AminoAcid Class Reference

It mplements a simple amino acid. More...

Inheritance diagram for AminoAcid:

Collaboration diagram for AminoAcid:

Public Member Functions
	AminoAcid ()
	AminoAcid (const AminoAcid &orig)
virtual	~AminoAcid ()
void	addAtom (Atom &a)
void	addMissingO ()
void	addTerminalOXT ()
void	adjustLeadingN ()
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)
virtual void	connectIn (AminoAcid *c, unsigned int offset=1)
virtual void	connectOut (AminoAcid *c, unsigned int offset=1)
void	constructSideChain (SideChain &sc, vector< double > chi)
void	constructSideChain (SideChain &sc, double chi1, double chi2, double chi3, double chi4, double chi5)
void	copy (const Bond &orig)
void	copy (const Group &orig)
virtual void	copy (const SimpleBond &orig)
void	copy (const Component &orig)
void	copy (const AminoAcid &orig)
const AminoAcid &	getInBond (unsigned int n) const
AminoAcid &	getInBond (unsigned int n)
virtual Atom &	getInBondRef (unsigned int n)
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 AminoAcid &	getOutBond (unsigned int n) const
AminoAcid &	getOutBond (unsigned int n)
virtual Atom &	getOutBondRef (unsigned int n)
virtual string	getType () const
virtual vgVector3< double >	getUpperBound (double dist=0.0)
bool	inSync ()
bool	isBond (const SimpleBond &c) const
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
AminoAcid &	operator= (const AminoAcid &orig)
void	patchBetaPosition (unsigned int n=0)
void	removeAtom (Atom &a)
void	removeHAtomsfromLeadingNH3 ()
void	setBonds (double NToCaLen, double CaToCLen, double CToOLen, double atCaToCAng, double CaToOAng)
bool	setBondsFromPdbCode (bool connect, AminoAcid *prev=NULL, bool permissive=false)
void	setDefault ()
void	setMaxInBonds (unsigned int m)
void	setMaxOutBonds (unsigned int m)
void	setOmega (double a)
void	setPhi (double a)
void	setPsi (double a)
void	setSideChain (SideChain &sc)
void	setStateFromTorsionAngles ()
void	setType (string _name)
unsigned int	sizeInBonds () const
unsigned int	sizeOpenInBonds () const
unsigned int	sizeOpenOutBonds () const
unsigned int	sizeOutBonds () const
virtual void	sync ()
virtual void	unbindIn (Bond &c)
virtual void	unbindIn (SimpleBond &c)
virtual void	unbindOut (Bond &c)
virtual void	unbindOut (SimpleBond &c)
virtual AminoAcid *	unconnectIn ()
virtual AminoAcid *	unconnectOut ()

Protected Member Functions
Atom *	pGetAtom (const AtomCode &ac) const
virtual void	pUnbindIn (SimpleBond &c)
virtual void	pUnbindOut (SimpleBond &c)
virtual void	resetBoundaries ()

Detailed Description

It mplements a simple amino acid.

Includes methods that allow to get and set angles, connections, bonds, side chain info, etc. NB: Angles are in degrees.

Constructor & Destructor Documentation

AminoAcid

(

)

Constructor

Parameters

none

AminoAcid

(

const AminoAcid &

orig

)

Constructor

Parameters

AminoAcid

~AminoAcid ( )

virtual

DESTRUCTOR

Parameters

none

Member Function Documentation

void addAtom ( Atom &  a )

inherited

Add an Atom the the Group. Sets the superior, and the lower/upperBound.

Parameters

a

(Atom&)

void addMissingO

(

)

adds an O atom, if missing

Parameters

none

Returns

void

void addTerminalOXT

(

)

adds an OXT atom to the C terminus

Parameters

none

Returns

void

void adjustLeadingN

(

)

adjusts the translation of the N atom, set trans for N relative to CA & C, adjust this' translation, the phi angle in leading structures is always undefined

Parameters

none

Returns

void

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 aa

Parameters

none

Returns

Component*

Reimplemented from Monomer.

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 connectIn ( AminoAcid *  a, unsigned int  offset = 1  )

virtual

Connects the aa to the reverse structure

Parameters

AminoAcid*,unsigned

int (use 0)

Returns

void

void connectOut ( AminoAcid *  a, unsigned int  offset = 1  )

virtual

Connects the aa to the structure

Parameters

AminoAcid*,unsigned

int (use 0)

Returns

void

void constructSideChain	(	SideChain &	sc,
		vector< double >	chi
	)

Construct side chain

Parameters

SideChain&

sc, vector<double> chi (values for chi, as much as needed, max 5)

Returns

void

void constructSideChain	(	SideChain &	sc,
		double	chi1,
		double	chi2,
		double	chi3,
		double	chi4,
		double	chi5
	)

Construct side chain

Parameters

SideChain&

sc, double chi1, double chi2, double chi3, double chi4, double chi5 (values for chi, as much as needed, max 5)

Returns

void

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 Group &  orig )

inherited

Copy a Group. See comments in the source.

