231, double atCaToCAng=111.6, double CaToOAng=120.80, double CtoNLen=1.33, double atCToNAng=116.4, double OToNAng=123.2, double atNToCaAng=121.9)

void	insertAminoBefore (string code, unsigned int p=0, double phi=-62, double psi=-41, double omega=180, double NToCaLen=1.458, double CaToCLen=1.52, double CToOLen=1.231, double atCaToCAng=111.6, double CaToOAng=120.80, double CtoNLen=1.33, double atCToNAng=116.4, double OToNAng=123.2, double atNToCaAng=121.9)

void	insertComponent (Component *c)

void	insertFirstSpacer (Spacer *sp)

void	insertSubSpacerAfter (Spacer *sp, unsigned int pos)

bool	inSync ()

bool	isBond (const SimpleBond &c) const

bool	isGap (int index)

bool	isInBond (const SimpleBond &c) const

bool	isIndirectBond (const SimpleBond &c) const

bool	isIndirectInBond (const SimpleBond &c) const

bool	isIndirectOutBond (const SimpleBond &c) const

bool	isOutBond (const SimpleBond &c) const

bool	isTorsionBond (const SimpleBond &c) const

void	load (Loader &l)

void	makeFlat ()

void	mergeSpacer (Spacer *s)

Spacer &	operator= (const Spacer &orig)

void	printComponents ()

void	printGaps ()

void	printSubSpacerList ()

void	removeAllGaps ()

void	removeComponent (Component *c)

void	removeComponentFromIndex (unsigned int i)

void	removeGap (int index)

void	save (Saver &s)

void	setAtomStartOffset (int _offset)

void	setDSSP (bool verbose)

void	setMaxInBonds (unsigned int m)

void	setMaxOutBonds (unsigned int m)

void	setRot (vgMatrix3< double > r)

void	setStartOffset (int _offset)

void	setStateFromSecondary (string sec)

void	setStateFromTorsionAngles ()

void	setTrans (vgVector3< double > t)

virtual void	setType (string _name)

const unsigned int	sizeAmino () const

unsigned int	sizeInBonds () const

unsigned int	sizeOpenInBonds () const

unsigned int	sizeOpenOutBonds () const

unsigned int	sizeOutBonds () const

const unsigned int	sizeSpacer () const

Spacer *	splitSpacer (unsigned int index, unsigned int count)

void	sync ()

virtual void	unbindIn (Bond &c)

virtual void	unbindIn (SimpleBond &c)

virtual void	unbindOut (Bond &c)

virtual void	unbindOut (SimpleBond &c)

Static Public Member Functions
static bool	NMRGetMinimumCADistanceVector (const string &strFileName, vector< double > *pNMR)

Protected Member Functions
void	getBackboneHbonds ()

pair< unsigned int, unsigned int >	getSubSpacerListEntry (unsigned int)

pair< unsigned int, unsigned int >	getSubSpacerListEntry (unsigned int) const

void	modifySubSpacerList (Spacer *, int)

virtual void	pUnbindIn (SimpleBond &c)

virtual void	pUnbindOut (SimpleBond &c)

void	resetBoundaries ()

void	updateSubSpacerList ()

Detailed Description

Implements a "Spacer" for a protein chain. Includes methods to obtain values from the atoms and its pdb information.

***Attention*** The current implementation allows for "1 to 1" spacers, ie. spacers composed of a single aminoacid chain. Class that develop the virtual methods from the parent class Polymer.

Constructor & Destructor Documentation

Spacer ( )

Basic constructor

Spacer ( const Spacer & orig )

constructor based in another object

Parameters

orig,reference to the original object to copy

~Spacer ( )

virtual

Basic destructor

Member Function Documentation

void acceptCalculator ( EnergyVisitor * v )

virtual

Sets the Spacer as part of the Energy Visitor object

Parameters

v,pointer to the Energy visitor object

Reimplemented from Polymer.

void acceptOptimizer ( OptimizationVisitor * v )

virtual

Sets the Spacer as part of the Optimization Visitor object

Parameters

v,pointer to the Optimization Visitor

Reimplemented from Polymer.

void addGap ( int index )

Modifier used to add a gap into the list of gaps.

