Package ffx.potential.bonded

Class Atom

java.lang.Object
javax.swing.tree.DefaultMutableTreeNode
ffx.potential.bonded.MSNode
ffx.potential.bonded.Atom
All Implemented Interfaces:
ROLS, Serializable, Cloneable, Comparable<Atom>, MutableTreeNode, TreeNode
public class Atom extends MSNode implements Comparable<Atom>
The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
Since:
1.0
Author:
Michael J. Schnieders
See Also:

  • Field Details

    • AtomColor

      public static final Map<Integer,org.jogamp.vecmath.Color3f> AtomColor
      Constant AtomColor

    • XYZIndexComparator

      public static Comparator<Atom> XYZIndexComparator
      Compare two atoms (implementation of the Comparator interface).

      First, if atom1.equals(atom2), then 0 is returned.

      Next, atoms are compared based on their atomic number. A heavier atom is greater than (comes after) a lighter atom.

      Finally, atoms are compared based on their XYZ index. A lower XYZ index is less than (comes before) a higher index.

  • Constructor Details

    • Atom

      public Atom(String name)
      Default constructor.
      Parameters:
      name - The Atom's PDB name.
      Since:
      1.0

    • Atom

      public Atom(int xyzIndex, String name, AtomType atomType, double[] xyz)
      Constructor used when parsing XYZ files.
      Parameters:
      xyzIndex - Contiguous, unique atom index between 1..nAtoms.
      name - The Atom's molecular mechanics name.
      atomType - Molecular mechanics atom type.
      xyz - Cartesian coordinates.
      Since:
      1.0

    • Atom

      public Atom(int xyzIndex, String name, Character altLoc, double[] xyz, String resName, int resSeq, Character chainID, double occupancy, double tempFactor, String segID)
      Constructor used when parsing PDB files.
      Parameters:
      xyzIndex - Contiguous, unique atom index between 1..nAtoms.
      name - The Atom's molecular mechanics name.
      altLoc - The alternate locations (' ' or 'A' or 'B' etc.).
      xyz - Cartesian coordinates.
      resName - Residue name.
      resSeq - Residue sequence number.
      chainID - Possible redundant chain ID.
      occupancy - Crystallographic occupancy.
      tempFactor - Crystallographic B-factor.
      segID - Unique segment ID.
      Since:
      1.0.

    • Atom

      public Atom(int xyzIndex, String name, Character altLoc, double[] xyz, String resName, int resSeq, Character chainID, double occupancy, double tempFactor, String segID, boolean built)
      Constructor for Atom.
      Parameters:
      xyzIndex - The atom's contiguous, unique index between 1..nAtoms.
      name - a String object.
      altLoc - a Character object.
      xyz - an array of
      invalid reference 
      double
      objects.
      resName - a String object.
      resSeq - The residue sequence number.
      chainID - a Character object.
      occupancy - The crystallographic occupancy.
      tempFactor - The crystallographic B-factor.
      segID - a String object.
      built - a boolean.

    • Atom

      public Atom(int xyzIndex, Atom copyFrom, double[] xyz, int resSeq, char chainID, String segID)
      Creates a new Atom similar to an existing Atom (e.g. for tiling a solvent box over a solute). Will not include some properties such as velocity, acceleration, etc.
      Parameters:
      xyzIndex - Index of the new Atom.
      copyFrom - Atom to copy attributes from.
      xyz - Cartesian coordinates to place this new Atom at.
      resSeq - Residue sequence number.
      chainID - Chain identifier.
      segID - Segment identifier.

  • Method Details

    • addToAnisouGradient

      public void addToAnisouGradient(double[] anisouGradient)
      addToAnisouGradient
      Parameters:
      anisouGradient - an array of double.

    • addToLambdaXYZGradient

      public void addToLambdaXYZGradient(double x, double y, double z)
      addToLambdaXYZGradient
      Parameters:
      x - a double.
      y - a double.
      z - a double.

    • addToOccupancyGradient

      public void addToOccupancyGradient(double occupancyGradient)
      addToOccupancyGradient
      Parameters:
      occupancyGradient - a double.

