Victor
 All Data Structures Functions Variables Friends Pages
Protein Class Reference

Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present). More...

+ Inheritance diagram for Protein:
+ Collaboration diagram for Protein:

Public Member Functions

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 Proteinclone ()
 
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 deleteComponent (Component *c)
 
char getChainLetter (unsigned int i)
 
unsigned int getChainNum (char c)
 
virtual const SimpleBondgetInBond (unsigned int n) const
 
virtual SimpleBondgetInBond (unsigned int n)
 
virtual AtomgetInBondRef (unsigned int n)
 
LigandSetgetLigandSet (char c)
 
LigandSetgetLigandSet (unsigned int n)
 
virtual vgVector3< double > getLowerBound (double dist=0.0)
 
unsigned int getMaxInBonds () const
 
unsigned int getMaxOutBonds () const
 
virtual AtomgetOpenInBondRef (unsigned int n=0)
 
virtual AtomgetOpenOutBondRef (unsigned int n=0)
 
virtual const SimpleBondgetOutBond (unsigned int n) const
 
virtual SimpleBondgetOutBond (unsigned int n)
 
virtual AtomgetOutBondRef (unsigned int n)
 
PolymergetPolymer (unsigned int n)
 
SpacergetSpacer (char c)
 
SpacergetSpacer (unsigned int n)
 
virtual string getType () const
 
virtual vgVector3< double > getUpperBound (double dist=0.0)
 
void insertComponent (Component *c)
 
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
 
void removeComponent (Component *c)
 
virtual void removeComponentFromIndex (unsigned int i)
 
void setMaxInBonds (unsigned int m)
 
void setMaxOutBonds (unsigned int m)
 
virtual void setType (string _name)
 
unsigned int sizeInBonds () const
 
unsigned int sizeOpenInBonds () const
 
unsigned int sizeOpenOutBonds () const
 
unsigned int sizeOutBonds () const
 
virtual void unbindIn (Bond &c)
 
virtual void unbindIn (SimpleBond &c)
 
virtual void unbindOut (Bond &c)
 
virtual void unbindOut (SimpleBond &c)
 

Protected Member Functions

virtual void pUnbindIn (SimpleBond &c)
 
virtual void pUnbindOut (SimpleBond &c)
 

Detailed Description

Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present).

Member Function Documentation

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
atomreference, 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
atomreference, bond reference, atom reference
Returns
void
void bindOut ( SimpleBond c)
virtualinherited

Sets and out-bond from this to c

Reimplemented in Atom.

Protein * clone ( )
virtual
Parameters

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
bondreference
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 deleteComponent ( Component c)
virtual
Parameters

Reimplemented from Polymer.

char getChainLetter ( unsigned int  i)

Returns the chainID by index

Parameters
i(unsigned int) index
Returns
The chainID (char)
unsigned int getChainNum ( char  c)

Returns the chain index by chainID

Parameters
c(char) chainID
Returns
The chainID index in the chains vector
const SimpleBond & getInBond ( unsigned int  n) const
virtualinherited

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getInBond ( unsigned int  n)
virtualinherited

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

Atom & getInBondRef ( unsigned int  n)
virtualinherited

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

Parameters
unsignedint
Returns
Atom reference
LigandSet * getLigandSet ( char  c)

Return a pointer to the LigandSet with the requested chainID

Parameters
c(char), the chainID
Returns
A pointer to the LiganSet
LigandSet * getLigandSet ( unsigned int  n)

Return a pointer to the LiganSet by an index in the Components vector.

Parameters
n(unsigned int), the index of the Polymer in the Components vector
Returns
A pointer to the LiganSet
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.

Atom & getOpenInBondRef ( unsigned int  n = 0)
virtualinherited

Returns reference to the i-th open in-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).

Parameters
unsignedint
Returns
Atom reference

Reimplemented in Spacer, and AminoAcid.

Atom & getOpenOutBondRef ( unsigned int  n = 0)
virtualinherited

Returns reference to the i-th open out-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).

Parameters
unsignedint
Returns
atom reference

Reimplemented in Spacer, and AminoAcid.

const SimpleBond & getOutBond ( unsigned int  n) const
virtualinherited

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getOutBond ( unsigned int  n)
virtualinherited

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

Atom & getOutBondRef ( unsigned int  n)
virtualinherited

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

Parameters
unsignedint
Returns
Atom reference
Polymer & getPolymer ( unsigned int  n)

Get the Polymer (Spacer + LigandSet) by an index.

Parameters
n(unsigned int), the index of the Polymer in the Components vector
Returns
The reference to the Polymer
Spacer * getSpacer ( char  c)

Return a pointer to the Spacer with the requested chainID

Parameters
c(char), the chainID
Returns
A pointer to the Spacer
Spacer * getSpacer ( unsigned int  n)

Return a pointer to the Spacer by an index in the Components vector.

Parameters
n(unsigned int), the index of the Polymer in the Components vector
Returns
A pointer to the Spacer
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 insertComponent ( Component p)
virtual

Insert a Polymer in the Protein. It is related to a single chain, and must contain a Spacer and possibly a LigandSet

Parameters
p(Component*)

Reimplemented from Polymer.

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)

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 removeComponent ( Component c)
virtual
Parameters

Reimplemented from Polymer.

void removeComponentFromIndex ( unsigned int  i)
virtualinherited
Parameters

Reimplemented in Spacer.

void setMaxInBonds ( unsigned int  m)
inherited

Sets maximum of in-bonds.

void setMaxOutBonds ( unsigned int  m)
inherited

Sets maximum of out-bonds.

void setType ( string  _name)
virtualinherited

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

Reimplemented in AminoAcid, Atom, and Nucleotide.

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 unbindIn ( Bond c)
virtualinherited

Remove in-going bond from this to c.

Parameters
bondreference
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
bondreference
Returns
void
void unbindOut ( SimpleBond c)
virtualinherited

Removes an out-bond from this to c.

Reimplemented in Atom.


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