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

N

N - Static variable in class conformation.Dssp

NO_RAND_PART_A_STATE - Static variable in class contrib.CBZip2InputStream

NO_RAND_PART_B_STATE - Static variable in class contrib.CBZip2InputStream

NO_RAND_PART_C_STATE - Static variable in class contrib.CBZip2InputStream

NP - Variable in class forcefield.DihedralType

NP - Variable in class forcefield.Dihedrals

Multiplicity of dihedral-angle torsion[num].

NUM_OVERSHOOT_BYTES - Static variable in interface contrib.BZip2Constants

N_GROUPS - Static variable in interface contrib.BZip2Constants

N_ITERS - Static variable in interface contrib.BZip2Constants

NearestImage - class core.pbc.NearestImage.

NearestImage() - Constructor for class core.pbc.NearestImage

nEgr - Variable in class io.g96.in.InEnergiesG96.G96Energies

the number of energy groups

nInUse - Variable in class contrib.CBZip2InputStream

name - Variable in class core.G96SolventTopology

name - Variable in class core.Particles

Particle name of Particle i in Topology.

name - Variable in class io.args.ArgumentTypeSpec

nameFormat - Static variable in class io.pdb.PDBAtomFormatter

namePattern - Static variable in class core.AtomSpecifier

namePatternString - Static variable in class core.AtomSpecifier

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

ArrayList to HashMap conversion.

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

Partitioning of tokens into name and number lists.

nearestImage(double[], double[], double[], int) - Method in class core.pbc.NearestImage

Return the nearest image of v2 with respect to v1.

nearestImage(double[], double[], double[]) - Method in class core.pbc.PBC

Return the nearest image of v2 with respect to v1.

nearestImage(double[], double[], double[]) - Method in class core.pbc.PBC_RectBox

nearestImage(double[], double[], double[]) - Method in class core.pbc.PBC_TruncOct

nearestImageRectangular(double[], double[], double[]) - Method in class core.pbc.NearestImage

The nearest image of v2 with respect to v1 under rectangular boundary conditions.

nearestImageTruncatedOctahedron(double[], double[], double[]) - Method in class core.pbc.NearestImage

The nearest image of v2 with respect to v1 under truncated octahedral boundary conditions.

nearestImageVacuum(double[], double[], double[]) - Method in class core.pbc.NearestImage

The nearest image of v2 with respect to v1.

neighbors - Variable in class esraMath.Statistics.Cluster

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

nist - Variable in class io.pdb.InPDB

noBound - Static variable in class io.args.ArgumentChecker

noPattern - Static variable in class io.args.ArgumentChecker

nonControl(String, int) - Method in class contrib.PrintfFormat

Return a substring starting at start and ending at either the end of the String s, the next unpaired percent sign, or at the end of the String if the last character is a percent sign.

nonb - Variable in class energy.Bornradii_STILL

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

the euclidean norm of a vector

norm2(double[]) - Static method in class esraMath.BLA

the squared euclidean norm of a vector

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

normalize a vector by scaling it by its inverse norm.

numAtoms - Variable in class core.G96SolventTopology

numDihedralTypes - Static variable in class conformation.AlkaneDihedrals

numFrames - Variable in class conformation.HydrogenBonds.HBTrajectoryStats

numHBonds - Variable in class conformation.HydrogenBonds.HBFrameStats

numMolecules - Variable in class core.Particles

Number of Molecules in Topology.

numResidues - Variable in class core.Particles

Total Number of residues.

number - Variable in class core.Particles

Total Number of solute Particles.

number - Variable in class forcefield.Angles

Number of Angles in the object.

number - Variable in class forcefield.Bonds

Number of Bonds in the object.

number - Variable in class forcefield.Dihedrals

Number of dihedral-angle torsions in the object.

number - Variable in class forcefield.ImproperDihedrals

Number of improper dihedral-angles in the object.

numberPattern - Static variable in class core.AtomSpecifier

numberPatternString - Static variable in class core.AtomSpecifier

nus - Variable in class io.pdb.InPDB