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

T

TOLERANCE - Variable in class conformation.DsspTest

TOLERANCE - Variable in class energy.FDPoissonBoltzmannTest

TOLERANCE - Static variable in class esraMath.BLA

TOLERANCE - Variable in class esraMath.BLA_test

TOLERANCE - Variable in class esraMath.FitTest

TOLERANCE - Variable in class esraMath.GeometryTest

TOLERANCE - Variable in class forcefield.BondsTest

TrajectoryWriter - class io.TrajectoryWriter.

TrajectoryWriter(String) - Constructor for class io.TrajectoryWriter

TrajectoryWriter(String, String) - Constructor for class io.TrajectoryWriter

Turn - Variable in class conformation.Dssp

tPos - Variable in class contrib.CBZip2InputStream

temperature - Variable in class energy.FDPoissonBoltzmann_Parameters

testAlignPrincipalAxes() - Method in class esraMath.FitTest

testAngle() - Method in class esraMath.BLA_test

testAngle() - Method in class esraMath.GeometryTest

testAssignUniqueSecondaryStructure() - Method in class conformation.DsspTest

testBonds() - Method in class forcefield.BondsTest

testCenterOfGeometry() - Method in class esraMath.GeometryTest

testCopies() - Method in class forcefield.BondsTest

testDetermineBoundaryAtoms() - Method in class io.g96.in.InTopoG96Test

testDetermineMoleculesFloyd() - Method in class io.g96.in.InTopoG96Test

testDetermineSixRingConformation() - Method in class conformation.RingConformationTest

testDihedral() - Method in class esraMath.GeometryTest

testDistance() - Method in class esraMath.GeometryTest

testDssp() - Method in class conformation.DsspTest

testFindBackBoneAtoms() - Method in class conformation.DsspTest

testFindBridges() - Method in class conformation.DsspTest

testFindHelices() - Method in class conformation.DsspTest

testFindTurns() - Method in class conformation.DsspTest

testFitAndRmsddoubleArrayArraydoubleArrayArraydoubleArray() - Method in class esraMath.GeometryTest

testFitdoubleArrayArraydoubleArrayArraydoubleArray() - Method in class esraMath.FitTest

testFitdoubleArrayArrayintArraydoubleArrayArrayintArraydoubleArray() - Method in class esraMath.FitTest

testGetBackboneCoords() - Method in class conformation.DsspTest

testGetBoundaryAtoms() - Method in class io.g96.in.InTopoG96Test

testGetDihedralType() - Method in class conformation.AlkaneDihedralsTest

testHbEnergy() - Method in class conformation.DsspTest

testInMol2() - Method in class io.mol2.InMol2Test

testInMol2String() - Method in class io.mol2.InMol2Test

testInertiaTensor() - Method in class esraMath.GeometryTest

testIsEclipsed() - Method in class conformation.AlkaneDihedralsTest

testIsStaggered() - Method in class conformation.AlkaneDihedralsTest

testIterativeRotationalFit() - Method in class esraMath.FitTest

testIupac2Math() - Method in class esraMath.GeometryTest

testJoin() - Method in class forcefield.BondsTest

testKabschSander() - Method in class conformation.DsspTest

testKabschSanderIntArrayArrayDoubleArrayArrayArrayIntArray() - Method in class conformation.DsspTest

