meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
Class RamachandranParametersList

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

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 RamachandranParametersList
extends ParametersList
implements CompositeTorsionsDefinitions

See Also:

Serialized Form

Field Summary

private SplinedPolynomialsLoader

spl

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

RamachandranParametersList(java.lang.String splinedPolynomialsFileName)

Method Summary

Parameters	createParameters(int residueType)
Parameters	createParameters(java.lang.String line) Energy term specific method to create a Parameters object from a line of the parameters file.
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 SplinedPolynomialsLoader spl

Constructor Detail

RamachandranParametersList

public RamachandranParametersList(java.lang.String splinedPolynomialsFileName)

Method Detail

createParameters

public Parameters createParameters(int residueType)

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(java.lang.String line)

Description copied from class: ParametersList

Energy term specific method to create a Parameters object from a line of the parameters file.

Specified by:

createParameters in class ParametersList