Package 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:

Jose Duarte

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
CrystalBuilder(Structure structure)
CrystalBuilder(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)	Special constructor for NCS-aware CrystalBuilder.

Method Summary

Modifier and Type	Method	Description
static void	expandNcsOps(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)	Apply the NCS operators in the given Structure adding new chains as needed.
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.
boolean	hasNcsOps()
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 Details

NCS_CHAINID_SUFFIX_CHAR

public static final String NCS_CHAINID_SUFFIX_CHAR

See Also:

• Constant Field Values

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 Details

CrystalBuilder

public CrystalBuilder(Structure structure,
 Map<String,String> chainOrigNames,
 Map<String,javax.vecmath.Matrix4d> chainNcsOps)

Special constructor for NCS-aware CrystalBuilder. The output list of interfaces will be pre-clustered by NCS-equivalence. Run expandNcsOps(Structure, Map, Map) first to extend the AU and get the equivalence information.

Parameters:

structure - NCS-extended structure

chainOrigNames - chain names mapped to the original chain names (pre-NCS extension)

chainNcsOps - chain names mapped to the ncs operators that was used to generate them

Since:

5.0.0

CrystalBuilder

public CrystalBuilder(Structure structure)

Method Details

hasNcsOps

public boolean hasNcsOps()

Returns:

true if this CrystalBuilder is NCS-aware.

Since:

5.0.0

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)

expandNcsOps

public static void expandNcsOps(Structure structure,
 Map<String,String> chainOrigNames,
 Map<String,javax.vecmath.Matrix4d> chainNcsOps)

Apply the NCS operators in the given Structure adding new chains as needed. All chains are (re)assigned ids of the form: original_chain_id+ncs_operator_index+"n".

Parameters:

structure - the structure to expand

chainOrigNames - new chain names mapped to the original chain names

chainNcsOps - new chain names mapped to the ncs operators that was used to generate them

Since:

5.0.0