io.g96.out
Class HBondFormatter

java.lang.Object
  io.g96.out.HBondFormatter

public class HBondFormatter

extends java.lang.Object

Author:

mika, vincent

Field Summary

(package private) static java.lang.String	end
(package private) static PrintfFormat	FormatAngle
(package private) static PrintfFormat	FormatAtomName
(package private) static PrintfFormat	FormatAtomNumber
(package private) static PrintfFormat	Formatdistance
(package private) static PrintfFormat	formatHBNum
(package private) static PrintfFormat	FormatMolNum
(package private) static PrintfFormat	FormatOccur
(package private) static PrintfFormat	FormatOccurPerc
(package private) static PrintfFormat	FormatResName
(package private) static PrintfFormat	FormatResNum
(package private) static java.lang.String	g96Comment
(package private) static PrintfFormat	hbFormat
(package private) static PrintfFormat	timeFormat

Constructor Summary

HBondFormatter()

Method Summary

static HydrogenBonds.HBDefinitions	getHBDefinitions(java.util.HashMap arguments, Particles particles, Bonds bondh) Get the hydrogen bond definitions from various sources (command line options etc.).
static java.lang.String	printStatistics(Particles particles, HydrogenBonds.HBDefinitions hbdef, HydrogenBonds.HBTrajectoryStats hbStats, double cutoff) Print the hydrogen bonding statistics in Gromos96 block format.
static java.lang.String	printTsFrame(boolean[] hbonds, double time) Print a frame of the hydrogen bond time series.
static java.lang.String	timeSeriesBlockName()
static java.lang.String	title(java.lang.String titleBlock, double maxDistance, double minAngle)

Methods inherited from class java.lang.Object

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

Field Detail

g96Comment

static final java.lang.String g96Comment

See Also:

Constant Field Values

formatHBNum

static final PrintfFormat formatHBNum

FormatMolNum

static final PrintfFormat FormatMolNum

FormatResNum

static final PrintfFormat FormatResNum

FormatResName

static final PrintfFormat FormatResName

FormatAtomNumber

static final PrintfFormat FormatAtomNumber

Formatdistance

static final PrintfFormat Formatdistance

FormatAtomName

static final PrintfFormat FormatAtomName

FormatAngle

static final PrintfFormat FormatAngle

FormatOccur

static final PrintfFormat FormatOccur

FormatOccurPerc

static final PrintfFormat FormatOccurPerc

timeFormat

static final PrintfFormat timeFormat

hbFormat

static final PrintfFormat hbFormat

end

static final java.lang.String end

See Also:

Constant Field Values

Constructor Detail

HBondFormatter

public HBondFormatter()

Method Detail

title

public static java.lang.String title(java.lang.String titleBlock,
                                     double maxDistance,
                                     double minAngle)

Parameters:

titleBlock -

timeSeriesBlockName

public static java.lang.String timeSeriesBlockName()

getHBDefinitions

public static HydrogenBonds.HBDefinitions getHBDefinitions(java.util.HashMap arguments,
                                                           Particles particles,
                                                           Bonds bondh)
                                                    throws java.io.IOException

Get the hydrogen bond definitions from various sources (command line options etc.). A hydrogen bond definition consists of just three int's: the atom numbers of the donor, the hydrogen and the acceptor.

Parameters:

arguments -

particles -

bondh -

Returns:

the corresponding hydrogen bond definitions

Throws:

java.io.IOException

printStatistics

public static java.lang.String printStatistics(Particles particles,
                                               HydrogenBonds.HBDefinitions hbdef,
                                               HydrogenBonds.HBTrajectoryStats hbStats,
                                               double cutoff)

Print the hydrogen bonding statistics in Gromos96 block format.

Parameters:

particles -

hbdef -

hbStats -

cutoff - cutoff in percent. if the hydrogen bond occurs less frequently than this, it's not printed

Returns:

printTsFrame

public static java.lang.String printTsFrame(boolean[] hbonds,
                                            double time)

Print a frame of the hydrogen bond time series.

Parameters:

hbonds -

time -