    • addToTempFactorGradient

      public void addToTempFactorGradient(double tempFactorGradient)
      addToTempFactorGradient
      Parameters:
      tempFactorGradient - a double.

    • addToXYZGradient

      public void addToXYZGradient(double x, double y, double z)
      addToXYZGradient
      Parameters:
      x - a double.
      y - a double.
      z - a double.

    • addToXYZGradient

      public void addToXYZGradient(int axis, double value)
      addToXYZGradient.
      Parameters:
      axis - The axis to add to.
      value - The value to add.

    • applyLambda

      public boolean applyLambda()
      applyLambda
      Returns:
      a boolean.

    • compareTo

      public int compareTo(Atom a)

      Implementation of the Comparable interface.

      Specified by:
      compareTo in interface Comparable<Atom>

    • describe

      public String describe(Atom.Descriptions type)
      describe.
      Parameters:
      type - a Atom.Descriptions object.
      Returns:
      a String object.

    • drawLabel

      public void drawLabel(org.jogamp.java3d.Canvas3D canvas, org.jogamp.java3d.J3DGraphics2D g2d, org.jogamp.java3d.Node node)
      drawLabel
      Specified by:
      drawLabel in interface ROLS
      Overrides:
      drawLabel in class MSNode
      Parameters:
      canvas - a Canvas3D object.
      g2d - a J3DGraphics2D object.
      node - a Node object.

    • equals

      public final boolean equals(Object o)

      MSNode equality := same class and same name. Consider replacing with a Comparator<MSNode> for cases where non-reference equality is desired.

      Overrides:
      equals in class MSNode

    • get12List

      public List<Atom> get12List()
      Get the list of 1-2 atoms ordered by XYZ index.
      Returns:
      Returns the 1-2 list.

    • get13List

      public List<Atom> get13List()
      Get the list of 1-3 atoms ordered by XYZ index.
      Returns:
      Returns the 1-3 list.

    • get14List

      public List<Atom> get14List()
      Get the list of 1-4 atoms ordered by XYZ index.
      Returns:
      Returns the 1-4 list.

    • get15List

      public List<Atom> get15List()
      Get the list of 1-5 atoms ordered by XYZ index.
      Returns:
      Returns the 1-5 list.

    • getAcceleration

      public void getAcceleration(double[] acceleration)
      Getter for the field acceleration.
      Parameters:
      acceleration - an array of double.

    • getAltLoc

      public Character getAltLoc()
      Getter for the field altLoc.
      Returns:
      a Character object.

    • setAltLoc

      public void setAltLoc(Character a)
      Setter for the field altLoc.
      Parameters:
      a - a Character object.

    • getAngle

      public Angle getAngle(Atom centralAtom, Atom endAtom)
      getAngle.
      Parameters:
      centralAtom - a Atom object.
      endAtom - a Atom object.
      Returns:
      a Angle object.

    • getAngles

      public List<Angle> getAngles()
      Getter for the field angles.
      Returns:
      a ArrayList object.

    • getAnisou

      public double[] getAnisou(double[] anisou)
      Getter for the field anisou.
      Parameters:
      anisou - an array of
      invalid reference 
      double
      objects.
      Returns:
      an array of double.

    • getAnisouAcceleration

      public double[] getAnisouAcceleration(double[] anisouAcceleration)
      Getter for the field anisouAcceleration.
      Parameters:
      anisouAcceleration - an array of
      invalid reference 
      double
      objects.
      Returns:
      an array of double.

    • getAnisouGradient

      public double[] getAnisouGradient(double[] anisouGradient)
      Getter for the field anisouGradient.
      Parameters:
      anisouGradient - an array of
      invalid reference 
      double
      objects.
      Returns:
      an array of double.

    • getAnisouPreviousAcceleration

      public double[] getAnisouPreviousAcceleration(double[] anisouPreviousAcceleration)
      Getter for the field anisouPreviousAcceleration.
      Parameters:
      anisouPreviousAcceleration - an array of
      invalid reference 
      double
      objects.
      Returns:
      an array of double.

