Serialized Form

  • Package edu.rit.io

  • Package edu.rit.mp

  • Package edu.rit.pj

  • Package edu.rit.pj.cluster

  • Package edu.rit.pj.job

  • Package edu.rit.pj.reduction

  • Package edu.rit.pj.replica

  • Package edu.rit.util

  • Package ffx

    • Class ffx.Main

      class Main extends JFrame implements Serializable

      • Serialized Fields

        • initGUI
          Runnable initGUI
          This Runnable is used to init the GUI using SwingUtilities.

  • Package ffx.potential

    • Class ffx.potential.MolecularAssembly

      class MolecularAssembly extends MSGroup implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • alternateLocation
          Character alternateLocation
        • archiveFile
          File archiveFile
        • atomLookUp
          Atom[] atomLookUp
        • base
          org.jogamp.java3d.BranchGroup base
        • branchGroup
          org.jogamp.java3d.BranchGroup branchGroup
        • childNodes
          org.jogamp.java3d.BranchGroup childNodes
        • currentCycle
          int currentCycle
        • cycles
          int cycles
        • file
          File file
        • forceField
          ForceField forceField
        • fractionalCoordinates
          double[][] fractionalCoordinates
        • fractionalMode
          MolecularAssembly.FractionalMode fractionalMode
        • headerLines
          List<String> headerLines
        • ionHashMap
          HashMap<String,Molecule> ionHashMap
        • ions
          MSNode ions
        • lineAttributes
          org.jogamp.java3d.LineAttributes lineAttributes
        • moleculeHashMap
          HashMap<String,Molecule> moleculeHashMap
        • molecules
          MSNode molecules
        • myNewShapes
          List<org.jogamp.java3d.BranchGroup> myNewShapes
        • offset
          org.jogamp.vecmath.Vector3d offset
        • originToRot
          org.jogamp.java3d.TransformGroup originToRot
        • originToRotT3D
          org.jogamp.java3d.Transform3D originToRotT3D
        • originToRotV3D
          org.jogamp.vecmath.Vector3d originToRotV3D
        • potentialEnergy
          ForceFieldEnergy potentialEnergy
        • properties
          org.apache.commons.configuration2.CompositeConfiguration properties
        • rotToCOM
          org.jogamp.java3d.TransformGroup rotToCOM
        • rotToCOMT3D
          org.jogamp.java3d.Transform3D rotToCOMT3D
        • rotToCOMV3D
          org.jogamp.vecmath.Vector3d rotToCOMV3D
        • switchGroup
          org.jogamp.java3d.Switch switchGroup
        • visible
          boolean visible
        • vrml
          org.jogamp.java3d.BranchGroup vrml
        • vrmlTd
          org.jogamp.java3d.Transform3D vrmlTd
        • vrmlTG
          org.jogamp.java3d.TransformGroup vrmlTG
        • water
          MSNode water
        • waterHashMap
          HashMap<String,Molecule> waterHashMap
        • wire
          org.jogamp.java3d.Shape3D wire

  • Package ffx.potential.bonded

    • Class ffx.potential.bonded.Angle

      class Angle extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • angleType
          AngleType angleType
          Force field parameters to compute the angle bending energy.
        • atom4
          Atom atom4
          Fourth atom for in-plane angles.
        • nh
          int nh
          Number of hydrogen on the central atom that are not part of this Angle.
        • rigidScale
          double rigidScale
          Scale factor to apply to angle bending.

    • Class ffx.potential.bonded.AngleTorsion

      class AngleTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • angleTorsionType
          AngleTorsionType angleTorsionType
          Angle Torsion force field type.
        • angleType1
          AngleType angleType1
          First angle force field type.
        • angleType2
          AngleType angleType2
          Second angle force field type.
        • constants
          double[] constants
          Angle Torsion force constants (may be reversed compared to storage in the AngleTorsionType instance).
        • dEdL
          double dEdL
          Value of dE/dL.
        • lambda
          double lambda
          Value of lambda.
        • lambdaTerm
          boolean lambdaTerm
          Flag to indicate lambda dependence.
        • tcos
          double[] tcos
        • torsionType
          TorsionType torsionType
          Torsion force field type.
        • tsin
          double[] tsin
          The AngleTorsion may use more sine and cosine terms than are defined in the TorsionType.