Parameters

index,amino acid number from on the pdb file

void addRot ( vgMatrix3< double > r )

virtual

Adds a rotation matrix

Parameters

r,the rotation matrix to add

Reimplemented from Polymer.

void addTrans ( vgVector3< double > t )

virtual

Adds a the translation vector

Parameters

t,the translation vector to add

Reimplemented from Polymer.

void bindIn	(	Atom &	_this,
		Bond &	c,
		Atom &	_other
	)

virtualinherited

In-going bond from this to c, from this' atom _this to c's _other atom.

Parameters

atom	reference, bond reference, atom reference

Returns: void

void bindIn ( SimpleBond & c )

virtualinherited

Sets and in-bond from this to c.

Reimplemented in Atom.

void bindOut	(	Atom &	_this,
		Bond &	c,
		Atom &	_other
	)

virtualinherited

Out-going bond from this to c, from this' atom _this to c's _other atom.

Parameters

atom	reference, bond reference, atom reference

Returns: void

void bindOut ( SimpleBond & c )

virtualinherited

Sets and out-bond from this to c

Reimplemented in Atom.

Component * clone ( )

virtual

clone the spacer

Returns: pointer to the new component

Reimplemented from Polymer.

bool collides	(	Component &	other,
		double	dist = `0.0`
	)

inherited

Is other within dist of this' bounding box?

Parameters

other	(Component)
dist	(double)

Returns: True, if the component collides with "OTHER"

void copy ( const Bond & orig )

inherited

Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.

Parameters

bond reference

Returns: void

void copy ( const Polymer & orig )

inherited

Parameters

void copy ( const SimpleBond & orig )

virtualinherited

Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.

void copy ( const Component & orig )

inherited

Copy the component. Attention: new elements have to be copied also in Monomer::copy() since it does NOT invoke this function (segmentation fault if it does).

Parameters

orig

void copy ( const Spacer & orig )

Copies the given the spacer

Parameters

orig,reference to the spacer to copy

void deleteComponent ( Component * c )

virtual

Similar to removeComponent but also free the component's memory space

Parameters

c,pointer to the Component to delete

Reimplemented from Polymer.

AminoAcid & getAmino ( unsigned int n )

Returns the aminoacid of the index

Parameters

n,AminoAcid index

Returns: aminoacid reference

const AminoAcid & getAmino ( unsigned int n ) const

Returns the aminoacid of index

Parameters

n,AminoAcid index

Returns: aminoacid reference

void getBackboneHbonds ( )

protected

Set the state from H bonds. H bond definition: Kabsch, Sander, Biopolymers. 1983 Dec;22(12):2577-637.

vector< pair< unsigned int, unsigned int > > getHelixData ( )

Predicate used to get the range for the Helix amino acids

Returns: vector containing the ranges

vector< pair< int, int > > getHoles ( )

This function returs a pair array that define holes into the PDB numbering. NOTE: The function returns exactly where an hole starts and ends.

Returns: vector of int pairs

const Spacer & getInBond ( unsigned int n ) const

virtual

Returns the reference to the spacer that contains the inBond for the n Atom

Parameters

n,index of the atom

Returns: reference to the spacer that contains the inBond information

Reimplemented from SimpleBond.

Spacer & getInBond ( unsigned int n )

virtual

Returns the reference to the spacer that contains the inBond for the n Atom

Parameters

n,index of the atom

Returns: reference to the spacer that contains the inBond information

Reimplemented from SimpleBond.

Atom & getInBondRef ( unsigned int n )

virtualinherited

Returns reference to the i-th in-bond atom.

Parameters

unsigned int

Returns: Atom reference

int getIndexFromPdbNumber ( int index )

Predicate used to get the internal array number corresponding to a given PDB aminoacid number (Residue sequence number, columns 23-26 of a pdb file).

Parameters

index,pdb number

Returns: the corresponding internal array number

vgVector3< double > getLowerBound ( double dist = 0.0 )

virtualinherited

Return the lower bound coordinates.

