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F

FDPoissonBoltzmann - class energy.FDPoissonBoltzmann.

FDPoissonBoltzmann() - Constructor for class energy.FDPoissonBoltzmann

The PoissonBoltzmann default class constructor.

FDPoissonBoltzmann(Particles, SimSystem, boolean) - Constructor for class energy.FDPoissonBoltzmann

FDPoissonBoltzmann(FDPoissonBoltzmann_Parameters, boolean) - Constructor for class energy.FDPoissonBoltzmann

FDPoissonBoltzmann(Particles, SimSystem, FDPoissonBoltzmann_Parameters, boolean) - Constructor for class energy.FDPoissonBoltzmann

The PoissonBoltzmann class constructor.

FDPoissonBoltzmannTest - class energy.FDPoissonBoltzmannTest.

FDPoissonBoltzmannTest() - Constructor for class energy.FDPoissonBoltzmannTest

FDPoissonBoltzmann_Boundary - class energy.FDPoissonBoltzmann_Boundary.

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

FDPoissonBoltzmann_Boundary(Particles, SimSystem, double) - Constructor for class energy.FDPoissonBoltzmann_Boundary

FDPoissonBoltzmann_ChargeGrid - class energy.FDPoissonBoltzmann_ChargeGrid.

FDPoissonBoltzmann_ChargeGrid(Particles, SimSystem, int) - Constructor for class energy.FDPoissonBoltzmann_ChargeGrid

FDPoissonBoltzmann_ChargeGrid(Particles, SimSystem, int, int, int, int) - Constructor for class energy.FDPoissonBoltzmann_ChargeGrid

FDPoissonBoltzmann_EpsGrid - class energy.FDPoissonBoltzmann_EpsGrid.

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

FDPoissonBoltzmann_ICCG - class energy.FDPoissonBoltzmann_ICCG.

FDPoissonBoltzmann_ICCG() - Constructor for class energy.FDPoissonBoltzmann_ICCG

FDPoissonBoltzmann_ICCG_NPBC - class energy.FDPoissonBoltzmann_ICCG_NPBC.

FDPoissonBoltzmann_ICCG_NPBC(int, int, int, int, int) - Constructor for class energy.FDPoissonBoltzmann_ICCG_NPBC

FDPoissonBoltzmann_Parameters - class energy.FDPoissonBoltzmann_Parameters.

FDPoissonBoltzmann_Parameters() - Constructor for class energy.FDPoissonBoltzmann_Parameters

FD_WriteGrid - class energy.FD_WriteGrid.

FD_WriteGrid(int, int, int) - Constructor for class energy.FD_WriteGrid

FEPS - Variable in class energy.Bornradii_STILL

FPEPSI - Variable in class core.SimSystem

1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) $\frac{1}{{4\pi \varepsilon _0 }}$

FPEPSI - Variable in class energy.FDPoissonBoltzmannTest

Fit - class esraMath.Fit.

Purpose: The Fit class Description: The Fit class provides routines for fitting.

Fit() - Constructor for class esraMath.Fit

FitTest - class esraMath.FitTest.

FitTest() - Constructor for class esraMath.FitTest

FormatAngle - Static variable in class io.g96.out.HBondFormatter

FormatAtomName - Static variable in class io.g96.out.HBondFormatter

FormatAtomNumber - Static variable in class io.g96.out.HBondFormatter

FormatMolNum - Static variable in class io.g96.out.HBondFormatter

FormatOccur - Static variable in class io.g96.out.HBondFormatter

FormatOccurPerc - Static variable in class io.g96.out.HBondFormatter

FormatResName - Static variable in class io.g96.out.HBondFormatter

FormatResNum - Static variable in class io.g96.out.HBondFormatter

Formatdistance - Static variable in class io.g96.out.HBondFormatter

f - Static variable in class conformation.Dssp

kabsch & sander hydrogen bond energy parameters

f2c(ArrayList) - Static method in class core.AtomSpecifier

Takes an ArrayList of Integer objects and creates a new ArrayList by subtracting 1 from each element (C-style indexing vs.