    • Class ffx.potential.bonded.Atom

      class Atom extends MSNode implements Serializable

      • Serialized Fields

        • acceleration
          double[] acceleration
        • active
          boolean active
          If active is true, the coordinates of this atom can be modified.
        • altLoc
          Character altLoc
          Array of altLoc identifiers defined for this atom.
          Since:
          1.0
        • angles
          List<Angle> angles
        • anisou
          double[] anisou
          Anisou tensor.
          Since:
          1.0
        • anisouAcceleration
          double[] anisouAcceleration
        • anisouGradient
          double[] anisouGradient
          Anisou gradient, velocity, accel and prev accel.
          Since:
          1.0
        • anisouPreviousAcceleration
          double[] anisouPreviousAcceleration
        • anisouVelocity
          double[] anisouVelocity
        • appearance
          org.jogamp.java3d.Appearance appearance
        • applyState
          boolean applyState
        • atomType
          AtomType atomType
          Force field AtomType.
        • axisAtomIndices
          int[] axisAtomIndices
          Local frame axis atom indices.
        • bonds
          List<Bond> bonds
        • branchGroup
          org.jogamp.java3d.BranchGroup branchGroup
        • built
          boolean built
          If built is true, this atom was built during the parsing of a file.
        • chainID
          Character chainID
          PDB "chainID" or "segID" record.
          Since:
          1.0
        • currentCol
          org.jogamp.vecmath.Color3f currentCol
        • detail
          int detail
        • electrostatics
          boolean electrostatics
          If electrostatics is true, include the charge, multipole and/or polarizability in electrostatics calculations.
        • formFactorIndex
          int formFactorIndex
        • formFactorWidth
          double formFactorWidth
        • formFactorWidth2
          double formFactorWidth2
        • hetatm
          boolean hetatm
          True if this Atom is a HETATM.
        • mass
          double mass
        • modres
          boolean modres
          True if this Atom is a member of modified residue.
        • moleculeNumber
          int moleculeNumber
        • multipoleType
          MultipoleType multipoleType
          Force field MultipoleType.
        • neuralNetwork
          boolean neuralNetwork
          If true, this atom is part of a molecule whose intramolecular energetics are treated by a neural network potential.
        • occupancy
          double occupancy
          Array of occupancy values for each altLoc.
          Since:
          1.0
        • occupancyAcceleration
          double occupancyAcceleration
        • occupancyGradient
          double occupancyGradient
          Array of occupancy gradients for each altLoc.
          Since:
          1.0
        • occupancyPreviousAcceleration
          double occupancyPreviousAcceleration
        • occupancyVelocity
          double occupancyVelocity
        • polarizeType
          PolarizeType polarizeType
          Force field PolarizeType.
        • polygonType
          RendererCache.ViewModel polygonType
        • previousAcceleration
          double[] previousAcceleration
        • previousCol
          org.jogamp.vecmath.Color3f previousCol
        • radius
          double radius
        • redXYZ
          double[] redXYZ
          Array of XYZ coordinates for the electron (van der Waals) centers of each atom: if null, methods will refer to xyz.
          Since:
          1.0
        • resName
          String resName
          PDB "resname" record.
          Since:
          1.0
        • resolution
          Atom.Resolution resolution
        • resSeq
          int resSeq
          PDB "resSeq" record.
          Since:
          1.0
        • scale
          double scale
        • segID
          String segID
        • soluteType
          SoluteType soluteType
          Force Field SoluteType.
        • specialPositionSymOps
          List<Integer> specialPositionSymOps
          If this List is not empty, then the atom is at a special position. The list contains the index of the symmetry operators that leave the atom (or an atom in this atom's molecule) at its special position.
        • sphere
          org.jogamp.java3d.Shape3D sphere
        • stale
          boolean stale
          "stale" is True if this Atom's J3D transforms need to be updated before making it visible
        • tempFactor
          double tempFactor
          Array of tempFactor values for each altLoc.
          Since:
          1.0
        • tempFactorAcceleration
          double tempFactorAcceleration
        • tempFactorGradient
          double tempFactorGradient
          Array fo tempFactorGradients
          Since:
          1.0
        • tempFactorPreviousAcceleration
          double tempFactorPreviousAcceleration
        • tempFactorVelocity
          double tempFactorVelocity
        • torsions
          List<Torsion> torsions
        • trajectory
          ArrayList<org.jogamp.vecmath.Vector3d> trajectory
        • transform3D
          org.jogamp.java3d.Transform3D transform3D
        • transformGroup
          org.jogamp.java3d.TransformGroup transformGroup
        • use
          boolean use
          If use is true, this atom should be included in target functions.
        • userColor
          org.jogamp.vecmath.Color3f userColor
        • vdwType
          VDWType vdwType
          Force Field VDWType.
        • vector3d
          org.jogamp.vecmath.Vector3d vector3d
        • velocity
          double[] velocity
          Array of velocities
        • viewModel
          RendererCache.ViewModel viewModel
        • xyz
          double[] xyz
          Array of XYZ coordinates.
          Since:
          1.0
        • xyzGradient
          double[] xyzGradient
          Array of XYZ gradient.
          Since:
          1.0
        • xyzIndex
          int xyzIndex
          Contiguous atom index ranging from 1..nAtoms.
          Since:
          1.0
        • xyzLambdaGradient
          double[] xyzLambdaGradient
          Array of XYZ lambda gradient.
          Since:
          1.0