Parameters

dist

Returns: The lowerBound vector (vgVector2<double>)

unsigned int getMaxInBonds ( ) const

inherited

Get maximum of in-bonds.

unsigned int getMaxOutBonds ( ) const

inherited

Get maximum of out-bonds.

const Atom & getOpenInBondRef ( unsigned int n = 0 ) const

virtual

used to obtain the corresponding reference to the InBond of the n amino acid

Parameters

n,index of the atom

Returns: atom reference

Reimplemented from Bond.

Atom & getOpenInBondRef ( unsigned int n = 0 )

virtual

used to obtain the corresponding reference to the InBond of the n amino acid

Parameters

n,index of the atom

Returns: atom reference

Reimplemented from Bond.

const Atom & getOpenOutBondRef ( unsigned int n = 0 ) const

virtual

used to obtain the corresponding reference to the OutBond of the n amino acid

Parameters

n,index of the atom

Returns: atom reference

Reimplemented from Bond.

Atom & getOpenOutBondRef ( unsigned int n = 0 )

virtual

used to obtain the corresponding reference to the OutBond of the n amino acid

Parameters

n,index of the atom

Returns: atom reference

Reimplemented from Bond.

const Spacer & getOutBond ( unsigned int n ) const

virtual

Returns the reference to the spacer that contains the outBond for the n Atom

Parameters

n,index of the atom

Returns: reference to the spacer that contains the outBond information

Reimplemented from SimpleBond.

Spacer & getOutBond ( unsigned int n )

virtual

Returns the reference to the spacer that contains the outBond for the n Atom

Parameters

n,index of the atom

Returns: reference to the spacer that contains the outBond information

Reimplemented from SimpleBond.

Atom & getOutBondRef ( unsigned int n )

virtualinherited

Returns reference to the i-th in-bond atom.

Parameters

unsigned int

Returns: Atom reference

int getPdbNumberFromIndex ( int index )

Predicate used to get the PDB aminoacid number (Residue sequence number, columns 23-26 of a pdb file) corresponding to a given internal array number

Parameters

index,internal array number

Returns: the corresponding PDB aminoacid number

Spacer & getSpacer ( unsigned int n )

Returns the spacer of the corresponding index

Parameters

n,the Spacer index

Returns: spacer reference

const Spacer & getSpacer ( unsigned int n ) const

Returns the spacer of the corresponding index

Parameters

n,Spacer index

Returns: spacer reference

vector< pair< unsigned int, unsigned int > > getStrandData ( )

Predicate used to get the range for the Strand amino acids

Returns: vector containing the ranges

pair< unsigned int, unsigned int > getSubSpacerListEntry ( unsigned int n )

protected

Returns the first and last aminoacid indexes from the sub-spacer in a <pair>. The difference (last - first) is the count of amino acids in the whole sub-spacer structure.

Parameters

n,corresponding index

Returns: the start and end indexes in the range

pair< unsigned int, unsigned int > getSubSpacerListEntry ( unsigned int n ) const

protected

Returns the first and last aminoacid index from the sub-spacer in a <pair>. The difference (last - first) is the count of amino acids in the whole sub-spacer structure.

Parameters

n,corresponding index

Returns: the start and end indexes in the range

string getType ( ) const

virtualinherited

Is c bonded to this ?

Reimplemented in SideChain.

vgVector3< double > getUpperBound ( double dist = 0.0 )

virtualinherited

Return the upper bound coordinates.

Parameters

dist

Returns: The upperBound vector (vgVector2<double>)

void groupLikeStateCode ( )

Group the spacer (and his sub-spacers) like the state codes of the aminoacids. After this the aminoacid structure is grouped in HELIX-spacer,STRANDS-spacer,COIL-spacer and TURN-spacer.

void insertAminoAfter	(	string	code,
		unsigned int	n = `9999`,
		double	phi = `-62`,
		double	psi = `-41`,
		double	omega = `180`,
		double	NToCaLen = `1.458`,
		double	CaToCLen = `1.52`,
		double	CToOLen = `1.231`,
		double	atCaToCAng = `111.6`,
		double	CaToOAng = `120.80`,
		double	CtoNLen = `1.33`,
		double	atCToNAng = `116.4`,
		double	OToNAng = `123.2`,
		double	atNToCaAng = `121.9`
	)

Insert a new aminoacid of type 'code' after position 'n'. Atoms are set according to lenght and angle cristallographic values. Torsion angles are given in input (DEFAULT: -62', -41') WARNING: This function is only implemented for 'flat' spacers. Ie. no subspacers can be handled. NB: This function is invoked by the Nazgul module to temporarily (!!!) fill gaps.