fFormatDigits(double) - Method in class contrib.PrintfFormat.ConversionSpecification

For f format, the flag character '-', means that the output should be left justified within the field.

fFormatString(double) - Method in class contrib.PrintfFormat.ConversionSpecification

An intermediate routine on the way to creating an f format String.

fieldWidth - Variable in class contrib.PrintfFormat.ConversionSpecification

If the converted value has fewer bytes than the field width, it will be padded with spaces or zeroes.

fieldWidthSet - Variable in class contrib.PrintfFormat.ConversionSpecification

Flag indicating whether or not the field width has been set.

fileName - Variable in class io.TrajectoryWriter

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

fileName - Variable in class io.mol2.InMol2

fileName - Variable in class io.pdb.InPDB

fileNameIterator - Variable in class io.g96.in.InTrajG96

fileNamePattern - Static variable in class io.args.ArgumentChecker

fileNames - Variable in class io.g96.in.InTrajG96

fill(int[], int, int, int) - Static method in class conformation.Dssp

fill a part of vector stuff with value.

findBackBoneAtoms(Particles) - Static method in class conformation.Dssp

Find indices of the protein backbone atoms.

findBends(double[][]) - Static method in class conformation.Dssp

Check if a residue is part of a bend.

findBridges(boolean[][]) - Static method in class conformation.Dssp

find bridges in the hydrogen bonding pattern.

findDonor(int, Bonds) - Static method in class conformation.HydrogenBonds

findDonors(int[], Bonds) - Static method in class conformation.HydrogenBonds

findHbonds(int[][], double[][][], int[], int) - Static method in class conformation.Dssp

Rather than directly inspecting structural characteristics, the dssp algorithm looks at the "energy" of a hydrogen bond to determine if it's there.

findHelices(int[], int, int) - Static method in class conformation.Dssp

Turns may be parts of helices.

findLaddersAndSheets(int[][]) - Static method in class conformation.Dssp

Find β-ladders and -sheets.

findTurns(boolean[][], int) - Static method in class conformation.Dssp

find turns in the hydrogen bonding pattern.

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

A fit of coords to refCoords (weighted by weights).

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

A fit of coords to refCoords (weighted by weights).

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

fit two structures and compute the rmsd.

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

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

floatPattern - Static variable in class io.args.ArgumentChecker

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

public Method floyd calculates the shortest path through an adjacency matrix.

fmt - Variable in class contrib.PrintfFormat.ConversionSpecification

Literal or control format string.

forcefield - package forcefield

format(double[]) - Method in class io.g96.out.G96BoxFormatter

format(String, String[]) - Static method in class io.g96.out.G96GenericFormatter

format(String, String[], String) - Static method in class io.g96.out.G96GenericFormatter

Generate a GROMOS block from an array of Strings.

format(double[][], String[], String[], int[]) - Method in class io.g96.out.G96PositionFormatter

format(double[][]) - Method in class io.g96.out.G96PositionredFormatter

format(int, double) - Method in class io.g96.out.G96TimestepFormatter

format(String) - Method in class io.g96.out.G96TitleFormatter

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

format(double[][], String[], String[], int[]) - Static method in class io.pdb.PDBAtomFormatter

Takes arrays of atomic positions and names as well as the corresponding residue names and numbers and attempt to generate pdb atomic coordinates from it.

format(String) - Static method in class io.pdb.PDBTitleFormatter

format(double[][]) - Method in class io.vmd.VMDAMFormatter

formatHBNum - Static variable in class io.g96.out.HBondFormatter

formatfloat - Variable in class energy.FD_WriteGrid

formatint - Variable in class energy.FD_WriteGrid

foundBadTimestep - Variable in class io.g96.in.InCorG96

foundZeroBox - Static variable in class io.g96.in.InCorG96