testLinerotationMatrix() - Method in class esraMath.GeometryTest

testParseAngleBlock() - Method in class io.g96.in.InTopoG96Test

testParseAtomTypeNameBlock() - Method in class io.g96.in.InTopoG96Test

testParseBondAngleTypeBlock() - Method in class io.g96.in.InTopoG96Test

testParseBondBlock() - Method in class io.g96.in.InTopoG96Test

testParseBondTypeBlock() - Method in class io.g96.in.InTopoG96Test

testParseDihedralBlock() - Method in class io.g96.in.InTopoG96Test

testParseDihedralTypeBlock() - Method in class io.g96.in.InTopoG96Test

testParseExclusionLine() - Method in class io.g96.in.InTopoG96Test

testParseImpDihedralTypeBlock() - Method in class io.g96.in.InTopoG96Test

testParseImproperBlock() - Method in class io.g96.in.InTopoG96Test

testParseLJBlock() - Method in class io.g96.in.InTopoG96Test

testParseResNameBlock() - Method in class io.g96.in.InTopoG96Test

testParseSoluteAtomBlock() - Method in class io.g96.in.InTopoG96Test

testParseSolventAtomBlock() - Method in class io.g96.in.InTopoG96Test

testParseSolventConstraintBlock() - Method in class io.g96.in.InTopoG96Test

testParseTopPhysConBlock() - Method in class io.g96.in.InTopoG96Test

testParseTopVersionBlock() - Method in class io.g96.in.InTopoG96Test

testParsefile() - Method in class io.mol2.InMol2Test

testReadMol2fromfile() - Method in class io.mol2.InMol2Test

testReadTopology() - Method in class io.g96.in.InTopoG96Test

testRgyr() - Method in class esraMath.GeometryTest

testRmsddoubleArrayArraydoubleArrayArray() - Method in class esraMath.GeometryTest

testRmsddoubleArrayArraydoubleArrayArraydoubleArray() - Method in class esraMath.GeometryTest

testRotate() - Method in class esraMath.GeometryTest

testRotationMatrix() - Method in class esraMath.FitTest

testRotationMatrixMcLachlan() - Method in class esraMath.FitTest

testRotationalFit2() - Method in class esraMath.FitTest

testRotationalFitdoubleArrayArraydoubleArrayArray() - Method in class esraMath.FitTest

testRotationalFitdoubleArrayArraydoubleArrayArraydoubleArray() - Method in class esraMath.FitTest

testShiftCoG() - Method in class esraMath.FitTest

testSubset() - Method in class forcefield.BondsTest

testTranslationalFit() - Method in class esraMath.FitTest

testdiagonalizesymmetric() - Method in class esraMath.BLA_test

testdoBorn() - Method in class energy.FDPoissonBoltzmannTest

testdoBornanalytic() - Method in class energy.FDPoissonBoltzmannTest

testlinerotation() - Method in class esraMath.BLA_test

th0 - Variable in class forcefield.Angles

Ideal angle of bond-angle[num].

th0 - Variable in class forcefield.BondAngleType

thousands - Variable in class contrib.PrintfFormat.ConversionSpecification

The integer portion of the result of a decimal conversion (i, d, u, f, g, or G) will be formatted with thousands' grouping characters.

threeTenHelixT - Static variable in class conformation.Dssp

thtopo - Variable in class forcefield.BondAngleType

time - Variable in class io.g96.G96Frame

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

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

timeSeriesBlockName() - Static method in class io.g96.out.HBondFormatter

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

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

title(String, double, double) - Static method in class io.g96.out.HBondFormatter

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

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

toString() - Method in class io.args.ArgumentTypeSpec

convert argument to String.

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

tokenize(String) - Static method in class core.AtomSpecifier

Parse and validate the atom specifier string obtained from the command line.

topversion - Variable in class forcefield.InteractionParameters

tot_charge - Variable in class energy.FDPoissonBoltzmann_Boundary

The PoissonBoltzmann class constructor.

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

QL algorithm with implicit shifts, to determine the eigenvalues and eigenvectors of a real, symmetric, tridiagonal matrix

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

Shift the center of geometry of a set of 3D-coordinates to the center of geometry of another set of 3D-coords, both weighted by the same weights.

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

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

tred2(double[][], double[], double[]) - Static method in class esraMath.BLA

Householder reduction of a real, symmetric matrix (double mat[][])

truncatedOctahedralType - Static variable in class core.pbc.NearestImage

tt - Variable in class contrib.CBZip2InputStream

turnT - Static variable in class conformation.Dssp

type - Variable in class io.args.ArgumentDescription

types - Variable in class forcefield.DenseExclusions

types() - Method in class forcefield.DenseExclusions

types - Variable in class forcefield.LJ14HashMap

types() - Method in class forcefield.LJ14HashMap

types - Variable in class forcefield.LJTypeHashMap

types() - Method in class forcefield.LJTypeHashMap