Victor
|
class manages the angle qualities and the energy More...
Public Member Functions | |
PhiPsiOmega (int SET_ARC1=10, string knownledge="data/tor.par") | |
virtual long double | calculateEnergy (Spacer &sp) |
virtual long double | calculateEnergy (Spacer &sp, unsigned int index1, unsigned int index2) |
virtual long double | calculateEnergy (AminoAcid &aa) |
virtual long double | calculateEnergy (AminoAcid &diheds, AminoAcidCode code) |
virtual double | calculateMaxEnergy (Spacer &sp) |
virtual double | calculateMaxEnergy (unsigned int amino) |
virtual double | calculateMinEnergy (Spacer &sp) |
virtual double | calculateMinEnergy (unsigned int amino) |
virtual vector< vector< ANGLES > > * | getOrderedEnergyTable () |
virtual double | pReturnMaxPropensities (int amino) |
virtual double | pReturnMinPropensities (int amino) |
virtual void | setArcStep (int n) |
virtual int | setRange_Omega (int n) |
Protected Member Functions | |
virtual double | getOmegaAngle (int prop, long RANGE_OMEGA) |
virtual double | getPhiPsiAngle (int prop, long SIZE_TABLE, int ARC_STEP) |
virtual void | pConstructData () |
virtual void | pConstructMaxPropensities () |
virtual void | pConstructMinPropensities () |
virtual double | pGetMaxPropensities (int amino) |
virtual double | pGetMinPropensities (int amino) |
virtual void | pResetData () |
void | sAddProp (int code, int x, int y, int z) |
int | sGetPropBin (double p) |
int | sGetPropOmegaBin (double p) |
class manages the angle qualities and the energy
This class implements a simple torsion potential based on the statistical preference of aminoacid types phi , psi and omega angles.
PhiPsiOmega | ( | int | SET_ARC1 = 10 , |
string | knownledge = "data/tor.par" |
||
) |
Constructor that sets the arc steps for the table's size
arc | values for table 1 and 2(int ,int), file name where torsion angles are, usually data/tor.par(string) |
|
virtual |
calculates energy for a protein
reference | to the spacer containing the protein (Spacer&) |
Implements TorsionPotential.
|
virtual |
calculates energy for part of the protein
reference | to the spacer that contains the protein(Spacer&) , start and end position of the protein part (unsigned int , unsigned int) |
Implements TorsionPotential.
|
virtual |
calculates energy for a specific amino acid
aminoacid | reference (AminoAcid&) |
Implements TorsionPotential.
|
virtual |
diheds | a (phi, psi, omega) triple of dihedral angles. code: an amino acid type. phi-psi-omega torsional energy of the amino acid whose (phi, psi, omega) triple is specified by 'diheds' and whose type is specified by code. |
Implements TorsionPotential.
|
virtualinherited |
Calculates the maximum energy for the amino acids in the spacer
spacer | reference(Spacer&) |
|
virtualinherited |
Calculates the maximum energy for an amino acid
index | of the amino acid, consider the enum list(unsigned int) |
|
virtualinherited |
Calculates the minimum energy for the amino acids in the spacer
spacer | reference(Spacer&) |
|
virtualinherited |
Calculates the minimum energy for an amino acid
index | of the amino acid, consider the enum list(unsigned int) |
|
protectedvirtual |
obtains the Omega angle for a given propensity value and Omega range
propensity | value (int), Omega range(long) |
Reimplemented from TorsionPotential.
|
virtual |
Returns asort energy table
none |
|
protectedvirtual |
Calculates the value os the psi , phi angle
propensity | value(int), long(not used),arc step(int) |
Reimplemented from TorsionPotential.
|
protectedvirtual |
Method that using the torsion file, creates the structure
none |
Implements TorsionPotential.
|
protectedvirtual |
@return |
|
protectedvirtual |
computes and stores the minimum propensities based on the max propensities based on knowledge
none |
|
protectedvirtual |
obtains the maximum propensity value for an amino acid type considering all the granularities
amino | acid code(int) |
|
protectedvirtual |
amino | the code of an amino acid type. value: minimum (phi, psi, omega) propensity of that type according to kwnowledge. |
|
protectedvirtual |
Resets all the propensities set previously
none |
Implements TorsionPotential.
|
virtual |
obtains the maximum propensity value for an amino acid type knowledge based
amino | acid code(int) |
Implements TorsionPotential.
|
virtual |
obtains the minimum propensity value for an amino acid type considering a given phi and psi values knowledge based
amino | acid code(int), values for the previous phi and psi angles(int , int) |
Reimplemented from TorsionPotential.
|
protected |
Adds propensity value for a amino acid type
corresponding | amino acid code(int), corresponding propensity values(int, int, int, int, int)) |
|
virtual |
@return |
|
virtual |
Sets the range for omega
parameter | for omega range, only 1,2, and 3 are posible(int) |
|
protected |
Returns the propensity binding value using table 1(granularity) for a specific angle
angle | in degrees |
|
protected |
@return |