meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Class SmoothRotamerLibraryParameters

java.lang.Object
  meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters

All Implemented Interfaces:

Parameters, CompositeTorsionsDefinitions

Direct Known Subclasses:

SmoothRotamerLibraryParametersChi0, SmoothRotamerLibraryParametersChi1, SmoothRotamerLibraryParametersChi2, SmoothRotamerLibraryParametersChi3, SmoothRotamerLibraryParametersChi4

public abstract class SmoothRotamerLibraryParameters
extends java.lang.Object
implements Parameters, CompositeTorsionsDefinitions

Parameters used with the SmoothRotamerLibraryEnergy term. Each parameters object contains all the information needed to calculate the term's energy value for a given residue type, between none and six polynomials. Because of the complexity of the energy term, there are several classes that inherit from this parent class, one for each number of possible sidechain torsion angles.

Field Summary

protected SplinedPolynomial[]	polynomials polynomials used
private int	residueType residue type

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

SmoothRotamerLibraryParameters(int residueType)
Updates residue type of parameters.

Method Summary

abstract double	evaluate(int derivVar, ResidueTorsions resTorsions) evaluates parameters for residue torsions.
int	getResidueType() returns rotamer's residue type
SplinedPolynomial	getSplinedPolynomial(int spType) retrieves specific polynomial.
protected abstract boolean	legalResidueType() verifies residue type is a legal residue types for class.
void	reportPolynomialsList() Reports contents of all polynomials.
java.lang.String	toString() Converts attributes of SmoothRotamerLibraryParameters to string.

Methods inherited from class java.lang.Object

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

Field Detail

residueType

private final int residueType

residue type

polynomials

protected SplinedPolynomial[] polynomials

polynomials used

Constructor Detail

SmoothRotamerLibraryParameters

public SmoothRotamerLibraryParameters(int residueType)

Updates residue type of parameters.

Method Detail

getResidueType

public int getResidueType()

returns rotamer's residue type

legalResidueType

protected abstract boolean legalResidueType()

verifies residue type is a legal residue types for class.

getSplinedPolynomial

public SplinedPolynomial getSplinedPolynomial(int spType)

retrieves specific polynomial.

evaluate

public abstract double evaluate(int derivVar,
                                ResidueTorsions resTorsions)

evaluates parameters for residue torsions. That is, calculate the energy value and derivatives. While the parameters class in MESHI is usually just a static storage, the complex nature of the energy calculations with the smooth rotamer library allows easier calculations here. Note that throughout evaluate() it is assumed that all the torsion angles required for calculation exist. This is most crucial for the first and last residue of the protein, which may not have phi and psi, respectively.

Parameters:

derivVar - torsion angle to be derived in calculation, zero for none.

resTorsions - all of the calculated residue's torsion angles

reportPolynomialsList

public void reportPolynomialsList()

Reports contents of all polynomials.

toString

public java.lang.String toString()

Converts attributes of SmoothRotamerLibraryParameters to string.

Overrides:

toString in class java.lang.Object