    • getAnisouVelocity

      public double[] getAnisouVelocity(double[] anisouVelocity)
      Getter for the field anisouVelocity.
      Parameters:
      anisouVelocity - an array of
      invalid reference 
      double
      objects.
      Returns:
      an array of double.

    • getArrayIndex

      public final int getArrayIndex()
      getArrayIndex.
      Returns:
      The index of this atom in the array of atoms (xyzIndex - 1).

    • getAtomList

      public List<Atom> getAtomList()
      Returns a List of all Atoms below the present MSNode.
      Overrides:
      getAtomList in class MSNode
      Returns:
      a new List object.

    • getAtomType

      public AtomType getAtomType()
      Getter for the field atomType.
      Returns:
      a AtomType object.

    • setAtomType

      public void setAtomType(AtomType atomType)
      Setter for the field atomType.
      Parameters:
      atomType - a AtomType object.

    • getAtomicNumber

      public int getAtomicNumber()
      Gets the Atomic Number
      Returns:
      Atomic Number

    • getAxisAtomIndices

      public int[] getAxisAtomIndices()
      Getter for the field axisAtomIndices.
      Returns:
      an array of
      invalid reference 
      int
      objects.

    • getBond

      public Bond getBond(Atom a)
      getBond
      Parameters:
      a - a Atom object.
      Returns:
      a Bond object.

    • getBonds

      public List<Bond> getBonds()
      Gets the list of the Bonds this Atom helps to form
      Returns:
      A list of the bonds this atom helps to form

    • getBuilt

      public boolean getBuilt()
      If true, this atom was built during PDB file parsing.
      Returns:
      true if this atom was built during parsing of a PDB file.

    • setBuilt

      public void setBuilt(boolean built)
      Setter for the field built.
      Parameters:
      built - a boolean.

    • getChainID

      public Character getChainID()
      Get the chain name
      Returns:
      String

    • setChainID

      public void setChainID(Character chainID)
      Set the chain name.
      Parameters:
      chainID - The chain ID of this atom.

    • getCharge

      public double getCharge() throws IllegalStateException
      Gets the partial atomic charge
      Returns:
      partial atomic charge
      Throws:
      IllegalStateException - If the atom does not have a known multipole type.

    • getCharge

      public double getCharge(ForceField ff)
      Gets the partial atomic charge.
      Parameters:
      ff - If multipole type has not yet been assigned, search this force field.
      Returns:
      partial atomic charge
      Throws:
      IllegalStateException - If a multipole type could not be found and ff is null.

    • getElectrostatics

      public boolean getElectrostatics()
      Getter for the field electrostatics.
      Returns:
      a boolean.

    • setElectrostatics

      public void setElectrostatics(boolean electrostatics)
      Setter for the field electrostatics.
      Parameters:
      electrostatics - a boolean.

    • getEpsilon

      public double getEpsilon()
      Gets the Epsilon value
      Returns:
      Epsilon value

    • getFormFactorIndex

      public int getFormFactorIndex()
      Getter for the field formFactorIndex.
      Returns:
      The index of the form factor in the form factor array.

    • setFormFactorIndex

      public void setFormFactorIndex(int formFactorIndex)
      Setter for the field formFactorIndex.
      Parameters:
      formFactorIndex - The index of the form factor in the form factor array.

    • getFormFactorWidth

      public double getFormFactorWidth()
      Getter for the field formFactorWidth.
      Returns:
      a double.

    • setFormFactorWidth

      public void setFormFactorWidth(double width)
      Setter for the field formFactorWidth.
      Parameters:
      width - a double.

    • getFormFactorWidth2

      public double getFormFactorWidth2()
      Getter for the field formFactorWidth.
      Returns:
      a double.

    • getHybridization

      public int getHybridization()
      Gets the Atomic Hybridization
      Returns:
      Atomic Hybridization

    • getIdent

      public String getIdent()
      Gets the atom ID
      Returns:
      atom ID

    • getIndex

      public final int getIndex()
      Getter for the field index.
      Returns:
      The index of this atom in the molecular assembly.