Parameters

code
n
phi
psi
omega
NToCaLen
CaToCLen
CToOLen
atCaToCAng
CaToOAng
CtoNLen
atCToNAng
OToNAng
atNToCaAng

void insertAminoAfterWithGaps	(	string	code,
		unsigned int	n = `9999`,
		double	phi = `-62`,
		double	psi = `-41`,
		double	omega = `180`,
		int	beginHole = `0`,
		int	endHole = `0`,
		vgVector3< double >	ca1 = `vgVector3<double>()`,
		vgVector3< double >	ca2 = `vgVector3<double>()`,
		string	target = `""`,
		Spacer *	refSpacer = `0`,
		Spacer *	pOriginalSpacer = `0`,
		double	NToCaLen = `1.458`,
		double	CaToCLen = `1.52`,
		double	CToOLen = `1.231`,
		double	atCaToCAng = `111.6`,
		double	CaToOAng = `120.80`,
		double	CtoNLen = `1.33`,
		double	atCToNAng = `116.4`,
		double	OToNAng = `123.2`,
		double	atNToCaAng = `121.9`
	)

Used to insert an amino after a GAP. The general idea is to develop a mixed function between inserting a new amino and connecting aminoacids in the spacer). The difference is placed into the parameters beginHole & endHole. They represent those two indices such that (beginHole+1..endHole-1) is an hole. We need these parameters for deciding how to change the internal numbering

Parameters

code
n
phi
psi
omega
beginHole
endHole
ca1
ca2
target
refSpacer
pOriginalSpacer
NToCaLen
CaToCLen
CToOLen
atCaToCAng
CaToOAng
CtoNLen
atCToNAng
OToNAng
atNToCaAng

void insertAminoBefore	(	string	code,
		unsigned int	p = `0`,
		double	phi = `-62`,
		double	psi = `-41`,
		double	omega = `180`,
		double	NToCaLen = `1.458`,
		double	CaToCLen = `1.52`,
		double	CToOLen = `1.231`,
		double	atCaToCAng = `111.6`,
		double	CaToOAng = `120.80`,
		double	CtoNLen = `1.33`,
		double	atCToNAng = `116.4`,
		double	OToNAng = `123.2`,
		double	atNToCaAng = `121.9`
	)

This function is only implemented for 'flat' spacers. Ie. no subspacers can be handled. NB: This function is invoked by the Nazgul module to temporarily (!!!) fill gaps. WARNING: this method still requires to be corrected: problems are found in positioning the O atom.

Parameters

code
p
phi
psi
omega
NToCaLen
CaToCLen
CToOLen
atCaToCAng
CaToOAng
CtoNLen
atCToNAng
OToNAng
atNToCaAng

void insertComponent ( Component * c )

virtual

Insert a component(only an Amino acid or Sapacer class type are allowed) in the spacer at the back side. It doesn't connect the components.

Parameters

c,pointer to the component to insert

Reimplemented from Polymer.

void insertFirstSpacer ( Spacer * sp )

insert a new sub spacer inside an empty spacer structure WARNING: this method works only with superior spacers which are made of other subspacers only (child components must be all spacers, the presence of aminoacids is not considered) (This assumption is sufficient for the Thor module)

Parameters

sp,spacer reference

void insertSubSpacerAfter	(	Spacer *	sp,
		unsigned int	pos
	)

insert a new sub spacer inside a spacer structure. N.B. spacers are not positioned, they maintain original coordinates WARNING: this method works only with superior spacers which are made of other subspacers only (child components must be all spacers, the presence of aminoacids is not considered) (This assumption is sufficient for the Thor module)

Parameters

sp,Spacer	reference
pos

bool inSync ( )

inherited

Checks the "Modified" flag in the component.

