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

S

SASA - Variable in class core.Particles

The SASA of atoms i.

SASAweight - Variable in class core.Particles

The SASA weight.

START_BLOCK_STATE - Static variable in class contrib.CBZip2InputStream

SimSystem - class core.SimSystem.

Contains the information for simulation system, such as number of dimensions, box dimension.

SimSystem() - Constructor for class core.SimSystem

Statistics - class esraMath.Statistics.

Statistics() - Constructor for class esraMath.Statistics

Statistics.Cluster - class esraMath.Statistics.Cluster.

litttle helper class for the clustering algorithm

Statistics.Cluster(int, ArrayList) - Constructor for class esraMath.Statistics.Cluster

StillradiibyIAC(Particles) - Static method in class energy.PositionUtils

StringUtils - class stuff.StringUtils.

StringUtils() - Constructor for class stuff.StringUtils

same(int, int) - Static method in class esraMath.BLA

initialize a vector of length ii with values value

same(int, double) - Static method in class esraMath.BLA

initialize a vector of length ii with values value

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

multiply all elements of a vector by some fixed number.

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

Scale a 3rd order tensor by some scalar.

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

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

returns a selected part of the array

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

returns a selected part of the array

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

returns a selected number of rows of the matrix

selector - Variable in class contrib.CBZip2InputStream

selectorMtf - Variable in class contrib.CBZip2InputStream

seqToUnseq - Variable in class contrib.CBZip2InputStream

setArgPosition() - Method in class contrib.PrintfFormat.ConversionSpecification

Store the digits n in %n$ forms.

setConversionCharacter() - Method in class contrib.PrintfFormat.ConversionSpecification

Check for a conversion character.

setDecompressStructureSizes(int) - Method in class contrib.CBZip2InputStream

setFieldWidth() - Method in class contrib.PrintfFormat.ConversionSpecification

Set the field width.

setFieldWidthArgPosition() - Method in class contrib.PrintfFormat.ConversionSpecification

Store the digits n in *n$ forms.

setFieldWidthWithArg(int) - Method in class contrib.PrintfFormat.ConversionSpecification

Set the field width with an argument.

setFlagCharacters() - Method in class contrib.PrintfFormat.ConversionSpecification

Set flag characters, one of '-+#0 or a space.

setGlobalCRC(int) - Method in class contrib.CRC

setLiteral(String) - Method in class contrib.PrintfFormat.ConversionSpecification

Set the String for this instance.

setOptionalHL() - Method in class contrib.PrintfFormat.ConversionSpecification

Check for an h, l, or L in a format.

setPrecision() - Method in class contrib.PrintfFormat.ConversionSpecification

Set the precision.

setPrecisionArgPosition() - Method in class contrib.PrintfFormat.ConversionSpecification

Store the digits n in *n$ forms.

setPrecisionWithArg(int) - Method in class contrib.PrintfFormat.ConversionSpecification

Set the precision with an argument.

set_pbc(boolean) - Method in class energy.FD_WriteGrid

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

setparams(double[]) - Method in class energy.Bornradii_STILL

setpermittivity(double, double) - Method in class energy.FDPoissonBoltzmann

static setpermittivity.

setupBlock() - Method in class contrib.CBZip2InputStream

setupCoords() - Static method in class esraMath.FitTest

setupGrid(FDPoissonBoltzmann_Parameters, boolean) - Method in class energy.FDPoissonBoltzmann

public void method setupGrid sets up a grid around the solute particles using the center of geometry as the grid center, along with the given gridspacing, ionic strength, solute/solven permittivities and the number of gridpoints along X,Y and Z.

setupNoRandPartA() - Method in class contrib.CBZip2InputStream

setupNoRandPartB() - Method in class contrib.CBZip2InputStream

setupNoRandPartC() - Method in class contrib.CBZip2InputStream

setupRandPartA() - Method in class contrib.CBZip2InputStream

setupRandPartB() - Method in class contrib.CBZip2InputStream

setupRandPartC() - Method in class contrib.CBZip2InputStream

setup_Interactions() - Method in class energy.Energy

private void method setup_Interactions() sets up the interaction types for the calculation

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

Add a N-vector change to each row of the M x N - Matrix positions.