    • getKey

      public String getKey()
      Gets the atom Key
      Returns:
      atom Key

    • getLambdaXYZGradient

      public void getLambdaXYZGradient(double[] x)
      getLambdaXYZGradient
      Parameters:
      x - an array of double.

    • getMass

      public double getMass()
      Gets the Atomic Mass.
      Returns:
      Atomic Mass

    • setMass

      public void setMass(double mass)
      Set the Atomic Mass.
      Parameters:
      mass - The mass of the atom.

    • getMoleculeNumber

      public int getMoleculeNumber()
      Getter for the field moleculeNumber.
      Returns:
      The molecule number of this atom.

    • setMoleculeNumber

      public void setMoleculeNumber(int molecule)
      Setter for the field moleculeNumber.
      Parameters:
      molecule - The molecule number of this atom.

    • getMultipoleType

      public MultipoleType getMultipoleType()
      Getter for the field multipoleType.
      Returns:
      a MultipoleType object.

    • setMultipoleType

      public void setMultipoleType(MultipoleType multipoleType)
      Setter for the field multipoleType.
      Parameters:
      multipoleType - a MultipoleType object.

    • getNumAngles

      public final int getNumAngles()
      getNumAngles
      Returns:
      The number of angles involving this atom.

    • getNumBonds

      public final int getNumBonds()
      Gets the number of atoms bonded to this Atom
      Returns:
      Number of atoms bonded to this atom

    • getNumDihedrals

      public final int getNumDihedrals()
      getNumDihedrals
      Returns:
      The number of dihedrals involving this atom.

    • getNumberOfBondedHydrogen

      public int getNumberOfBondedHydrogen()
      Count the number of bonded hydrogen.
      Returns:
      the count.

    • getOccupancy

      public double getOccupancy()
      Getter for the field occupancy.
      Returns:
      a double.

    • setOccupancy

      public void setOccupancy(double occupancy)
      Setter for the field occupancy.
      Parameters:
      occupancy - a double.

    • getOccupancyAcceleration

      public double getOccupancyAcceleration()
      Getter for the field occupancyAccelerationy.
      Returns:
      a double.

    • setOccupancyAcceleration

      public void setOccupancyAcceleration(double occupancyAcceleration)
      Setter for the field occupancyAcceleration.
      Parameters:
      occupancyAcceleration - a double.

    • getOccupancyGradient

      public double getOccupancyGradient()
      Getter for the field occupancyGradient.
      Returns:
      a double.

    • setOccupancyGradient

      public void setOccupancyGradient(double occupancyGradient)
      Setter for the field occupancyGradient.
      Parameters:
      occupancyGradient - a double.

    • getOccupancyPreviousAcceleration

      public double getOccupancyPreviousAcceleration()
      Getter for the field occupancyPreviousAccelerationy.
      Returns:
      a double.

    • setOccupancyPreviousAcceleration

      public void setOccupancyPreviousAcceleration(double occupancyPreviousAcceleration)
      Setter for the field occupancyPreviousAcceleration.
      Parameters:
      occupancyPreviousAcceleration - a double.

    • getOccupancyVelocity

      public double getOccupancyVelocity()
      Getter for the field occupancyVelocity.
      Returns:
      a double.

    • setOccupancyVelocity

      public void setOccupancyVelocity(double occupancyVelocity)
      Setter for the field occupancyVelocity.
      Parameters:
      occupancyVelocity - a double.

    • getPolarizeType

      public PolarizeType getPolarizeType()
      Getter for the field polarizeType.
      Returns:
      a PolarizeType object.

    • setPolarizeType

      public void setPolarizeType(PolarizeType polarizeType)
      Setter for the field polarizeType.
      Parameters:
      polarizeType - a PolarizeType object.

    • getPreviousAcceleration

      public void getPreviousAcceleration(double[] previousAcceleration)
      Getter for the field previousAcceleration.
      Parameters:
      previousAcceleration - an array of double.

    • getRedX

      public final double getRedX()
      Gets the reduced x coordinate (van der Waals center). Will refer to xyz[] if not initialized.
      Returns:
      Reduced x coordinate

    • getRedXYZ

      public void getRedXYZ(double[] x)
      getRedXYZ
      Parameters:
      x - an array of double.

