Index (molecularjava 1.0-SNAPSHOT API)

A B C D E F G H I J L M N O P R S T V W X
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A

accepted - Variable in class com.molecular_java.StepVars: Tells wheter the system was accepted or not.
angle(Ball, Ball, Ball) - Static method in class com.molecular_java.Physics: Method counts angle between the tree given balls.
angleOfRotation - Variable in class com.molecular_java.StepVars: Random angle of rotation
avgFile - Variable in class com.molecular_java.SimSpace: avg file writer.
avgFileReader - Variable in class com.molecular_java.SimSpace: Avgs for postprocessing.

B

Ball - Class in com.molecular_java: The class represents balls/particles in the system, so each balls is an object of this class.
Ball() - Constructor for class com.molecular_java.Ball: Only for testing.
Ball(Ball) - Constructor for class com.molecular_java.Ball: This constructor is used to make a copy of given ball.
Ball(Double[]) - Constructor for class com.molecular_java.Ball: Makes a "ball" representation of the center of mass in the system.
Ball(Random, double, Hashtable<Character, Integer>, char) - Constructor for class com.molecular_java.Ball: The basic constructor which makes an object of class Ball accordingly to the SimulationBox properties and sets its diameter.
balls - Variable in class com.molecular_java.SimSpace: An array which contains balls in the simulation space.
basicPotential - Variable in class com.molecular_java.StepVars: Potentials count for the system.
bendingAngleOffsetCos - Variable in class com.molecular_java.SimSpace: Cosinus of angle of bond.
bendingConst - Variable in class com.molecular_java.SimSpace: Constant for bending potential.
bendingPotential - Variable in class com.molecular_java.StepVars: Potentials count for the system.
bendingPotential(SimSpace, Ball, Ball, Ball) - Static method in class com.molecular_java.Physics: This function is used to count bending potential over three balls, assuming, that ball1 has bond to ball2 and ball2 has bond to ball3.
bendingPotentialInSystem(SimSpace, double, List<Ball>) - Static method in class com.molecular_java.Physics: Method counts bending potential of the system represented by balls in a list.
bendingPotentialTable - Variable in class com.molecular_java.SimSpace: Table with potential values (index 1) for given angle values (index 0).
boltzman - Variable in class com.molecular_java.StepVars: Force, pressure, prob and boltzman (used for accepting/rejecting of the stay).
boltzmannsFactor(SimSpace) - Static method in class com.molecular_java.Physics: The Boltzmann's factor is count from the temperature and the difference between potentials.

C

calculatePotential(SimSpace, List<Ball>, int, int, Double) - Static method in class com.molecular_java.Physics: This method calculates potential for 2 functions -- PotentialInSystem and Pressure in system.
centerOfMass(SimSpace) - Static method in class com.molecular_java.Physics: Computes a position of center of mass of balls in given simulation space.
close() - Method in class com.molecular_java.MyWriter: Closes MyWriter.buffy.
code - Variable in class com.molecular_java.Ball: Code for indexing.
com.molecular_java - package com.molecular_java
constantDihedralAngle - Variable in class com.molecular_java.SimSpace: Constant used in formula to count dihedral angle potential by "atan2" method.
constantSinDihedralAngle - Variable in class com.molecular_java.SimSpace: Constant used in formula to count dihedral angle potential by "sin" method.
contourLength - Variable in class com.molecular_java.StepVars: Gyration radius and distance between the last and the first ball in the system.
coordinates - Variable in class com.molecular_java.Ball: Position of the ball.
CountAdditionalParams(SimSpace) - Method in class com.molecular_java.StepVars: In this method some additional parameters about the simulation are count.
crossProduct(double[], double[]) - Static method in class com.molecular_java.Physics: Cross product for 3D vectors.

D

dataFile - Variable in class com.molecular_java.SimSpace: Data file writer.
dataFileHeader - Variable in class com.molecular_java.SimSpace: A header for the data file.
dataFileName - Variable in class com.molecular_java.SimSpace: Name of the data file.
dataFileNrOfColumns - Variable in class com.molecular_java.SimSpace: Number of columns of the data file.
dataFileReader - Variable in class com.molecular_java.SimSpace: Data file reader.
DATAFreq - Variable in class com.molecular_java.SimSpace: Specifies how often the DATA will be noted.
DataRange - Class in com.molecular_java: A simple class used in the CountErrBlockMethod(SimSpace s) method to select ranges in data file for each block.
DataRange(int, int) - Constructor for class com.molecular_java.DataRange: Straith forward constructor of the data range.
diameter - Variable in class com.molecular_java.Ball: Diameter of the ball.
dihedralPotential - Variable in class com.molecular_java.StepVars: Potentials count for the system.
dihedralPotentialTable - Variable in class com.molecular_java.SimSpace: Table with potential values (index 1) for given angle values (index 0).
distanceOfTwoBalls(SimSpace, Ball, Ball) - Static method in class com.molecular_java.Physics: A method to count distance of two given molecules.
dot(double[], double[]) - Static method in class com.molecular_java.Physics: Dot for 3D vectors in an array.