Returns: True, if the component coordinates have been already syncronized. Checks also for the "superior" class status.

bool isBond ( const SimpleBond & c ) const

inherited

Is c bonded to this ?

bool isGap ( int index )

Predicate used to determine if there is a gap in a given position/PDB aminoacid number

Parameters

index,given position to evaluate

Returns: result from the verification

bool isInBond ( const SimpleBond & c ) const

inherited

Is c in-bonded to this ?

bool isIndirectBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isIndirectInBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isIndirectOutBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isOutBond ( const SimpleBond & c ) const

inherited

Is c out-bonded to this ?

bool isTorsionBond ( const SimpleBond & c ) const

inherited

Checks if this is torsion bond to c. (ie. A to D if A indirect bond C and C bond D)

void load ( Loader & l )

virtual

Loads the Spacer from a Loader

Parameters

l,reference of the Loader

Reimplemented from Polymer.

void makeFlat ( )

Rearrange the spacer (and all sub-spacers) as a flat tree. After this there are no more sub-spacers..

void mergeSpacer ( Spacer * s )

Merge the components of the sub-spacer <s> at the place of <s> in the spacer <this>..

Parameters

s,spacer reference

void modifySubSpacerList	(	Spacer *	s,
		int	count
	)

protected

If something has changed in the spacer structure, this method updates the spacer given as a parameter .

Parameters

s,pointer	to the spacer to modify(Spacer*),
count,number	of aminoacids which has inserted (positive value) or deleted (negativ value)

bool NMRGetMinimumCADistanceVector	(	const string &	strFileName,
		vector< double > *	pNMR
	)

static

This helper function, is used to implement an optimization to mjollnir. What it does is simple and it works only for NMR PDB files. We load it and we read the number of different models stored. After it, we load every single model and once we did it, we calculate every single distance between Ca atoms. We return a position-related array, where each position is the minimum distance between each pair of Ca.

Parameters

strFileName,PDB	file name
pNMR,the	reference vector for the result values

Returns: true if the function does the job

Spacer & operator= ( const Spacer & orig )

Assign the spacer to another spacer.

Parameters

orig,reference for the original spacer

Returns: reference to the new spacer

void printComponents ( )

Prints the components.

void printGaps ( )

Predicate used to a list of the positions/pdb amino acid numbers where a gap is present

Returns: prints the corresponding values

void printSubSpacerList ( )

Prints the subspacer list.

void pUnbindIn ( SimpleBond & c )

protectedvirtualinherited

Private method to find the matching in-bond from c to this to remove.

void pUnbindOut ( SimpleBond & c )

protectedvirtualinherited

Private method to find the matching out-bond from c to this to remove.

void removeAllGaps ( )

Modifier used to remove all gaps from the gap list.

void removeComponent ( Component * c )

virtual

Removes the corresponding component

Parameters

c,pointer to the component to remove, usually the object that is calling the method.

Reimplemented from Polymer.

void removeComponentFromIndex ( unsigned int i )

virtual

Removes the corresponding component in the corresponding index

Parameters

i,index to the component to remove, usually the index of the object that is calling the method.

Reimplemented from Polymer.

void removeGap ( int index )

Modifier used to remove a specific gap from the gaps list created.

Parameters

index,amino acid number

void resetBoundaries ( )

protectedvirtual

Reset the amino acids boundaries

Reimplemented from Polymer.

void save ( Saver & s )

virtual

Saves the information from the saver into the Spacer

Parameters

s,reference to the saver

Reimplemented from Polymer.

void setAtomStartOffset ( int _offset )

Set the atom offset

Parameters

_offset

void setDSSP ( bool verbose )

Set the secondary structure (states) from H bonds.