    • getRedXYZ

      public double[] getRedXYZ()
      getRedXYZ
      Returns:
      an array of double.

    • setRedXYZ

      public void setRedXYZ(double[] redXYZ)
      setXYZ
      Parameters:
      redXYZ - an array of double.

    • getRedY

      public final double getRedY()
      Gets the reduced y coordinate (van der Waals center). Will refer to xyz[] if not initialized.
      Returns:
      Reduced y coordinate

    • getRedZ

      public final double getRedZ()
      Gets the reduced z coordinate (van der Waals center). Will refer to xyz[] if not initialized.
      Returns:
      Reduced z coordinate

    • getResidueName

      public String getResidueName()
      Get the residue name
      Returns:
      String

    • getResidueNumber

      public int getResidueNumber()
      getResidueNumber
      Returns:
      The residue number of this atom.

    • setResidueNumber

      public void setResidueNumber(int resNumber)
      setResidueNumber
      Parameters:
      resNumber - this atom's residue number.

    • getResolution

      public Atom.Resolution getResolution()
      Getter for the field resolution.
      Returns:
      a Atom.Resolution object.

    • setResolution

      public void setResolution(Atom.Resolution resolution)
      Setter for the field resolution.
      Parameters:
      resolution - a Atom.Resolution object.

    • getSegID

      public String getSegID()
      Getter for the field segID.
      Returns:
      a String object.

    • setSegID

      public void setSegID(String segID)
      Set this atom's seg ID.
      Parameters:
      segID - The segID of this atom.

    • getSigma

      public double getSigma()
      Gets the Sigma value
      Returns:
      Sigma value

    • getTempFactor

      public double getTempFactor()
      Getter for the field tempFactor.
      Returns:
      a double.

    • setTempFactor

      public void setTempFactor(double tempFactor)
      Setter for the field tempFactor.
      Parameters:
      tempFactor - a double.

    • getTempFactorAcceleration

      public double getTempFactorAcceleration()
      Getter for the field tempFactorAcceleration.
      Returns:
      a double.

    • setTempFactorAcceleration

      public void setTempFactorAcceleration(double tempFactorAcceleration)
      Setter for the field tempFactorAcceleration.
      Parameters:
      tempFactorAcceleration - a double.

    • getTempFactorGradient

      public double getTempFactorGradient()
      Getter for the field tempFactorGradient.
      Returns:
      a double.

    • setTempFactorGradient

      public void setTempFactorGradient(double tempFactorGradient)
      Setter for the field tempFactorGradient.
      Parameters:
      tempFactorGradient - a double.

    • getTempFactorPreviousAcceleration

      public double getTempFactorPreviousAcceleration()
      Getter for the field tempFactorPreviousAcceleration.
      Returns:
      a double.

    • setTempFactorPreviousAcceleration

      public void setTempFactorPreviousAcceleration(double tempFactorPreviousAcceleration)
      Setter for the field tempFactorPreviousAcceleration.
      Parameters:
      tempFactorPreviousAcceleration - a double.

    • getTempFactorVelocity

      public double getTempFactorVelocity()
      Getter for the field tempFactorVelocity.
      Returns:
      a double.

    • setTempFactorVelocity

      public void setTempFactorVelocity(double tempFactorVelocity)
      Setter for the field tempFactorVelocity.
      Parameters:
      tempFactorVelocity - a double.

    • getTorsion

      public Torsion getTorsion(Atom atom2, Atom atom3, Atom atom4)
      Finds a Torsion which contains this atom, and atoms 2, 3, and 4.
      Parameters:
      atom2 - Atom number 2.
      atom3 - Atom number 3.
      atom4 - Atom number 4.
      Returns:
      Torsion the Torsion if found, or null if not found.

    • getTorsions

      public List<Torsion> getTorsions()
      Getter for the field torsions.
      Returns:
      a ArrayList object.

    • getTrajectoryCoords

      public org.jogamp.vecmath.Vector3d getTrajectoryCoords(int position)
      getTrajectoryCoords
      Parameters:
      position - The position in the trajectory.
      Returns:
      a Vector3d object.

