io.g96.out
Class OutTopoG96

java.lang.Object
  io.g96.out.OutTopoG96

public class OutTopoG96

extends java.lang.Object

Field Summary

(package private) Particles	atoms
(package private) java.lang.String	format
(package private) InteractionParameters	intpara
(package private) java.text.NumberFormat	nf
(package private) PrintfFormat	PfF
(package private) java.io.PrintWriter	pw
(package private) int	size
(package private) SimSystem	sys

Constructor Summary

OutTopoG96()

OutTopoG96(Particles atoms, SimSystem sys, InteractionParameters intpar, java.lang.String fileName)

Method Summary

private int	add(int i)
(package private) void	close()
(package private) void	end()
private void	printangle(java.lang.String type, Angles ang)
void	printBondBlock(java.lang.String type, Bonds bond)
private void	printdih(java.lang.String type, Dihedrals dh)
private void	printimpdih(java.lang.String type, ImproperDihedrals idh)
(package private) void	println(java.lang.String what)
static java.lang.String[]	soluteAtomFormatter(int numAtoms, int[] atomNumbers, int[] residueNumbers, java.lang.String[] atomNames, int[] IAC, double[] masses, double[] charges, int[] chargeGroups, DenseExclusions exclusions, DenseExclusions one4Exclusions)
void	writeTopo()
void	writeTopo(G96SolventTopology solvent)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

format

final java.lang.String format

See Also:

Constant Field Values

size

final int size

pw

java.io.PrintWriter pw

atoms

Particles atoms

sys

SimSystem sys

intpara

InteractionParameters intpara

PfF

final PrintfFormat PfF

nf

final java.text.NumberFormat nf

Constructor Detail

OutTopoG96

public OutTopoG96(Particles atoms,
                  SimSystem sys,
                  InteractionParameters intpar,
                  java.lang.String fileName)
           throws java.io.IOException

OutTopoG96

public OutTopoG96()
           throws java.io.IOException

Method Detail

soluteAtomFormatter

public static java.lang.String[] soluteAtomFormatter(int numAtoms,
                                                     int[] atomNumbers,
                                                     int[] residueNumbers,
                                                     java.lang.String[] atomNames,
                                                     int[] IAC,
                                                     double[] masses,
                                                     double[] charges,
                                                     int[] chargeGroups,
                                                     DenseExclusions exclusions,
                                                     DenseExclusions one4Exclusions)

end

final void end()

println

final void println(java.lang.String what)

writeTopo

public final void writeTopo()
                     throws java.io.IOException

Throws:

java.io.IOException

writeTopo

public final void writeTopo(G96SolventTopology solvent)
                     throws java.io.IOException

Throws:

java.io.IOException

printBondBlock

public final void printBondBlock(java.lang.String type,
                                 Bonds bond)

Parameters:

type -

bond -

printangle

private final void printangle(java.lang.String type,
                              Angles ang)

printimpdih

private final void printimpdih(java.lang.String type,
                               ImproperDihedrals idh)

printdih

private final void printdih(java.lang.String type,
                            Dihedrals dh)

add

private final int add(int i)

close

void close()