    • Class ffx.potential.bonded.Bond

      class Bond extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bondType
          BondType bondType
          The force field BondType for this bond.
        • branchGroup
          org.jogamp.java3d.BranchGroup branchGroup
        • cy1
          org.jogamp.java3d.Shape3D cy1
        • cy1t3d
          org.jogamp.java3d.Transform3D cy1t3d
        • cy1tg
          org.jogamp.java3d.TransformGroup cy1tg
        • cy2
          org.jogamp.java3d.Shape3D cy2
        • cy2t3d
          org.jogamp.java3d.Transform3D cy2t3d
        • cy2tg
          org.jogamp.java3d.TransformGroup cy2tg
        • detail
          int detail
        • formsAngleWith
          ArrayList<Bond> formsAngleWith
          List of Bonds that this Bond forms angles with
        • la
          org.jogamp.java3d.LineArray la
        • lineIndex
          int lineIndex
        • rigidScale
          double rigidScale
          Rigid Scale factor.
        • scale
          org.jogamp.vecmath.Vector3d scale
        • viewModel
          RendererCache.ViewModel viewModel
        • wireVisible
          boolean wireVisible

    • Class ffx.potential.bonded.BondedTerm

      class BondedTerm extends MSNode implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • atoms
          Atom[] atoms
          Atoms that are used to form this term.
        • bonds
          Bond[] bonds
          Bonds that are used to form this term.
        • energy
          double energy
          Energy of the term (kcal/mol).
        • id
          String id
          ID of this BondedTerm.
        • isConstrained
          boolean isConstrained
          Flag indicating if this term is constrained.
        • value
          double value
          Value of the term (e.g. bond length, angle, dihedral angle, etc).

    • Exception Class ffx.potential.bonded.BondedUtils.MissingAtomTypeException

      class MissingAtomTypeException extends Exception implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Exception Class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException

      class MissingHeavyAtomException extends Exception implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

    • Class ffx.potential.bonded.ImproperTorsion

      class ImproperTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • improperType
          ImproperTorsionType improperType
          Force field parameters to compute the ImproperTorsion energy.
        • scaleFactor
          double scaleFactor
          Scale factor.

    • Class ffx.potential.bonded.Joint

      class Joint extends MSNode implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • group1
          MSGroup group1
          First group forming this Joint
        • group2
          MSGroup group2
          Second group forming this Joint

    • Class ffx.potential.bonded.Molecule

      class Molecule extends MSGroup implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • chainID
          Character chainID
          Possibly redundant chainID assigned in PDB files.
        • residueName
          String residueName
          Residue name assigned in PDB files.
        • residueNum
          int residueNum
          Residue number assigned in PDB files.
        • segID
          String segID
          Unique segID.

    • Class ffx.potential.bonded.MSGroup

      class MSGroup extends MSNode implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • angleNode
          MSNode angleNode
        • angleTorsionNode
          MSNode angleTorsionNode
        • atomNode
          MSNode atomNode
          Constructs the Geometry of this MultiScaleGroup and stores the terms as children in the Term node.
        • bondNode
          MSNode bondNode
        • center
          double[] center
          Center of the MultiScaleGroup
        • danglingAtomList
          List<Atom> danglingAtomList
          List of under-constrained Atoms
        • finalized
          boolean finalized
          Whether the terms are current.
        • improperTorsionNode
          MSNode improperTorsionNode
        • joints
          List<Joint> joints
          List of Joints.
        • outOfPlaneBendNode
          MSNode outOfPlaneBendNode
        • piOrbitalTorsionNode
          MSNode piOrbitalTorsionNode
        • stretchBendNode
          MSNode stretchBendNode
        • stretchTorsionNode
          MSNode stretchTorsionNode
        • termNode
          MSNode termNode
        • torsionNode
          MSNode torsionNode
        • torsionTorsionNode
          MSNode torsionTorsionNode
        • ureyBradleyNode
          MSNode ureyBradleyNode