    • getTrajectoryLength

      public int getTrajectoryLength()
      getTrajectoryLength
      Returns:
      The length of the trajectory.

    • getType

      public int getType()
      getType
      Returns:
      The type of this atom.

    • getUse

      public boolean getUse()
      If true, this atom should be used in potential energy functions.
      Returns:
      true if this atom should be included in the potential energy.

    • setUse

      public void setUse(boolean use)
      If true, this atom should be used in potential energy functions.
      Parameters:
      use - a boolean.

    • getV3D

      public void getV3D(org.jogamp.vecmath.Vector3d temp)
      Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates
      Parameters:
      temp - a Vector3d object.

    • getVDWR

      public double getVDWR()
      Gets the van der Waals radius.
      Returns:
      a double.

    • getVDWType

      public VDWType getVDWType()
      getVDWType
      Returns:
      a VDWType object.

    • setVDWType

      public void setVDWType(VDWType vdwType)
      setVDWType
      Parameters:
      vdwType - a VDWType object.

    • getSoluteType

      public SoluteType getSoluteType()
      getSoluteType
      Returns:
      a SoluteType object.

    • setSoluteType

      public void setSoluteType(SoluteType soluteType)
      setSoluteType
      Parameters:
      soluteType - a SoluteType object.

    • getVelocity

      public void getVelocity(double[] velocity)
      Getter for the field velocity.
      Parameters:
      velocity - an array of double.

    • getX

      public final double getX()
      Gets the x coordinate
      Returns:
      x coordinate

    • getXYZ

      public double[] getXYZ(@Nullable double[] xyz)
      getXYZ
      Parameters:
      xyz - an array of double.
      Returns:
      the original array with updated coordinates, or a new array if xyz was null.

    • getXYZ

      public Double3 getXYZ()
      getXYZ
      Returns:
      a new Double3 containing this Atom's coordinates.

    • setXYZ

      public void setXYZ(double[] xyz)
      setXYZ
      Parameters:
      xyz - an array of double.

    • getXYZGradient

      public void getXYZGradient(double[] x)
      getXYZGradient
      Parameters:
      x - an array of double.

    • getXyzIndex

      public final int getXyzIndex()
      Getter for the field xyzIndex.
      Returns:
      The index of this atom in XYZ files.

    • setXyzIndex

      public final void setXyzIndex(int set)
      Setter for the field xyzIndex.
      Parameters:
      set - The index of this atom in XYZ files.

    • getY

      public final double getY()
      Gets the y coordinate
      Returns:
      y coordinate

    • getZ

      public final double getZ()
      Gets the z coordinate
      Returns:
      z coordinate

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class MSNode

    • isActive

      public boolean isActive()
      If active, the coordinates of this atom can be modified.
      Returns:
      true if this atom's coordinates, b-factors, etc. can be modified.

    • setActive

      public void setActive(boolean active)
      If active, the coordinates of this atom can be modified.
      Parameters:
      active - a boolean.

    • isNeuralNetwork

      public boolean isNeuralNetwork()
      If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
      Returns:
      true if this atom is part of a molecule whose intramolecular interactions are handled by a neural network.

    • setNeuralNetwork

      public void setNeuralNetwork(boolean neuralNetwork)
      If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
      Parameters:
      neuralNetwork - a boolean.

    • isSpecialPosition

      public boolean isSpecialPosition()
      If true, this atom is at a special position.
      Returns:
      True if this atom is at a special position.

    • setSpecialPositionSymOps

      public void setSpecialPositionSymOps(List<Integer> specialPositionSymOps)
      Set the symmetry operations that leave this atom's molecule at a special position.
      Parameters:
      specialPositionSymOps - The symmetry operations that leave this atom's molecule at a special position.

    • isSpecialPositionSymOp

      public boolean isSpecialPositionSymOp(int symOp)
      If true, this atom is at a special position for the specified symmetry operation.
      Parameters:
      symOp - The symmetry operation to check.
      Returns:
      True if this atom is at a special position for the specified symmetry operation.