E

end() - Method in class com.molecular_java.MyWatches: The method notes the current time as the end time and sets the elapsed time as a difference of end and start time.

F

force - Variable in class com.molecular_java.StepVars: Force, pressure, prob and boltzman (used for accepting/rejecting of the stay).
from - Variable in class com.molecular_java.DataRange: Tells in which cycle the block starts.
fSequence - Variable in class com.molecular_java.SimSpace: FASTA sequence of the simulated peptide.

G

getPotentialFromTable(Double[][], Double) - Static method in class com.molecular_java.Physics: For given value of angle (rad) returns a potentials value from the given table.

H

hardSpheresForce(Double, Double) - Static method in class com.molecular_java.Physics: Counting of force by the "Hard-Spheres" method.
hardSpheresPotential(Double, Double) - Static method in class com.molecular_java.Physics: Counts "Hard-Spheres potential".

I

inputFile - Variable in class com.molecular_java.SimSpace: Reader for the input file.
inputFileName - Variable in class com.molecular_java.SimSpace: Name of the input file.
inputFolder - Variable in class com.molecular_java.SimSpace: Input folder path.

J

JSONInput - Variable in class com.molecular_java.SimSpace: Input file reader.

L

lengthOfBond - Variable in class com.molecular_java.SimSpace: Specifies how long are the bonds between the balls.
lennardJonesForce(Double, Double, Double) - Static method in class com.molecular_java.Physics: Counting of force by the "Lennard-Jones" formula.
lennardJonesPotential(SimSpace, Ball, Ball, Double) - Static method in class com.molecular_java.Physics: Method to count "Lennard-Jones potential".
loadPotentialFromCSV(String) - Method in class com.molecular_java.SimSpace: Method which takes a filename of potential csv matrix as an argument and gives a table with the values as the output.
logFile - Variable in class com.molecular_java.SimSpace: Dog file writer.

M

makeAvgs(SimSpace) - Method in class com.molecular_java.SimRunVars: Counts the averages from the sums in the end of the simulation.
makeTclScript() - Method in class com.molecular_java.SimSpace
MyWatches - Class in com.molecular_java: A class for time meassurement.
MyWatches() - Constructor for class com.molecular_java.MyWatches
MyWriter - Class in com.molecular_java: This class is used to write to files instead of standard BufferedWriter.
MyWriter(BufferedWriter) - Constructor for class com.molecular_java.MyWriter: Constructor which takes a BufferedWriter and uses it as an attribute.

N

noteFreq - Variable in class com.molecular_java.SimSpace: Specifies how often the XYZ positions will be noted.
nrOfBalls - Variable in class com.molecular_java.SimSpace: Number of balls in the simulation space.
numberOfCycles - Variable in class com.molecular_java.SimSpace: Number of cycles of the simulation.

O

optimalDihedralAngle - Variable in class com.molecular_java.SimSpace: Meassured "optimal" dihedral angle.
optimalSinDihedralAngle - Variable in class com.molecular_java.SimSpace: Meassured "optimal" dihedral angle.
outputFolder - Variable in class com.molecular_java.SimSpace: Output folder path.

P

Physics - Class in com.molecular_java: This class makes the "physical engine" behind the simulation.
Physics() - Constructor for class com.molecular_java.Physics
potential - Variable in class com.molecular_java.StepVars: Potentials count for the system.
potentialInSystem(SimSpace, double, List<Ball>) - Static method in class com.molecular_java.Physics: Method counts a potential in a system represented by balls in list.
potentialMatrix - Variable in class com.molecular_java.SimSpace: A matrix of pairwise potentials between AAs.
pressure - Variable in class com.molecular_java.StepVars: Force, pressure, prob and boltzman (used for accepting/rejecting of the stay).

