meshi.molecularElements.ca
Class CaResidue

java.lang.Object
  meshi.molecularElements.Residue
      meshi.molecularElements.ca.CaResidue

All Implemented Interfaces:

java.lang.Comparable, ResidueCreator, MeshiPotential, Attributable, MeshiAttribute

public class CaResidue
extends Residue

Field Summary

Atom	CA
static CaResidue	creator

Fields inherited from class meshi.molecularElements.Residue

atoms, bonds, head, mode, name, nextAtom, prevAtom, tail, type

Fields inherited from interface meshi.parameters.MeshiPotential

ACCESSIBLE, ALPHA_ANGLE_PARAMETERS, ALPHA_TORSION_PARAMETERS, ANGLE_PARAMETERS, ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, BOND_PARAMETERS, BURIED, COIL, COMPOSITE_PROPENSITY_2D_PARAMETERS, COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS, COMPOSITE_PROPENSITY_PARAMETERS, COMPOSITE_TORSIONS_PARAMETERS, CONTACTS_ENVIRONMENT_PARAMETERS, CONTACTS_PARAMETERS, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, COOPERATIVE_PROPENSITY_PARAMETERS, COOPERATIVE_RAMACHANDRAN_PARAMETERS, ELECTROSTATICS_PARAMETERS, EXCLUDED_VOL_PARAMETERS, FLAT_RAMACH_PARAMETERS, HELIX, HELIX_OR_COIL, HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS, HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS, HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE, LENNARD_JONES_PARAMETERS, LENNARD_JONES_PARAMETERS_BACKBONE, LENNARD_JONES_PARAMETERS_CA, LJ_ENVIRONMENT_PARAMETERS, LJ_ENVIRONMENT_PARAMETERS_BACKBONE, LJ_ENVIRONMENT_PARAMETERS_CA, ONE_ANGLE_PARAMETERS, OUT_OF_PLANE_PARAMETERS, PLANE_PARAMETERS, PROPENSITY_ANGLE_PARAMETERS, PROPENSITY_TORSION_PARAMETERS, SHEET, SHEET_OR_COIL, SOLVATE_LONG_HB_PARAMETERS, SOLVATE_MINIMIZE_HB_PARAMETERS, SOLVATE_NOHB_PARAMETERS, SOLVATE_PARAMETERS, SOLVATE_SC_PARAMETERS, TWO_ANGLES_PARAMETERS, TWO_TORSIONS_PARAMETERS

Fields inherited from interface meshi.util.MeshiAttribute

BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE

Constructor Summary

CaResidue(java.lang.String name)
Use this constructor to instantiate a creator object..

CaResidue(java.lang.String name, ResidueType type, ResidueIdentifier id, AtomList atomList, ResidueMode mode)

Method Summary

Residue	create(AtomList atoms, ResidueIdentifier id, ResidueMode mode) create a residue based on an atoms list.
Distance	distance(CaResidue other)
int	getContacts(ResidueList residueList, double contactDistance)
static AtomList	getNewAtomList(AtomList oldAL, ResidueType type)
void	moveTo(double x, double y, double z)
void	setCoordinates(Atom from)
void	setCoordinates(CaResidue from)

Methods inherited from class meshi.molecularElements.Residue

accessibility, addAttribute, amideH, amideN, atoms, bonds, ca, carbonylC, carbonylO, cb, cg, chain, comment, compareTo, defrost, dummy, equals, find, find, get, getAtom, getAttribute, getMode, head, ID, initiateAtoms, key, nextAtom, number, position, prevAtom, reliability, secondaryStructure, setAccessibility, setAccessibility, setNextAtom, setPrevAtom, setPrevNextAtomsToNull, setReliability, setResidueInAtoms, setSecondaryStructure, setSecondaryStructure, tail, test, toString, type

Methods inherited from class java.lang.Object

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

Field Detail

creator

public static final CaResidue creator

CA

public final Atom CA

Constructor Detail

CaResidue

public CaResidue(java.lang.String name)

 Use this constructor to instantiate a creator object..

CaResidue

public CaResidue(java.lang.String name,
                 ResidueType type,
                 ResidueIdentifier id,
                 AtomList atomList,
                 ResidueMode mode)

Method Detail

getNewAtomList

public static AtomList getNewAtomList(AtomList oldAL,
                                      ResidueType type)

getContacts

public int getContacts(ResidueList residueList,
                       double contactDistance)

setCoordinates

public void setCoordinates(CaResidue from)

setCoordinates

public void setCoordinates(Atom from)

distance

public Distance distance(CaResidue other)

moveTo

public void moveTo(double x,
                   double y,
                   double z)

create

public Residue create(AtomList atoms,
                      ResidueIdentifier id,
                      ResidueMode mode)

Description copied from class: Residue

create a residue based on an atoms list. creates a dummyResidue if the list is null or empty.

Specified by:

create in interface ResidueCreator

Overrides:

create in class Residue