    • Class ffx.potential.bonded.MSNode

      class MSNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • MultiScaleLevel
          int MultiScaleLevel
          The multiscale level of this node.
        • name
          String name
          The name of this node.
        • selected
          boolean selected
          True if this node is selected.
        • totalMass
          double totalMass
          Total mass of this node and its children.

    • Class ffx.potential.bonded.MSRoot

      class MSRoot extends MSNode implements Serializable
      serialVersionUID:
      1L

    • Class ffx.potential.bonded.MultiResidue

      class MultiResidue extends Residue implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • activeResidue
          Residue activeResidue
          The active residue.
        • consideredResidues
          List<Residue> consideredResidues
          List of residues under consideration.
        • forceField
          ForceField forceField
          The force field in use.
        • originalRotamer
          Rotamer originalRotamer
          The original rotamer.
        • rotamers
          Rotamer[] rotamers
          Current rotamers.

    • Class ffx.potential.bonded.OutOfPlaneBend

      class OutOfPlaneBend extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • outOfPlaneBendType
          OutOfPlaneBendType outOfPlaneBendType
          Force field parameters to compute the Out-of-Plane Bend energy.

    • Class ffx.potential.bonded.PiOrbitalTorsion

      class PiOrbitalTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • dEdL
          double dEdL
          Current value of dE/dL.
        • lambda
          double lambda
          Current value of lambda.
        • lambdaTerm
          boolean lambdaTerm
          Flag to indicate use of lambda dependence.
        • piOrbitalTorsionType
          PiOrbitalTorsionType piOrbitalTorsionType
          A reference to the Pi-Torsion type in use.

    • Class ffx.potential.bonded.Polymer

      class Polymer extends MSGroup implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • chainID
          Character chainID
          The ChainID of this Polymer.
        • link
          boolean link
          Flag to indicate the residues in the polymer should be joined.
        • polymerNumber
          int polymerNumber
          The number of this Polymer.

    • Class ffx.potential.bonded.Residue

      class Residue extends MSGroup implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • aa
          AminoAcidUtils.AminoAcid3 aa
          3-letter amino acid code.
        • C1sCoords
          double[] C1sCoords
          These arrays store default coordinates for certain atoms in nucleic acid Residues. C1', O4', and C4' are the critical sugar atoms off which every other atom is drawn when applyRotamer is called. The backbone corrections, however, move these atoms, so they must be reverted to their original coordinates each time applyRotamer is called.

          O3' North and South coordinates are technically non-essential, as they could be derived from C1', O4', C4', and a given sugar pucker, however, it is much less computationally expensive to calculate them once and then store them.

          TODO: Add O3' coordinates for the DNA C3'-exo configuration.

        • C4sCoords
          double[] C4sCoords
          These arrays store default coordinates for certain atoms in nucleic acid Residues. C1', O4', and C4' are the critical sugar atoms off which every other atom is drawn when applyRotamer is called. The backbone corrections, however, move these atoms, so they must be reverted to their original coordinates each time applyRotamer is called.

          O3' North and South coordinates are technically non-essential, as they could be derived from C1', O4', C4', and a given sugar pucker, however, it is much less computationally expensive to calculate them once and then store them.

          TODO: Add O3' coordinates for the DNA C3'-exo configuration.

        • chainID
          Character chainID
          Possibly redundant PDB chain ID.
        • currentRotamer
          Rotamer currentRotamer
          The current rotamer in use.
        • na
          NucleicAcidUtils.NucleicAcid3 na
          3-letter nucleic acid code.
        • O3sNorthCoords
          double[] O3sNorthCoords
          These arrays store default coordinates for certain atoms in nucleic acid Residues. C1', O4', and C4' are the critical sugar atoms off which every other atom is drawn when applyRotamer is called. The backbone corrections, however, move these atoms, so they must be reverted to their original coordinates each time applyRotamer is called.