    • isBonded

      public boolean isBonded(Atom a)
      Checks to see if an Atom is bonded to this Atom
      Parameters:
      a - Atom to check
      Returns:
      True if Atom a is bonded to thisthis atom

    • isDeuterium

      public boolean isDeuterium()
      isDeuterium
      Returns:
      a boolean.

    • isHeavy

      public boolean isHeavy()
      isHeavy checks whether this Atom is a heavy (non-hydrogen) atom.
      Returns:
      True if this is a heavy atom.

    • isHetero

      public boolean isHetero()
      isHetero
      Returns:
      a boolean.

    • setHetero

      public void setHetero(boolean hetatm)
      setHetero
      Parameters:
      hetatm - a boolean.

    • isHydrogen

      public boolean isHydrogen()
      isHydrogen
      Returns:
      a boolean.

    • isHalogen

      public boolean isHalogen()
      Check if this atom is a Halogen (F, Cl, Br, I)
      Returns:
      a boolean.

    • isModRes

      public boolean isModRes()
      isModRes
      Returns:
      a boolean.

    • setModRes

      public void setModRes(boolean modres)
      setModRes
      Parameters:
      modres - a boolean.

    • isRing

      public boolean isRing(Atom a2)
      Determine if atom is in a ring with second atom WARNING: Does not work for 8+ membered rings...
      Parameters:
      a2 - a Atom object.
      Returns:
      a boolean.

    • isStale

      public boolean isStale()
      isStale
      Returns:
      a boolean.

    • isTrigonal

      public boolean isTrigonal()
      isTrigonal
      Returns:
      a boolean.

    • isVisible

      public boolean isVisible()
      isVisible

      True if this Atom's Sphere or Vector is visible

      Returns:
      a boolean.

    • is_12_or_13

      public boolean is_12_or_13(Atom a)
      is_12_or_13
      Parameters:
      a - a Atom object.
      Returns:
      a boolean.

    • is_1_3

      public boolean is_1_3(Atom atom)
      is_1_3
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • is_1_4

      public boolean is_1_4(Atom atom)
      Are these atoms 1-4 bonded?
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • is_1_5

      public boolean is_1_5(Atom atom)
      Are these atoms 1-5 bonded?
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • is_1_6

      public boolean is_1_6(Atom atom)
      Are these atoms 1-6 bonded?
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • is_1_7

      public boolean is_1_7(Atom atom)
      Are these atoms 1-7 bonded?
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • is_1_8

      public boolean is_1_8(Atom atom)
      Are these atoms 1-8 bonded?
      Parameters:
      atom - a Atom object.
      Returns:
      a boolean.

    • move

      public void move(double[] d)
      Add a vector to the Atom's current position vector
      Parameters:
      d - Vector to add to the current position

    • moveTo

      public void moveTo(double a, double b, double c)
      moveTo
      Parameters:
      a - a double.
      b - a double.
      c - a double.

    • moveTo

      public void moveTo(double[] d)
      Moves the atom to the specified location
      Parameters:
      d - Location to move this Atom to

    • moveTo

      public void moveTo(org.jogamp.vecmath.Vector3d v)
      moveTo
      Parameters:
      v - a Vector3d object.

    • print

      public final void print()
      Prints the MSNode's name

      Prints the atom identity and Cartesian coordinates to the logger.

      Overrides:
      print in class MSNode

    • print

      public final void print(Level logLevel)

    • removeFromParent

      public void removeFromParent()
      Specified by:
      removeFromParent in interface MutableTreeNode
      Overrides:
      removeFromParent in class DefaultMutableTreeNode

    • rotate

      public void rotate(double[][] d)
      rotate.
      Parameters:
      d - an array of
      invalid reference 
      double
      objects.

    • setAcceleration

      public void setAcceleration(double[] acceleration)
      Setter for the field acceleration.
      Parameters:
      acceleration - an array of double.

    • setAcceleration

      public void setAcceleration(double x, double y, double z)
      Setter for the field acceleration.
      Parameters:
      x - X-acceleration
      y - Y-acceleration
      z - Z-acceleration

    • setAngle

      public void setAngle(Angle a)
      setAngle
      Parameters:
      a - a Angle object.

