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

R

RAND_PART_A_STATE - Static variable in class contrib.CBZip2InputStream

RAND_PART_B_STATE - Static variable in class contrib.CBZip2InputStream

RAND_PART_C_STATE - Static variable in class contrib.CBZip2InputStream

RUNA - Static variable in interface contrib.BZip2Constants

RUNB - Static variable in interface contrib.BZip2Constants

RingConformation - class conformation.RingConformation.

Simple ring conformation analysis.

RingConformation() - Constructor for class conformation.RingConformation

RingConformationTest - class conformation.RingConformationTest.

RingConformationTest() - Constructor for class conformation.RingConformationTest

rNToGo - Variable in class contrib.CBZip2InputStream

rNums - Static variable in interface contrib.BZip2Constants

rTPos - Variable in class contrib.CBZip2InputStream

rad() - Method in class energy.Energy_GBorn

radP - Variable in class core.SimSystem

water probe radius; default 0.14 nm.

radius - Variable in class core.Particles

The atomic radii.

radius - Variable in class energy.FDPoissonBoltzmannTest

radiusboundaryEPSI(double, double[], double, double, double[]) - Method in class energy.FDPoissonBoltzmann_EpsGrid

radiusboundaryEPSJ(double, double[], double, double, double[]) - Method in class energy.FDPoissonBoltzmann_EpsGrid

radiusboundaryEPSK(double, double[], double, double, double[]) - Method in class energy.FDPoissonBoltzmann_EpsGrid

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

range(int) - Static method in class esraMath.BLA

rangePattern - Static variable in class core.AtomSpecifier

rangePatternString - Static variable in class core.AtomSpecifier

rcsb - Variable in class io.pdb.InPDB

read() - Method in class contrib.CBZip2InputStream

readEnergyBlock() - Method in class io.g96.in.InEnergiesG96

readFrame() - Method in class io.g96.in.InCorG96

Read and parse a Gromos96 frame from file.

readFrame(boolean) - Method in class io.g96.in.InCorG96

readFrame() - Method in class io.g96.in.InTrajG96

readFrame(boolean) - Method in class io.g96.in.InTrajG96

read a frame from file.

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

readMol2fromfile() - Method in class io.mol2.InMol2

Method readMol2fromfile() reads a single mol2 file and stores any encountered \@ATOM or @BOND block.

readPDBfromWEB(double[][], boolean) - Method in class io.pdb.InPDB

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

Gromos files are usually headed by a TITLE block.

readTitle() - Method in class io.g96.in.InTrajG96

readTopology(String) - Static method in class io.g96.in.InTopoG96

readVolumePressureBlock() - Method in class io.g96.in.InEnergiesG96

readinputfile(String) - Static method in class io.args.ArgumentParser

slurp contents of an input file, stripping comments

rectangularType - Static variable in class core.pbc.NearestImage

recvDecodingTables() - Method in class contrib.CBZip2InputStream

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

required - Variable in class io.args.ArgumentTypeSpec

residueNameFormat - Static variable in class io.g96.out.G96PositionFormatter

residueNumberFormat - Static variable in class io.g96.out.G96PositionFormatter

residueNumberFormat - Static variable in class io.pdb.PDBAtomFormatter

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

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

rhogrid - Variable in class energy.FDPoissonBoltzmann

rhogrid[GPX*GPY*GPZ] stores the charges assigned to each grid point divided by the gridspacing @f$ h @f$

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

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

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

computes the rmsd matrix for a trajectory.

rname - Variable in class core.Particles

Residue name of Particle i in Topology.

rnum - Variable in class core.Particles

Residue number of Particle i in Topology.

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

Rotate point using a supplied rotationmatrix.

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

Rotate point using a supplied rotationmatrix.

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

SEE A.D.

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

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

SEE A.D.

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

The atoms of the simulation system are rotated about the origin such that the (weighted) rmsd is minimized.

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

SEE A.D.

run() - Method in class energy.Energy_Angle

public void Method run calls protected void Method calc.

run() - Method in class energy.Energy_Bond

public void Method run calls protected void Method calc.

run() - Method in class energy.Energy_Dihedral

public void Method run calls protected void Method calc.

run() - Method in class energy.Energy_GBorn

run() - Method in class energy.Energy_ImpDihedral

public void Method run calls protected void Method calc.

run() - Method in interface energy.InteractionsEnergy

rutgers - Variable in class io.pdb.InPDB