org.biojava.nbio.structure.xtal

Class CrystalBuilder

java.lang.Object

org.biojava.nbio.structure.xtal.CrystalBuilder

public class CrystalBuilder
extends Object

A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators

Author:

duarte_j

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEF_NUM_CELLS
static double	DEFAULT_INTERFACE_DISTANCE_CUTOFF Default maximum distance between two chains to be considered an interface.
static javax.vecmath.Matrix4d	IDENTITY

Constructor Summary

Constructors

Constructor and Description
CrystalBuilder(Structure structure)

Method Summary

Modifier and Type	Method and Description
StructureInterfaceList	getUniqueInterfaces() Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
StructureInterfaceList	getUniqueInterfaces(double cutoff) Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
void	setNumCells(int numCells) Set the number of neighboring crystal cells that will be used in the search for contacts
void	translate(javax.vecmath.Matrix4d m, javax.vecmath.Vector3d translation)

Methods inherited from class java.lang.Object

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

Field Detail

DEF_NUM_CELLS

public static final int DEF_NUM_CELLS

See Also:

Constant Field Values

DEFAULT_INTERFACE_DISTANCE_CUTOFF

public static final double DEFAULT_INTERFACE_DISTANCE_CUTOFF

Default maximum distance between two chains to be considered an interface.

See Also:

getUniqueInterfaces(double), Constant Field Values

IDENTITY

public static final javax.vecmath.Matrix4d IDENTITY

Constructor Detail

CrystalBuilder

public CrystalBuilder(Structure structure)

Method Detail

setNumCells

public void setNumCells(int numCells)

Set the number of neighboring crystal cells that will be used in the search for contacts

Parameters:

numCells -

getUniqueInterfaces

public StructureInterfaceList getUniqueInterfaces()

Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the default cutoff distance.

Returns:

See Also:

DEFAULT_INTERFACE_DISTANCE_CUTOFF

getUniqueInterfaces

public StructureInterfaceList getUniqueInterfaces(double cutoff)

Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the given cutoff distance.

Parameters:

cutoff - the distance cutoff for 2 chains to be considered in contact

Returns:

translate

public void translate(javax.vecmath.Matrix4d m,
                      javax.vecmath.Vector3d translation)