meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Class SmoothRotamerLibraryParametersList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Parameters>
              meshi.energy.simpleEnergyTerms.ParametersList
                  meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Parameters>, java.util.Collection<Parameters>, java.util.List<Parameters>, java.util.RandomAccess, CompositeTorsionsDefinitions

public class SmoothRotamerLibraryParametersList
extends ParametersList
implements CompositeTorsionsDefinitions

See Also:

Serialized Form

Field Summary

private static SplinedPolynomialsLoader

spl Loader contains all of the polynomials in the data file.

Fields inherited from class java.util.AbstractList

modCount

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

SmoothRotamerLibraryParametersList(java.lang.String splinedPolynomialsFileName)
Create a new parameters file from the polynomials parameters data file.

Method Summary

Parameters	createParameters(int residueType) Creates a SmoothRotamerLibraryParameters for residue type.
Parameters	createParameters(java.lang.String line) Obsolete in SmoothRotamerLibraryParametersList.
Parameters	parameters(java.lang.Object Obj) Returns parameters for ResidueTorsions object according to residue type.

Methods inherited from class meshi.energy.simpleEnergyTerms.ParametersList

add, getParameters, iterator, sort

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

spl

private static SplinedPolynomialsLoader spl

Loader contains all of the polynomials in the data file.

Constructor Detail

SmoothRotamerLibraryParametersList

public SmoothRotamerLibraryParametersList(java.lang.String splinedPolynomialsFileName)

Create a new parameters file from the polynomials parameters data file.

Method Detail

parameters

public Parameters parameters(java.lang.Object Obj)

Returns parameters for ResidueTorsions object according to residue type.

Specified by:

parameters in class ParametersList

createParameters

public Parameters createParameters(int residueType)

Creates a SmoothRotamerLibraryParameters for residue type.

createParameters

public Parameters createParameters(java.lang.String line)

Obsolete in SmoothRotamerLibraryParametersList.

Specified by:

createParameters in class ParametersList