          O3' North and South coordinates are technically non-essential, as they could be derived from C1', O4', C4', and a given sugar pucker, however, it is much less computationally expensive to calculate them once and then store them.

          TODO: Add O3' coordinates for the DNA C3'-exo configuration.

        • O3sSouthCoords
          double[] O3sSouthCoords
          These arrays store default coordinates for certain atoms in nucleic acid Residues. C1', O4', and C4' are the critical sugar atoms off which every other atom is drawn when applyRotamer is called. The backbone corrections, however, move these atoms, so they must be reverted to their original coordinates each time applyRotamer is called.

          O3' North and South coordinates are technically non-essential, as they could be derived from C1', O4', C4', and a given sugar pucker, however, it is much less computationally expensive to calculate them once and then store them.

          TODO: Add O3' coordinates for the DNA C3'-exo configuration.

        • O4sCoords
          double[] O4sCoords
          These arrays store default coordinates for certain atoms in nucleic acid Residues. C1', O4', and C4' are the critical sugar atoms off which every other atom is drawn when applyRotamer is called. The backbone corrections, however, move these atoms, so they must be reverted to their original coordinates each time applyRotamer is called.

          O3' North and South coordinates are technically non-essential, as they could be derived from C1', O4', C4', and a given sugar pucker, however, it is much less computationally expensive to calculate them once and then store them.

          TODO: Add O3' coordinates for the DNA C3'-exo configuration.

        • residueType
          Residue.ResidueType residueType
          Residue type.
        • resNumber
          int resNumber
          The residue number of this residue in a chain.
        • rotamers
          Rotamer[] rotamers
          The rotamers for this residue.
        • segID
          String segID
          Unique segID.
        • shortString
          String shortString
          Short string describing this residue.
        • titrationUtils
          TitrationUtils titrationUtils
          If this is set, then ASP, GLU, LYS and HIS Rotamers will be titratable.

    • Class ffx.potential.bonded.RestrainDistance

      class RestrainDistance extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bondType
          BondType bondType
        • crystal
          Crystal crystal
        • d2EdL2
          double d2EdL2
        • dEdL
          double dEdL
        • dEdXdL
          double[][] dEdXdL
        • lambda
          double lambda
        • lambdaTerm
          boolean lambdaTerm
        • restraintLambdaStart
          double restraintLambdaStart
        • restraintLambdaStop
          double restraintLambdaStop
        • restraintLambdaWindow
          double restraintLambdaWindow
        • rlwInv
          double rlwInv
        • switchd2UdL2
          double switchd2UdL2
        • switchdUdL
          double switchdUdL
        • switchingFunction
          UnivariateSwitchingFunction switchingFunction
        • switchVal
          double switchVal

    • Class ffx.potential.bonded.RestraintTorsion

      class RestraintTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • atoms
          Atom[] atoms
        • d2EdL2
          double d2EdL2
        • dEdL
          double dEdL
        • lambda
          double lambda
        • lambdaTerm
          boolean lambdaTerm
        • lamMapper
          DoubleUnaryOperator lamMapper
        • torsionType
          TorsionType torsionType
        • units
          double units

    • Class ffx.potential.bonded.ROLSP

      class ROLSP extends MSNode implements Serializable
      serialVersionUID:
      1L

    • Class ffx.potential.bonded.StretchBend

      class StretchBend extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • angle
          Angle angle
          Angle this Stretch-Bend is based on.
        • angleEq
          double angleEq
          Equilibrium angle.
        • bond0Eq
          double bond0Eq
          First equilibrium bond distance.
        • bond1Eq
          double bond1Eq
          Second equilibrium bond distance.
        • force0
          double force0
          Force constant.
        • force1
          double force1
          Force constant.
        • rigidScale
          double rigidScale
          Rigid scale factor to apply to the force constant.
        • stretchBendType
          StretchBendType stretchBendType
          Force field parameters to compute the Stretch-Bend energy.

    • Class ffx.potential.bonded.StretchTorsion

      class StretchTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • bondType1
          BondType bondType1
          First bond force field type.
        • bondType2
          BondType bondType2
          Second bond force field type.
        • bondType3
          BondType bondType3
          Third bond force field type.
        • constants
          double[] constants
          Stretch Torsion force constants (may be reversed compared to storage in the StretchTorsionType instance).
        • dEdL
          double dEdL
          Value of dE/dL.
        • lambda
          double lambda
          Value of lambda.
        • lambdaTerm
          boolean lambdaTerm
          Flag to indicate lambda dependence.
        • stretchTorsionType
          StretchTorsionType stretchTorsionType
          Stretch Torsion force field type.
        • tcos
          double[] tcos
        • torsionType
          TorsionType torsionType
          Torsion force field type.
        • tsin
          double[] tsin
          The StretchTorsion may use more sine and cosine terms than are defined in the TorsionType.