shiftCOGin1stquadrant(Particles, SimSystem) - Static method in class energy.PositionUtils

shiftCoG(double[][], double[], double[]) - Static method in class esraMath.Fit

Shift the center of geometry of a set of 3D-coordinates and massses to some point in 3D-space.

size - Variable in class conformation.HydrogenBonds.HBDefinitions

size - Variable in class conformation.HydrogenBonds.HBFrameStats

size - Variable in class energy.Energy

size - Variable in class energy.FDPoissonBoltzmann_EpsGrid

The PoissonBoltzmannn_EpsGrid class constructor.

size() - Method in class forcefield.DenseExclusions

size() - Method in class forcefield.LJ14HashMap

size() - Method in class forcefield.LJTypeHashMap

size - Variable in class io.g96.out.OutTopoG96

skipBlock(String) - Static method in class io.g96.in.InCorG96

We don't care about any blocks except the TIMESTEP, POSITION(RED) and the BOX block.

skipLine(String) - Method in class io.g96.in.InBlock

slurp() - Method in class io.g96.in.InBlock

slurp the whole contents of the file into a list of blocks

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

reduce the size of a matrix by averaging over blocks.

soluteAtomFormatter(int, int[], int[], String[], int[], double[], double[], int[], DenseExclusions, DenseExclusions) - Static method in class io.g96.out.OutTopoG96

solvate(Particles, double[][]) - Method in class core.G96SolventTopology

solveforpotential(int, double) - Method in class energy.FDPoissonBoltzmann

public boolean solveforpotential solves the linearized Poisson-Boltzmann equation for the electrostatic potential phigrid using the incomplete cholesky conjugate gradient algorithm

solvent - Variable in class io.g96.in.InTopoG96.Topology

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

sprintf(Object[]) - Method in class contrib.PrintfFormat

Format an array of objects.

sprintf() - Method in class contrib.PrintfFormat

Format nothing.

sprintf(int) - Method in class contrib.PrintfFormat

Format an int.

sprintf(long) - Method in class contrib.PrintfFormat

Format an long.

sprintf(double) - Method in class contrib.PrintfFormat

Format a double.

sprintf(String) - Method in class contrib.PrintfFormat

Format a String.

sprintf(Object) - Method in class contrib.PrintfFormat

Format an Object.

sqrt_sum(double, double) - Static method in class esraMath.BLA

Return the (a^2 + b^2)^(1/2) without over- or underflow

startPattern - Variable in class io.g96.in.InBlock

startSymbolicCarry(char[], int, int) - Method in class contrib.PrintfFormat.ConversionSpecification

Start the symbolic carry process.

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

A naive implementation for calculating a naive measure for the standard deviation.

step - Variable in class io.g96.G96Frame

stepFormat - Variable in class io.g96.out.G96TimestepFormatter

store - Variable in class forcefield.DenseExclusions

store - Variable in class forcefield.LJ14HashMap

store - Variable in class forcefield.LJTypeHashMap

storedBlockCRC - Variable in class contrib.CBZip2InputStream

storedCombinedCRC - Variable in class contrib.CBZip2InputStream

stream - Variable in class io.g96.in.InBlock

streamEnd - Variable in class contrib.CBZip2InputStream

stuff - package stuff

subset(int[]) - Method in class core.Particles

Select a subset of particles.

subset(int[], int) - Method in class forcefield.Bonds

generate a new set of those bonds which only connect the atoms we're interested in.

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

subtract two vectors (bb - aa).

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

subtract two matrices.

suite() - Static method in class esraMath.BLA_test

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

sumchrg - Variable in class energy.FDPoissonBoltzmann_ChargeGrid

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

sybylToG96IAC - Static variable in class io.mol2.InMol2

synPeriPlanarType - Static variable in class conformation.AlkaneDihedrals

synType - Static variable in class conformation.AlkaneDihedrals

sys - Variable in class energy.Bornradii_STILL

sys - Variable in class energy.Energy

sys - Variable in class energy.Energy_GBorn

sys - Variable in class energy.FDPoissonBoltzmann

sys - Variable in class io.g96.out.OutTopoG96

system - Variable in class io.g96.in.InTopoG96.Topology