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B

BLA - class esraMath.BLA.

Provides basic linear algebra routines such as vector additions, multiplications, inner, outer products, basic matrix operations such as transposition, inversion etc.

BLA() - Constructor for class esraMath.BLA

BLA_test - class esraMath.BLA_test.

BLA_test() - Constructor for class esraMath.BLA_test

BZip2Constants - interface contrib.BZip2Constants.

Base class for both the compress and decompress classes.

BondAngleType - class forcefield.BondAngleType.

Contains the Angle information from the topology.

BondAngleType() - Constructor for class forcefield.BondAngleType

BondAngleType - Variable in class forcefield.InteractionParameters

HashTable for BondAngleType look-up.

BondType - class forcefield.BondType.

The BondType class contains all the Bond information from the topology.

BondType() - Constructor for class forcefield.BondType

BondType - Variable in class forcefield.InteractionParameters

HashTable for BondType look-up.

Bondblock - Variable in class io.mol2.InMol2

Bonds - class forcefield.Bonds.

The Bonds class contains all the Bond information from the sytem.

Bonds(int) - Constructor for class forcefield.Bonds

The Bonds class contructor.

BondsTest - class forcefield.BondsTest.

BondsTest() - Constructor for class forcefield.BondsTest

Bornradii_STILL - class energy.Bornradii_STILL.

Bornradii_STILL(Particles, SimSystem) - Constructor for class energy.Bornradii_STILL

b0 - Variable in class forcefield.BondType

b0 - Variable in class forcefield.Bonds

Ideal bond length of bond[num].

b02 - Variable in class forcefield.BondType

badBGLengths() - Static method in class contrib.CBZip2InputStream

badBlockHeader() - Static method in class contrib.CBZip2InputStream

base - Variable in class contrib.CBZip2InputStream

baseBlockSize - Static variable in interface contrib.BZip2Constants

bbAN - Variable in class conformation.Dssp

the backbone atom numbers

bendT - Static variable in class conformation.Dssp

bin(double[], double, double, int) - Static method in class esraMath.Statistics

bitStreamEOF() - Static method in class contrib.CBZip2InputStream

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

blockNamePattern - Static variable in class io.args.ArgumentChecker

blockOverrun() - Static method in class contrib.CBZip2InputStream

blockRandomised - Variable in class contrib.CBZip2InputStream

blockSize100k - Variable in class contrib.CBZip2InputStream

bo - Variable in class energy.Energy_Bond

boatType - Static variable in class conformation.RingConformation

boh - Variable in class energy.Energy_Bond

boltz - Variable in class energy.FDPoissonBoltzmann_Parameters

Boltzmann's constant @f$k_B @f$.

bond - Variable in class core.SimSystem

All Bonds involving non-hydrogen atoms.

bondh - Variable in class core.SimSystem

All Bonds involving hydrogen atoms.

bondlength - Variable in class energy.Bornradii_STILL

bonds - Variable in class energy.Bornradii_STILL

bornrad - Variable in class energy.Energy_GBorn

bornradii - Variable in class energy.Energy_GBorn

bornradius - Variable in class energy.Bornradii_STILL

boundaryAtoms - Variable in class core.Particles

Last atom[m] i of Molecule m in Topology.

box - Variable in class core.SimSystem

Box dimension.

box - Variable in class io.g96.G96Frame

boxCheck(double[]) - Static method in class core.pbc.NearestImage

boxCheck(double[]) - Static method in class core.pbc.PBC

boxFormatter - Static variable in class io.g96.out.OutPosG96

boxFormatter - Variable in class io.g96.out.OutTrajG96

bsBuff - Variable in class contrib.CBZip2InputStream

bsFinishedWithStream() - Method in class contrib.CBZip2InputStream

bsGetInt32() - Method in class contrib.CBZip2InputStream

bsGetIntVS(int) - Method in class contrib.CBZip2InputStream

bsGetUChar() - Method in class contrib.CBZip2InputStream

bsGetint() - Method in class contrib.CBZip2InputStream

bsLive - Variable in class contrib.CBZip2InputStream

bsR(int) - Method in class contrib.CBZip2InputStream

bsSetStream(InputStream) - Method in class contrib.CBZip2InputStream

bsStream - Variable in class contrib.CBZip2InputStream

bt - Variable in class forcefield.Bonds

String of the BondType.

buf - Variable in class energy.FD_WriteGrid