Victor
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class manages the angle qualities and the energy More...
Public Member Functions | |
PhiPsiOmegaPreAngle (int SET_ARC1=10, int SET_ARC2=40, 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 double | calculateMaxEnergy (Spacer &sp) |
virtual double | calculateMaxEnergy (unsigned int amino) |
virtual double | calculateMinEnergy (Spacer &sp) |
virtual double | calculateMinEnergy (unsigned int amino) |
virtual double | pReturnMaxPropensities (int amino) |
virtual double | pReturnMaxPropensitiesPreAngle (int amino, int prephi, int prepsi) |
virtual void | setArcStep (int n) |
virtual int | setRange_Omega (int n) |
virtual int | sGetPropBin2 (double p) |
Protected Member Functions | |
virtual void | pConstructData () |
virtual void | pConstructMaxPropensities () |
virtual double | pGetMaxPropensities (int amino) |
virtual double | pGetMaxPropensities (int amino, int prephi, int prepsi) |
virtual void | pResetData () |
virtual void | sAddProp (int code, int x, int y, int z, int m, int n) |
virtual int | sGetPropBin (double p) |
virtual 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 for phi, psi, omega, prephi and pre psi angles.
PhiPsiOmegaPreAngle | ( | int | SET_ARC1 = 10 , |
int | SET_ARC2 = 40 , |
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string | knownledge = "data/tor.par" |
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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) |
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virtual |
calculates energy for a protein
reference | to the spacer containing the protein (Spacer&) |
Implements TorsionPotential.
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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.
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virtual |
calculates energy for a specific amino acid
aminoacid | reference (AminoAcid&) |
Implements TorsionPotential.
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virtualinherited |
Calculates the maximum energy for the amino acids in the spacer
spacer | reference(Spacer&) |
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virtualinherited |
Calculates the maximum energy for an amino acid
index | of the amino acid, consider the enum list(unsigned int) |
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virtualinherited |
Calculates the minimum energy for the amino acids in the spacer
spacer | reference(Spacer&) |
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virtualinherited |
Calculates the minimum energy for an amino acid
index | of the amino acid, consider the enum list(unsigned int) |
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protectedvirtual |
Method that using the torsion file, creates the structure
none |
Implements TorsionPotential.
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protectedvirtual |
Creates the maximum propensities based on the max propensities based on knowledge
none |
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protectedvirtual |
obtains the maximum propensity value for an amino acid type considering all the granularities
amino | acid code(int) |
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protectedvirtual |
obtains the maximum propensity value for an amino acid type considering a given phi and psi values considering all the granularities
amino | acid code(int), values for the previous phi and psi angles(int , int) |
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protectedvirtual |
Resets all the propensities set previously
none |
Implements TorsionPotential.
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virtual |
obtains the maximum propensity value for an amino acid type knowledge based
amino | acid code(int) |
Implements TorsionPotential.
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virtual |
obtains the maximum 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.
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protectedvirtual |
Adds propensity value for a amino acid type
corresponding | amino acid code(int), corresponding propensity values(int, int, int, int, int)) |
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virtual |
Sets the arc step, needed to define the Size table
quantity | of steps(int) |
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virtual |
Sets the range for omega
parameter | for omega range, only 1,2, and 3 are posible(int) |
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protectedvirtual |
Returns the propensity binding value using table 1(granularity) for a specific angle
angle | in degrees |
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virtual |
Returns the propensity binding using table 2(granularity for i-1 aa) value for a specific angle
angle | in degrees(double) |
Reimplemented from TorsionPotential.
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protectedvirtual |
Returns the propensity Omega binding using
omega | angle in degrees(double) |