    • Class ffx.potential.bonded.Torsion

      class Torsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • dEdL
          double dEdL
          Value of dE/dL.
        • lambda
          double lambda
          Value of lambda.
        • lambdaMapper
          DoubleUnaryOperator lambdaMapper
          Maps global lambda to either itself or 1 - global lambda.
        • lambdaTerm
          boolean lambdaTerm
          Flag to indicate lambda dependence.
        • torsionScale
          double torsionScale
          Scale up the torsional energy by this factor.
        • torsionType
          TorsionType torsionType
          The force field Torsion type in use.

    • Class ffx.potential.bonded.TorsionTorsion

      class TorsionTorsion extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • dEdL
          double dEdL
          Value of dE/dL.
        • lambda
          double lambda
          Value of lambda.
        • lambdaTerm
          boolean lambdaTerm
          Flag to indicate lambda dependence.
        • torsions
          Torsion[] torsions
          The two torsions that are coupled.
        • torsionTorsionType
          TorsionTorsionType torsionTorsionType
          The force field Torsion-Torsion type in use.

    • Class ffx.potential.bonded.UreyBradley

      class UreyBradley extends BondedTerm implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • angle
          Angle angle
          The Angle this UreyBradley term is based on.
        • rigidScale
          double rigidScale
          Scale factor to apply to Urey-Bradley term.
        • ureyBradleyType
          UreyBradleyType ureyBradleyType
          Force field parameters to compute the Stretch-Bend energy.

  • Package ffx.potential.nonbonded

    • Class ffx.potential.nonbonded.RestrainPosition

      class RestrainPosition extends BondedTerm implements Serializable

      • Serialized Fields

        • a1
          double[] a1
        • d2EdL2
          double d2EdL2
        • d2LambdaPow
          double d2LambdaPow
        • dEdL
          double dEdL
        • dLambdaPow
          double dLambdaPow
        • dx
          double[] dx
        • equilibriumCoordinates
          double[][] equilibriumCoordinates
        • flatBottom
          double flatBottom
          Flat bottom radius in Angstroms.
        • forceConstant
          double forceConstant
          Force constant variable stores K/2 in Kcal/mol/A. E = K/2 * dx^2.
        • lambda
          double lambda
        • lambdaExp
          double lambdaExp
        • lambdaGradient
          double[] lambdaGradient
        • lambdaPow
          double lambdaPow
        • lambdaTerm
          boolean lambdaTerm
        • nAtoms
          int nAtoms

  • Package ffx.potential.utils

  • Package ffx.ui

  • Package ffx.ui.commands

    • Class ffx.ui.commands.SimulationDefinition

      class SimulationDefinition extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • atomic
          int[] atomic
        • charge
          double[] charge
        • connectivity
          int[][] connectivity
        • coordinates
          double[][] coordinates
        • file
          String file
        • forcefield
          String forcefield
        • keywords
          String[] keywords
        • mass
          double[] mass
        • name
          String[] name
        • numatoms
          int numatoms
        • numkeys
          int numkeys
        • read
          boolean read
        • story
          String[] story
        • types
          int[] types

    • Class ffx.ui.commands.SimulationMessage

      class SimulationMessage extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • message
          int message
        • step
          int step
        • time
          double time
        • type
          int type

    • Class ffx.ui.commands.SimulationUpdate

      class SimulationUpdate extends Object implements Serializable
      serialVersionUID:
      1L

      • Serialized Fields

        • acceleration
          double[][] acceleration
        • amoeba
          boolean amoeba
        • coordinates
          double[][] coordinates
        • density
          double density
        • energy
          double energy
        • gradients
          double[][] gradients
        • induced
          double[][] induced
        • intermolecular
          double intermolecular
        • kinetic
          double kinetic
        • numatoms
          int numatoms
        • potential
          double potential
        • pressure
          double pressure
        • read
          boolean read
        • step
          int step
        • temperature
          double temperature
        • time
          double time
        • type
          int type
        • velocity
          double[][] velocity