R

radiusOfGyration(SimSpace) - Static method in class com.molecular_java.Physics: This method counts the gyration radius of the balls in system.
random - Variable in class com.molecular_java.SimSpace: A Random object used in the simulations.
randomProb - Variable in class com.molecular_java.StepVars: Force, pressure, prob and boltzman (used for accepting/rejecting of the stay).
rangeOfAngleForRotation - Variable in class com.molecular_java.SimSpace: Parameter of the simulation which specifies how much the chain of balls can be rotated in one step.
Re - Variable in class com.molecular_java.StepVars: Gyration radius and distance between the last and the first ball in the system.
resNumberOfCycles - Variable in class com.molecular_java.SimSpace: How many active cycles do we have
restorePozitionsFromXYZ(String) - Method in class com.molecular_java.SimSpace: This method is called if option "--restore" is given as an argument.
Rg - Variable in class com.molecular_java.StepVars: Gyration radius and distance between the last and the first ball in the system.

S

SimRunVars - Class in com.molecular_java: You can store vars, which you need during the run of the simulation in objects of this class.
SimRunVars() - Constructor for class com.molecular_java.SimRunVars: Constructor which initializes all the variables except averages by zero values.
SimSpace - Class in com.molecular_java: A class for containment of important parameters, constants and I/O files to process the simulation.
SimSpace() - Constructor for class com.molecular_java.SimSpace: Only for testing.
SimSpace(String, String, String) - Constructor for class com.molecular_java.SimSpace: The constructor gets a name of the simulation, opens input files and output files and loads parameters from the input file.
simulationName - Variable in class com.molecular_java.SimSpace: Simulation name.
skippedCycles - Variable in class com.molecular_java.SimSpace: Specifies how many cycles are not count to averages and are not also used for the error estimation.
springConst - Variable in class com.molecular_java.SimSpace: Parameter of the spring bond potential count.
squareWellForce(Double, Double, Double, Double) - Static method in class com.molecular_java.Physics: Counting of force by the "Square-Well" method.
squareWellPotential(Double, Double, Double, Double) - Static method in class com.molecular_java.Physics: A little bit more complex potential function with discrete stays.
st - Variable in class com.molecular_java.SimSpace: Contains variables important for each step.
st_new - Variable in class com.molecular_java.SimSpace: Contains new variables for each step.
start() - Method in class com.molecular_java.MyWatches: On start, the method notes the current time for further counting.
StepVars - Class in com.molecular_java: A class for storing variables important for each step of the simulation.
StepVars() - Constructor for class com.molecular_java.StepVars: Non-standard constructor, used only to count everything in the initial stay of the system to note it.
StepVars(SimSpace) - Constructor for class com.molecular_java.StepVars: Standard constructor of the StepVars.

T

tclScript - Variable in class com.molecular_java.SimSpace: tcl script for the simulation.
temperatureFinal - Variable in class com.molecular_java.SimSpace: Parameter of the simulation which specifies how easily the unprobable stays will be accepted.
temperatureInit - Variable in class com.molecular_java.SimSpace: Parameter of the simulation which specifies how easily the unprobable stays will be accepted.
timeElapsed - Variable in class com.molecular_java.MyWatches: Elapsed time in millis (count in the MyWatches.end()) method.
to - Variable in class com.molecular_java.DataRange: Tells in which cycle the block ends.
type - Variable in class com.molecular_java.Ball: Type of the ball (e.g.
typeOfPotential - Variable in class com.molecular_java.SimSpace: Defines which type of potential we want to use.
typeOfSimulation - Variable in class com.molecular_java.SimSpace: Defines which type of simulation we are going to make.

V

v - Variable in class com.molecular_java.SimSpace: Contains variables which are changed, but also important during the simulation and in postprocessing.
vectorLength(double[]) - Static method in class com.molecular_java.Physics: Counts a length of given 3D vector.
vectorMultip(double[], double) - Static method in class com.molecular_java.Physics: 3D Vector multiplication.

W

watches - Variable in class com.molecular_java.SimSpace: Object used for time meassurement.
weight - Variable in class com.molecular_java.Ball: Weight of the ball.
writeAll(BufferedReader) - Method in class com.molecular_java.MyWriter: Prints all lines of the given file to the MyWriter.buffy.
writeLine(String) - Method in class com.molecular_java.MyWriter: Writes given String as a line to a buffy.

X

xyzFile - Variable in class com.molecular_java.SimSpace: xyz file writer.

A B C D E F G H I J L M N O P R S T V W X
All Classes and Interfaces|All Packages