conformation
Class HydrogenBonds

java.lang.Object
  conformation.HydrogenBonds

public class HydrogenBonds

extends java.lang.Object

Author:

vincent

Nested Class Summary

class	HydrogenBonds.HBDefinitions
class	HydrogenBonds.HBFrameStats
class	HydrogenBonds.HBTrajectoryStats

Constructor Summary

HydrogenBonds()

Method Summary

static double[]	checkHBond(int donor, int hydrogen, int acceptor, double[][] pos, double maxDistance, double minAngle) Is there a hydrogen bond involving the three atoms?
static int	findDonor(int hydrogen, Bonds bondh)
static int[]	findDonors(int[] hydrogens, Bonds bondh)
static HydrogenBonds.HBDefinitions	getDefs(int size) Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.
static HydrogenBonds.HBDefinitions	getDefs(int[] hydrogens, int[] acceptors, Bonds bondh) Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.
static HydrogenBonds.HBFrameStats	getFrameStats(int size) Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.
static HydrogenBonds.HBTrajectoryStats	getTrajStats(int size) Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.
static HydrogenBonds.HBFrameStats	inspectFrame(HydrogenBonds.HBDefinitions def, double[][] pos, double maxDistance, double minAngle) Looks for hydrogen bonds in the supplied frame.
static int[][]	removeIntraMolecularHBonds(int[] hydrogens, int[] acceptors, int[] molecules)

Methods inherited from class java.lang.Object

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

Constructor Detail

HydrogenBonds

public HydrogenBonds()

Method Detail

getDefs

public static HydrogenBonds.HBDefinitions getDefs(int[] hydrogens,
                                                  int[] acceptors,
                                                  Bonds bondh)

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.

Parameters:

hydrogens - the atom indices of the "hydrogens"

acceptors - the atom indices of the "acceptors"

bondh - the bonds involving hydrogens

Returns:

the definitions

getDefs

public static HydrogenBonds.HBDefinitions getDefs(int size)

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.

Parameters:

size - the number of (uninitialized) hydrogen bonds

Returns:

the definitions

getFrameStats

public static HydrogenBonds.HBFrameStats getFrameStats(int size)

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.

Parameters:

size -

Returns:

new statistics object

getTrajStats

public static HydrogenBonds.HBTrajectoryStats getTrajStats(int size)

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.

Parameters:

size - the number of hydrogen bonds

Returns:

stats object

findDonor

public static int findDonor(int hydrogen,
                            Bonds bondh)

Parameters:

hydrogen -

bondh - bonds involving hydrogens

Returns:

the atom that the hydrogen is bound to

findDonors

public static int[] findDonors(int[] hydrogens,
                               Bonds bondh)

Parameters:

hydrogens -

bondh -

Returns:

the atoms the hydrogens are bound to

See Also:

findDonor(int, Bonds)

removeIntraMolecularHBonds

public static int[][] removeIntraMolecularHBonds(int[] hydrogens,
                                                 int[] acceptors,
                                                 int[] molecules)

checkHBond

public static double[] checkHBond(int donor,
                                  int hydrogen,
                                  int acceptor,
                                  double[][] pos,
                                  double maxDistance,
                                  double minAngle)

Is there a hydrogen bond involving the three atoms?

Parameters:

donor -

hydrogen -

acceptor -

pos -

maxDistance -

minAngle -

Returns:

{bond lenght, bond angle} if it's a hydrogen bond, otherwise null.

inspectFrame

public static HydrogenBonds.HBFrameStats inspectFrame(HydrogenBonds.HBDefinitions def,
                                                      double[][] pos,
                                                      double maxDistance,
                                                      double minAngle)

Looks for hydrogen bonds in the supplied frame. Assumes gathered positions.

Parameters:

def -

pos -

maxDistance -

minAngle -

Returns:

statistics for this frame