Parameters

orig

(Group&)

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 AminoAcid &

orig

)

Copies an aa

Parameters

const

AminoAcid& (copy from the orig)

Returns

void

const AminoAcid & getInBond ( unsigned int  n ) const

virtual

Returns i-th in-bond.

Reimplemented from Group.

AminoAcid & getInBond ( unsigned int  n )

virtual

Returns i-th in-bond.

Reimplemented from Group.

Atom & getInBondRef ( unsigned int  n )

virtualinherited

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

Parameters

unsigned

int

Returns

Atom reference

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

Returns the atom corresponding to N, aminoacids have only a single possible, hard coded, open in-bond

Parameters

unsigned

int

Returns

const Atom&

Reimplemented from Bond.

Atom & getOpenInBondRef ( unsigned int  n = 0 )

virtual

Returns the atom corresponding to N, aminoacids have only a single possible, hard coded, open in-bond

Parameters

unsigned

int

Returns

Atom&

Reimplemented from Bond.

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

virtual

Returns the atom corresponding to C, aminoacids have only a single possible, hard coded, open in-bond

Parameters

unsigned

int

Returns

const Atom&

Reimplemented from Bond.

Atom & getOpenOutBondRef ( unsigned int  n = 0 )

virtual

Returns the atom corresponding to C, aminoacids have only a single possible, hard coded, open in-bond

Parameters

unsigned

int

Returns

Atom&

Reimplemented from Bond.

const AminoAcid & getOutBond ( unsigned int  n ) const

virtual

Returns i-th out-bond.

Reimplemented from Group.

AminoAcid & getOutBond ( unsigned int  n )

virtual

Returns i-th out-bond.

Reimplemented from Group.

Atom & getOutBondRef ( unsigned int  n )

virtualinherited

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

Parameters

unsigned

int

Returns

Atom reference

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>)

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 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)

AminoAcid & operator=

(

const AminoAcid &

orig

)

Operator =, assign the aa

Parameters

AminoAcid

reference

Returns

AminoAcid

void patchBetaPosition

(

unsigned int

n = 0

)

adds a CB atom to the sidechain, if necessary

Parameters

unsigned

int n (value of number to set)

Returns

void

Atom * pGetAtom ( const AtomCode &  ac ) const

protectedinherited

Returns the reference to the Atom with the corresponding AtomCode

Parameters

ac	(AtomCode)

Returns

Atom reference

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 removeAtom ( Atom &  a )

inherited

Removes an atom from the group.

Parameters

a

(Atom)

void removeHAtomsfromLeadingNH3

(

)

removeHAtomsfromLeadingNH3, check for NH3+ and, if so, remove superfluous H (i.e. 2H, 3H) atoms

Parameters

none

Returns

void

void resetBoundaries ( )

protectedvirtual

Reset the boundaries

Parameters

none

Returns

void

Reimplemented from Monomer.

void setBonds	(	double	NToCaLen,
		double	CaToCLen,
		double	CToOLen,
		double	atCaToCAng,
		double	CaToOAng
	)

Set the bonds based on lengths and angles given as params

Parameters

double

NToCaLen, double CaToCLen, double CToOLen, double atCaToCAng, double CaToOAng

Returns

void

bool setBondsFromPdbCode	(	bool	connect,
		AminoAcid *	prev = NULL,
		bool	permissive = false
	)

sets the bond structure for an aminoacid, and connect it (if connect is true)

Parameters

connect,if	True connect the AminoAcid with previous AminoAcid (set "Trans" and "Coords")
prev,the	previous AminoAcid
permissive,allows	to operate on an incomplete AminoAcid

Returns

True, if the AminoAcid has been connected with the previous AminoAcid

void setDefault

(

)

set bond length and angles to cristallographic values

Parameters

none

Returns

void

void setMaxInBonds ( unsigned int  m )

inherited

Sets maximum of in-bonds.

void setMaxOutBonds ( unsigned int  m )

inherited

Sets maximum of out-bonds.

void setOmega

(

double

a

)

Sets Omega angle

Parameters

double

a (angle value)

Returns

void

void setPhi

(

double

a

)

Sets phi angle

Parameters

double

a (angle value)

Returns

void

void setPsi

(

double

a

)

Sets Psi angle

Parameters

double

a (angle value)

Returns

void

void setSideChain

(

SideChain &

sc

)

Sets side chain

Parameters

SideChain&

Returns

void

void setStateFromTorsionAngles

(

)

Sets the state from torsion angles from definition was taken from McGuffin et al., Bioinformatics (17):63-72 (2001)

Parameters

none

Returns

void

void setType ( string  _name )

virtual

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

Reimplemented from SimpleBond.

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 ?

void sync ( )

virtual

Syncronize and sets boundaries

Parameters

none

Returns

void

Reimplemented from Group.

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.

AminoAcid * unconnectIn ( )

virtual

unconnect aminoacid from predecessor

Parameters

none

Returns

AminoAcid*

Reimplemented from Component.

AminoAcid * unconnectOut ( )

virtual

unconnect aminoacid from the follower

Parameters

none

Returns

AminoAcid*

Reimplemented from Component.

---

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

• Biopool/Sources/AminoAcid.h
• Biopool/Sources/AminoAcid.cc