    • setAnisou

      public void setAnisou(double[] anisou)
      Setter for the field anisou.
      Parameters:
      anisou - an array of double.

    • setAnisouAcceleration

      public void setAnisouAcceleration(double[] anisouAcceleration)
      Setter for the field anisouAcceleration.
      Parameters:
      anisouAcceleration - an array of double.

    • setAnisouGradient

      public void setAnisouGradient(double[] anisouGradient)
      Setter for the field anisouGradient.
      Parameters:
      anisouGradient - an array of double.

    • setAnisouPreviousAcceleration

      public void setAnisouPreviousAcceleration(double[] anisouPreviousAcceleration)
      Setter for the field anisouPreviousAcceleration.
      Parameters:
      anisouPreviousAcceleration - an array of double.

    • setAnisouVelocity

      public void setAnisouVelocity(double[] anisouVelocity)
      Setter for the field anisouVelocity.
      Parameters:
      anisouVelocity - an array of double.

    • setApplyLambda

      public void setApplyLambda(boolean applyState)
      setApplyLambda
      Parameters:
      applyState - a boolean.

    • setAxisAtoms

      public void setAxisAtoms(Atom... set)
      Setter for the field axisAtoms.
      Parameters:
      set - a Atom object.

    • setBond

      public void setBond(Bond b)
      Specify that this Atom is part of a Bond
      Parameters:
      b - Bond that this Atom is part of

    • setColor

      public void setColor(RendererCache.ColorModel newColorModel, org.jogamp.vecmath.Color3f newCol, org.jogamp.java3d.Material newMat)
      setColor

      Polymorphic setColor method.

      Specified by:
      setColor in interface ROLS
      Overrides:
      setColor in class MSNode
      Parameters:
      newColorModel - a RendererCache.ColorModel object.
      newCol - a Color3f object.
      newMat - a Material object.

    • setCurrentCycle

      public void setCurrentCycle(int cycle)
      setCurrentCycle
      Parameters:
      cycle - Sets the current cycle to the specified value.

    • setLambdaXYZGradient

      public void setLambdaXYZGradient(double x, double y, double z)
      setLambdaXYZGradient
      Parameters:
      x - a double.
      y - a double.
      z - a double.

    • setPreviousAcceleration

      public void setPreviousAcceleration(double[] previousAcceleration)
      Setter for the field previousAcceleration.
      Parameters:
      previousAcceleration - an array of double.

    • setResName

      public void setResName(String resName)
      Setter for the field resName.
      Parameters:
      resName - a String object.

    • setSelected

      public void setSelected(boolean selected)
      Setter for the field selected.
      Overrides:
      setSelected in class MSNode
      Parameters:
      selected - a boolean.

    • setTorsion

      public void setTorsion(Torsion torsion)
      setTorsion
      Parameters:
      torsion - a Torsion object.

    • setVelocity

      public void setVelocity(double[] velocity)
      Setter for the field velocity.
      Parameters:
      velocity - an array of double.

    • setVelocity

      public void setVelocity(double x, double y, double z)
      Setter for the field velocity.
      Parameters:
      x - X-velocity
      y - Y-velocity
      z - Z-velocity

    • setView

      public void setView(RendererCache.ViewModel newViewModel, List<org.jogamp.java3d.BranchGroup> newShapes)
      setView

      Polymorphic setView method.

      Specified by:
      setView in interface ROLS
      Overrides:
      setView in class MSNode
      Parameters:
      newViewModel - a RendererCache.ViewModel object.
      newShapes - a List object.

    • setXYZGradient

      public void setXYZGradient(double x, double y, double z)
      setXYZGradient
      Parameters:
      x - a double.
      y - a double.
      z - a double.

    • toString

      public String toString()

      Overridden toString method returns the MSNode's name

      Overrides:
      toString in class MSNode

    • update

      public void update()
      update

      Java3D transforms are not updated unless they are visible. This allows better performance for rendering partial structures during an interactive dynamics run or during trajectory playback.

      Specified by:
      update in interface ROLS
      Overrides:
      update in class MSNode