A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

D

DIM - Static variable in class core.SimSystem

Number of dimensions used.

DIM - Variable in class energy.Energy

DIM - Static variable in class esraMath.Fit

DebyeHueckel(double, double[], double, double[]) - Method in class energy.FDPoissonBoltzmann_Boundary

DenseExclusions - class forcefield.DenseExclusions.

meant for storing the exclusions of the particles (atoms) in the system.

DenseExclusions(int, int) - Constructor for class forcefield.DenseExclusions

typically i == j

DihedralType - class forcefield.DihedralType.

The DihedralType class contains all the Dihedral information from the topology.

DihedralType() - Constructor for class forcefield.DihedralType

DihedralType - Variable in class forcefield.InteractionParameters

HashTable for DihedralType look-up.

Dihedrals - class forcefield.Dihedrals.

The Dihedrals class contains all the Dihedral information from the sytem.

Dihedrals(int) - Constructor for class forcefield.Dihedrals

The Dihedrals class contructor.

Dssp - class conformation.Dssp.

DSSP: Determine Secondary Structure of Proteins.

Dssp(Particles) - Constructor for class conformation.Dssp

DsspTest - class conformation.DsspTest.

DsspTest() - Constructor for class conformation.DsspTest

d - Variable in class io.pdb.InPDB

dGelec(boolean) - Method in class energy.FDPoissonBoltzmann

public boolean dGelec calculates the electrostatic free energy [G] for the system from the electrostatic potential (phigrid) calculated above.

debug - Variable in class energy.FDPoissonBoltzmann

defaultDigits - Static variable in class contrib.PrintfFormat.ConversionSpecification

Default precision.

defaultValue - Variable in class io.args.ArgumentTypeSpec

definitions - Variable in class io.args.ArgumentParser

description - Variable in class io.args.ArgumentTypeSpec

det3x3(double[][]) - Static method in class esraMath.BLA

determineMolecules(Particles, Bonds) - Static method in class io.g96.in.InTopoG96

Fast method for determining molecule bounds.

determineMoleculesFloyd(Particles, Bonds) - Static method in class io.g96.in.InTopoG96

slow (N^3) but accurate molecule bounds method.

determineSixRingConformation(double[][]) - Static method in class conformation.RingConformation

a ring conformation specification.

dfs - Variable in class contrib.PrintfFormat

Character position.

diagonal(double[]) - Static method in class esraMath.BLA

generate a diagonal matrix with the elements of diag on its diagonal.

diagonalMatmul(double[], double[][]) - Static method in class esraMath.BLA

fuctionally equivalent to matmul(diagonal(vector), matrix) but better performance

diagonalizeSymmetric(double[][], double[]) - Static method in class esraMath.BLA

public Method diagonalizeSymmetric diagonalizes a symmetric matrix by first reducing it to tridiagonal form (private void method: tred2) and then evaluating eigenvalues and eigenvectors using the QL algorithm (private void method tqli).

dih - Variable in class core.SimSystem

All Dihedrals involving non-hydrogen atoms.

dih - Variable in class energy.Energy_Dihedral

dihedral(double[], double[], double[], double[]) - Static method in class esraMath.Geometry

The dihedral angle following IUPAC-IUB convention.

dihh - Variable in class core.SimSystem

All Dihedrals involving hydrogen atoms.

dihh - Variable in class energy.Energy_Dihedral

distance(double[], double[]) - Static method in class esraMath.BLA

the distance between two vectors.

distance(double[], double[]) - Static method in class esraMath.Geometry

distances - Variable in class conformation.HydrogenBonds.HBFrameStats

dogather(double[][], int[], double[]) - Method in class core.pbc.PBC.ByMoleculeGatherer

dogather(double[][], int[], double[]) - Method in class core.pbc.PBC.CoGGatherer

dogather(double[][], int[], double[]) - Method in class core.pbc.PBC.G96Gatherer

replace the position of each atom by its nearest image to the previous atom.

dogather(double[][], int[], double[]) - Method in interface core.pbc.PBC.Gatherer

dogather(double[][], int[], double[]) - Method in class core.pbc.PBC.InBoxGatherer

donor - Static variable in class conformation.Dssp

hydrogen bond indices

donors - Variable in class conformation.HydrogenBonds.HBDefinitions

dot(double[], double[]) - Static method in class esraMath.BLA

the dot product of two vectors

dt - Variable in class forcefield.Dihedrals

String of the DihedralType.

dumpgridtopdb(double[], int, int, int, String) - Method in class energy.FD_WriteGrid