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

C

C - Static variable in class conformation.Dssp

backbone atom indices

C12 - Variable in class forcefield.LJType

Lennard-Jones C12 parameter (repulsion)

C6 - Variable in class forcefield.LJType

Lennard-Jones C6 parameter (attraction)

CA - Static variable in class conformation.Dssp

CBZip2InputStream - class contrib.CBZip2InputStream.

An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.

CBZip2InputStream(InputStream) - Constructor for class contrib.CBZip2InputStream

CRC - class contrib.CRC.

A simple class the hold and calculate the CRC for sanity checking of the data.

CRC() - Constructor for class contrib.CRC

CS12 - Variable in class forcefield.LJType

Lennard-Jones C12 parameter for the 1-4 interactions (repulsion)

CS6 - Variable in class forcefield.LJType

Lennard-Jones C6 parameter for the 1-4 interactions (attraction)

Calc_COSPHI(double, int) - Method in class energy.Energy_Dihedral

cPos - Variable in class contrib.PrintfFormat

Character position.

cadvise() - Static method in class contrib.CBZip2InputStream

calc() - Method in class energy.Bornradii_STILL

calc(Angles) - Method in class energy.Energy_Angle

protected void Method calc evaluates the Angle Energy as (GROMOS96 manual pages II-17ff):

calc(Bonds) - Method in class energy.Energy_Bond

protected void Method calc evaluates the Bond Energy as (GROMOS96 manual pages II-12ff):

calc(Dihedrals) - Method in class energy.Energy_Dihedral

protected void Method calc evaluates the dihedral force as (GROMOS96 manual pages II-25ff):

calc(ImproperDihedrals) - Method in class energy.Energy_ImpDihedral

protected void Method calc evaluates the improper dihdral force as (GROMOS96 manual pages II-21ff):

calcBornradii() - Method in class energy.Bornradii_STILL

calcEnergy() - Method in class energy.Energy

public void method calcEnergy() calculates the bonded and non-bonded forces
by looping over the interactions interface parsed in the constructor

calcOverlap(int, int, double) - Method in class energy.Bornradii_STILL

calcVolume() - Method in class energy.Bornradii_STILL

calcrad() - Method in class energy.Energy_GBorn

capitalsPattern - Static variable in class io.args.ArgumentChecker

center - Variable in class energy.FDPoissonBoltzmann_Parameters

center - Variable in class esraMath.Statistics.Cluster

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

Compute the center of geometry of a set of 3D-coordinates and massses.

centermode - Variable in class energy.FDPoissonBoltzmann_Parameters

ch2 - Variable in class contrib.CBZip2InputStream

chPrev - Variable in class contrib.CBZip2InputStream

chairType - Static variable in class conformation.RingConformation

charge - Variable in class core.G96SolventTopology

charge - Variable in class core.Particles

Charge of Particle i.

charge - Variable in class energy.FDPoissonBoltzmannTest

chargeGridtrilinear(double, double[], double[]) - Method in class energy.FDPoissonBoltzmann_ChargeGrid

check(String, ArrayList, int, int, String) - Static method in class io.args.ArgumentChecker

assert that argValues has the right (min < x < max) number of arguments, and that all arguments match regex.

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

Check to see if the digits that are going to be truncated because of the precision should force a round in the preceding digits.

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

Is there a hydrogen bond involving the three atoms?

checkHelp(HashMap) - Method in class io.args.ArgumentParser

if the arguments contain the help keyword, print a usage text and exit.

checkInputFile(HashMap) - Method in class io.args.ArgumentParser

if the arguments contain the f keyword, read the corresponding input file.

checkPattern(String, String, String) - Static method in class io.args.ArgumentChecker

assert that argument matches regex.

checkValues() - Method in class io.args.ArgumentParser

assert that all the supplied arguments conform to the argument value definitions.

chgrp - Variable in class core.Particles

Charge Group of Particle i in Topology.

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

{x1, x2, -breakiterator , xn} -> {x(n - m), x(n - m + 1), breakiterator , x1, x2, breakiterator , x(n - m - 1)}

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

close the file stream and reset the file name

close() - Method in class io.g96.out.OutTopoG96

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

cluster analysis

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

Method cog calculates the center of geometry for the system

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

Method cog calculates the center of mass for the system

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

commentFormat - Static variable in class io.g96.out.G96GenericFormatter

commentFormat - Variable in class io.g96.out.G96PositionredFormatter

compare(HashMap, HashMap) - Static method in class io.args.ArgumentComparer

assert that all non-optional defined have been supplied and that no non-defined arguments have been supplied.

compareArgs(HashMap) - Method in class io.args.ArgumentParser

compare the supplied arguments with the defined arguments

complete() - Method in class contrib.CBZip2InputStream

compressedStreamEOF() - Static method in class contrib.CBZip2InputStream

computedBlockCRC - Variable in class contrib.CBZip2InputStream

computedCombinedCRC - Variable in class contrib.CBZip2InputStream

conformation - package conformation

constraints - Variable in class core.G96SolventTopology

continuationFormat - Static variable in class io.pdb.PDBTitleFormatter

contrib - package contrib

conversionCharacter - Variable in class contrib.PrintfFormat.ConversionSpecification

Control string type.

converttoG96() - Method in class forcefield.BondAngleType

converttoG96() - Method in class forcefield.ImpDihedralType

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

coordFormat - Variable in class io.g96.out.G96PositionredFormatter

coordFormat - Static variable in class io.pdb.PDBAtomFormatter

coordFormat - Static variable in class io.vmd.VMDAMFormatter

copies(int, int) - Method in class forcefield.Bonds

copy(int) - Method in class core.Particles

Generate a (multiple) of the particles.

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

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

core - package core

core.pbc - package core.pbc

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

the cos(angle) between two vectors.

count - Variable in class contrib.CBZip2InputStream

count - Variable in class io.vmd.VMDAMFormatter

crc32Table - Static variable in class contrib.CRC

crcError() - Static method in class contrib.CBZip2InputStream

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

the cross product of two 3-vectors.

currentChar - Variable in class contrib.CBZip2InputStream

currentState - Variable in class contrib.CBZip2InputStream