SS definition: Kabsch, Sander, Biopolymers. 1983 Dec;22(12):2577-637.

n-Turn: T = (i,i+n) n=3,4,5 3 = (n = 3) 4 = (n = 4) 5 = (n = 5)

Bridge: B = (i-1,i,i+1) (j-1,j,j+1) nonoverlapping P = parallel (i-1,j) && (j,i+1) || (j-1,i) && (i,j+1) A = anti (i,j) && (j,i) || (i-1,j+1) && (j-1,i+1)

Helices at least 2 consecutive n-Turns (longer helices by overlapping) G = 3-helix : (i-1,i+2) && (i,i+3) H = 4-helix at i: (i-1,i+3) && (i,i+4) I = 5-helix : (i-1,i+4) && (i,i+5)

Ladder: B = Consecutive bridges of identical type Sheet: E = One or more ladders connected by shared residues Bend: S = angle { CA(i)-CA(i-2), CA(i+2)-CA(i) } > 70

Structure Priority (switched E and B): H E B G I T S

TODO: check for chain breaks. TODO: remove small helices. TODO: check for bulges.

void setMaxInBonds ( unsigned int m )

inherited

Sets maximum of in-bonds.

void setMaxOutBonds ( unsigned int m )

inherited

Sets maximum of out-bonds.

void setRot ( vgMatrix3< double > r )

virtual

Sets the rotation matrix

Parameters

r,the rotation matrix to set

Reimplemented from Polymer.

void setStartOffset ( int _offset )

Set the start offset, considers the first amino acid number in the pdb file

Parameters

_offset,value for the offset

void setStateFromSecondary ( string sec )

Set the state (HELIX or STRAND ...) from the string sec which may be generated for example by DSSP.

Parameters

sec,secondary structure sequence

void setStateFromTorsionAngles ( )

Set the state (HELIX or STRAND ...) from the torsion angles of the aminoacids (phi/psi angles).

void setTrans ( vgVector3< double > t )

virtual

Sets the translation vector

Parameters

t,the translation vector to set

Reimplemented from Polymer.

void setType ( string _name )

virtualinherited

Sets type (eg. C atom, GLY amino acid, etc.) of this.

Reimplemented in AminoAcid, Atom, and Nucleotide.

const unsigned int sizeAmino ( ) const

Returns the count of all aminoacids in the spacer

Returns: Quantity of amino acids in the spacer

unsigned int sizeInBonds ( ) const

inherited

How many in-bonds are there ?

unsigned int sizeOpenInBonds ( ) const

inherited

Returns the number of open in-bonds, ie. how many in-bonds can still be added.

Parameters

void

Returns: unsigned int

unsigned int sizeOpenOutBonds ( ) const

inherited

Returns the number of open out-bonds, ie. how many out-bonds can still be added.

Parameters

void

Returns: unsigned int

unsigned int sizeOutBonds ( ) const

inherited

How many out-bonds are there ?

const unsigned int sizeSpacer ( ) const

Allows to know if there is a spacer in the protein or not.

Returns: quantity of spacers, possible values are 0 or 1

Spacer * splitSpacer	(	unsigned int	start,
		unsigned int	end
	)

Create a new sub-spacer at the place of <start> and put all components between <start> and <end> in the new sub-spacer. The method returns the pointer at the new sub-spacer.

Parameters

start
end

Returns: spacer reference

void sync ( )

virtual

Synchronizes coords with structure

Reimplemented from Polymer.

void unbindIn ( Bond & c )

virtualinherited

Remove in-going bond from this to c.

Parameters

bond reference

Returns: void

void unbindIn ( SimpleBond & c )

virtualinherited

Removes an in-bond from this to c.

Reimplemented in Atom.

void unbindOut ( Bond & c )

virtualinherited

Remove out-going bond from this to c.

Parameters

bond reference

Returns: void

void unbindOut ( SimpleBond & c )

virtualinherited

Removes an out-bond from this to c.

Reimplemented in Atom.

void updateSubSpacerList ( )

protected

Update the internal structure of a spacer after a change in the structure of a spacer.

The documentation for this class was generated from the following files:

Biopool/Sources/Spacer.h
Biopool/Sources/Spacer.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation