Victor
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class manages the angle qualities and the energy More...
Public Member Functions | |
PhiPsi (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 &aa, double phi, double psi) |
virtual long double | calculateEnergy (AminoAcid &diheds, AminoAcidCode code) |
virtual long double | calculateEnergySmooth (AminoAcid &aa) |
virtual double | calculateMaxEnergy (Spacer &sp) |
virtual double | calculateMaxEnergy (unsigned int amino) |
virtual double | calculateMinEnergy (Spacer &sp) |
virtual double | calculateMinEnergy (unsigned int amino) |
double | getEnergyFromPhiPsi (AminoAcidCode code, double phi, double psi) |
virtual double | pReturnMaxPropensities (int amino) |
virtual double | pReturnMinPropensities (int amino) |
virtual void | setArcStep (int n) |
int | sGetPropBinDiff (double p, double &diff) |
Protected Member Functions | |
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 | sGetPropBin (double p) |
class manages the angle qualities and the energy
Includes methods that allow to obtain information about the angle and the energy. This class implements a simple torsion potential based on the statistical preference of aminoacid types for phi and psi angles.
PhiPsi | ( | int | SET_ARC1 = 10 , |
string | knownledge = "data/tor.par" |
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) |
@return |
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virtual |
calculates the total energy for the amino acids in the spacer
spacer | reference(Sapcer(&) |
Implements TorsionPotential.
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virtual |
calculates the total energy for the amino acids in a portion of the spacer
spacer | reference(Sapcer(&), positions for start and end of the Sapcer portion (unsigned int, unsigned int) |
Implements TorsionPotential.
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virtual |
calculates the total energy for the amino acid
the | amino acid reference (AminoAcir&) |
Implements TorsionPotential.
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virtual |
calculates the total energy for the amino acid, considering a specific phi an psi value
the | amino acid reference (AminoAcir&), values for phi and psi (double) |
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virtual |
Calculates the psi-psi torsional energy of the amino acid whose (phi, psi) pair is specified by 'diheds' and whose type is specified by code.
pair | of dihedral angles(AminoAcir&), the amino acid code(AminoAcidCode) |
Implements TorsionPotential.
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virtual |
calculates the total energy for the amino acid
the | amino acid reference (AminoAcir&) |
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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) |
double getEnergyFromPhiPsi | ( | AminoAcidCode | code, |
double | phi, | ||
double | psi | ||
) |
calculates the energy from the PhiPsi angles of an amino acid
code | of the amino acid(AminoAcidCode), values for phi and psi(double,double) |
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protectedvirtual |
Sets all the information need for the class
none |
Implements TorsionPotential.
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protectedvirtual |
fill an array containing max propensities for each amino
none |
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protectedvirtual |
fill an array containing min propensities for each amino
none |
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protectedvirtual |
Calculates the Maximum propensities value of the amino acid
amino | acid index corresponding to the enum (int) |
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protectedvirtual |
Calculates the Minimum propensities value of the amino acid
amino | acid index corresponding to the enum (int) |
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protectedvirtual |
Clears all the set data
none |
Implements TorsionPotential.
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virtual |
returns the maximum propensities for the corresponding amino
amino | index from the enum (int) |
Implements TorsionPotential.
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virtual |
returns the minimum propensities for the corresponding amino
amino | index from the enum (int) |
Reimplemented from TorsionPotential.
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protected |
Adds a propensity for a specific amino acid type
code | of the amion acid(int), coordinates (int,int,int), values to set (int, int) |
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virtual |
Sets the step for the arc
the | step value(int) |
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protected |
Calculates the propensity binding value for a specific angle
angle | value (double) |
int sGetPropBinDiff | ( | double | p, |
double & | diff | ||
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Calculates the differenciated propensity binding and the
angle | value(double), reference to the calculated diff propensity binding(double&) |