meshi.energy.simpleEnergyTerms.compositeTorsions
Class SplinedPolynomial

java.lang.Object
  meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial

All Implemented Interfaces:

CompositeTorsionsDefinitions

public class SplinedPolynomial
extends java.lang.Object
implements CompositeTorsionsDefinitions

Polynomial for calculating energy values for a given amino acid, and given torsion angles.

Field Summary

private int	aac
private double[][]	breaks
private double[]	coefs
private int	numVariables
private int[]	order
private double[][]	quickPowerMatrix
private int	ssType
private int[]	torsionAngles

Fields inherited from interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions

ALL, CHI_1, CHI_2, CHI_3, CHI_4, COIL, HELIX, NUM_SIDECHAIN_TORSIONS, OMG, OMNI, PHI, POLYNOMIAL_CHI_1, POLYNOMIAL_CHI_1_CHI_2, POLYNOMIAL_CHI_1_CHI_2_TORSIONS, POLYNOMIAL_CHI_1_CHI_3, POLYNOMIAL_CHI_1_CHI_3_TORSIONS, POLYNOMIAL_CHI_1_CHI_4, POLYNOMIAL_CHI_1_CHI_4_TORSIONS, POLYNOMIAL_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI, POLYNOMIAL_PHI_PSI_CHI_1, POLYNOMIAL_PHI_PSI_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI_TORSIONS, PREPRO, PSI, SHEET, TOTAL_TORSION_ANGLES, UNIDENTIFIED_TORSION_TYPE

Constructor Summary

SplinedPolynomial(int numVariables, int aac, int[] torsionAngles, int ssType, double[][] breaks, double[] coefs)
Creates a new splined polynomial.

Method Summary

int	findBin(double[] breaks, double torsion) Find break index (bin) for torsion angle.
double	fixTorsionToBin(double[] breaks, double torsion, int bin) Fixes a torsion to be inside its bin.
boolean	isPolynomialNeeded(int aac, int[] torsionAngles, int ssType) checks whether this polynomial is of the parameters needed.
private static double	quickPower(double torsion, int power) Raises a double by the power, with 0 <= power <= 3.
java.lang.String	toString() Converts attributes of polynomial to string.
double	value(int derivVar, double... args) Calculates polynomial's derivation for given variable with value for list of arguments.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

numVariables

private int numVariables

aac

private int aac

torsionAngles

private int[] torsionAngles

ssType

private int ssType

breaks

private double[][] breaks

coefs

private double[] coefs

quickPowerMatrix

private double[][] quickPowerMatrix

order

private int[] order

Constructor Detail

SplinedPolynomial

public SplinedPolynomial(int numVariables,
                         int aac,
                         int[] torsionAngles,
                         int ssType,
                         double[][] breaks,
                         double[] coefs)

Creates a new splined polynomial.

Method Detail

isPolynomialNeeded

public boolean isPolynomialNeeded(int aac,
                                  int[] torsionAngles,
                                  int ssType)

checks whether this polynomial is of the parameters needed.

value

public double value(int derivVar,
                    double... args)

Calculates polynomial's derivation for given variable with value for list of arguments.

Parameters:

derivVar - variable to be derived (zero for calculation of polynomial).

findBin

public int findBin(double[] breaks,
                   double torsion)

Find break index (bin) for torsion angle.

Returns:

left bound of break, -1 if no break found.

fixTorsionToBin

public double fixTorsionToBin(double[] breaks,
                              double torsion,
                              int bin)

Fixes a torsion to be inside its bin. Since some of the breaks are not from -pi to pi (due to the varied grid construction method) we need this addition to verify the polynomial is calculated correctly.

toString

public java.lang.String toString()

Converts attributes of polynomial to string.

Overrides:

toString in class java.lang.Object

quickPower

private static double quickPower(double torsion,
                                 int power)

Raises a double by the power, with 0 <= power <= 3. For the special exception of power=-1, returns 0 (as it eases polynomial derivation calculations).