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LoopTableEntry Class Reference

Implements an entry for the loop table (equivalent to the old "ProteinTableEntry" from the previous version. More...

Public Member Functions

 LoopTableEntry ()
 
 LoopTableEntry (const LoopTableEntry &orig)
 
virtual ~LoopTableEntry ()
 
double calculateDeviation (const LoopTableEntry &, unsigned int nAmino=0) const
 
LoopTableEntry concatenate (const LoopTableEntry &, unsigned int)
 
void copy (const LoopTableEntry &orig)
 
float getBOND_ANGLE_AT_CALPHA_TO_CPRIME ()
 
float getBOND_ANGLE_AT_CPRIME_TO_N ()
 
float getBOND_ANGLE_AT_N_TO_CALPHA ()
 
float getBOND_LENGTH_CALPHA_TO_CPRIME ()
 
float getBOND_LENGTH_CPRIME_TO_N ()
 
float getBOND_LENGTH_N_TO_CALPHA ()
 
LoopTableEntryoperator= (const LoopTableEntry &orig)
 
vgVector3< float > & operator[] (unsigned int n)
 
const vgVector3< float > & operator[] (unsigned int n) const
 
void printTable (unsigned int k=0) const
 
void rotate (const vgVector3< float > &axis, const double angle)
 
void rotate (const vgMatrix3< float > &rotationMatrix)
 
float rotateIntoXYPlane (VectorTransformation &vt)
 
LoopTableEntry setToOrigin (LoopTableEntry &, unsigned int, VectorTransformation &vt)
 
void setToSingleAminoAcid ()
 

Detailed Description

Implements an entry for the loop table (equivalent to the old "ProteinTableEntry" from the previous version.

The two structs below serve to store a single entry in the protein table. To this end they contain endPoint, endDirection and normal, which are required for successful concatenation. The main difference between these two structs is that CompressedProteinTableEntry contains a table entry which had to be packed due to memory restrictions, hence the name. ProteinTableEntry contains two helper functions to concatenate a single amino acid combination and to rotate its endPoint back into the XY plane.

Constructor & Destructor Documentation

basic constructor

LoopTableEntry ( const LoopTableEntry orig)

Constructor based on the copy of another original object

Parameters
referenceto the original object(const LoopTableEntry&)
~LoopTableEntry ( )
virtual

basic destructor

Member Function Documentation

double calculateDeviation ( const LoopTableEntry other,
unsigned int  nAmino = 0 
) const

Calculates the deviation between src1 and src2 (the object data and the one given parameter )

Parameters
referenceto the Loop Table entry(const LoopTableEntry&) , number of amino acids(unsigned int)
Returns
corresponding value(double)
LoopTableEntry concatenate ( const LoopTableEntry dest,
unsigned int  nChain 
)

Concatenates the table entry this with dest, the result is returned as function value. dest is aligned with this before concatenation. The Omega torsion angle is to be twisted considered for even nChain starting points of src.

Parameters
referenceto the loop table entry(const LoopTableEntry&),number of chains(unsigned int)
Returns
the resulting loop table entry(LoopTableEntry)
void copy ( const LoopTableEntry orig)

copies an original object into the structure

Parameters
referenceto the original object(const LoopTableEntry&)
Returns
changes are made internally(void)
float getBOND_ANGLE_AT_CALPHA_TO_CPRIME ( )

returns the value of BOND_ANGLE_AT_CALPHA_TO_CPRIME

Parameters
none
Returns
corresponding value ( float)
float getBOND_ANGLE_AT_CPRIME_TO_N ( )

returns the value of BOND_ANGLE_AT_CPRIME_TO_N

Parameters
none
Returns
corresponding value ( float)
float getBOND_ANGLE_AT_N_TO_CALPHA ( )

returns the value of BOND_ANGLE_AT_N_TO_CALPHA

Parameters
none
Returns
corresponding value ( float)
float getBOND_LENGTH_CALPHA_TO_CPRIME ( )

returns the BOND_LENGTH_CALPHA_TO_CPRIME

Parameters
none
Returns
corresponding value ( float)
float getBOND_LENGTH_CPRIME_TO_N ( )

returns the value of BOND_LENGTH_CPRIME_TO_N

Parameters
none
Returns
corresponding value ( float)
float getBOND_LENGTH_N_TO_CALPHA ( )

returns the value of BOND_LENGTH_N_TO_CALPHA

Parameters
none
Returns
corresponding value ( float)
LoopTableEntry & operator= ( const LoopTableEntry orig)

Assigns one original Entry table into another

Parameters
theoriginal loop entry table reference(const LoopTableEntry& )
Returns
reference to the resulting loop table entry(LoopTableEntry)
vgVector3< float > & operator[] ( unsigned int  i)

Obtains the corresponding value depending of the index

Parameters
index(unsigned int)
Returns
reference to the resulting vector(vgVector3<float>&)
const vgVector3< float > & operator[] ( unsigned int  i) const

Obtains the corresponding value depending of the index

Parameters
index(unsigned int)
Returns
reference to the resulting vector(vgVector3<float>&)
void printTable ( unsigned int  k = 0) const

Prints an entry data

Parameters
indexof the entry
Returns
the output is printed
void rotate ( const vgVector3< float > &  axis,
const double  _angle 
)

Rotates this along axis by angle. Axis can be any valid vector, angle is indicated in radians.

Parameters
referenceto the axis(const vgVector3<float>&), angle to rotate(const double)
Returns
changes are made internally(void)
void rotate ( const vgMatrix3< float > &  rotationMatrix)

rotates this by angle along axis

Parameters
referenceto the rotation matrix( const vgMatrix3<float>&)
Returns
changes are made internally(void)
float rotateIntoXYPlane ( VectorTransformation vt)

Rotates the endPoint of this back into the X,Y plane and updates endDirection, normal accordingly. rotate EP into the x,y plane (and update ED & N accordingly) by using the arccos of the x-element of EP as reference for the required angle

Parameters
referenceto the transformation vector(VectorTransformation&)
Returns
corresponding value
LoopTableEntry setToOrigin ( LoopTableEntry dest,
unsigned int  nChain,
VectorTransformation vt 
)

setToOrigin is the dual method to concatenate. It reverses the concatenation held there, ie. the source is 'subtracted' from destination.

Parameters
referenceto the loop table entry(const LoopTableEntry&),number of chains(unsigned int)
Returns
the resulting loop table entry(LoopTableEntry)
void setToSingleAminoAcid ( )

Defaults the protein table entry to the simple case where it is a single amino acid.

Parameters
none
Returns
changes are made internally(void)

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