org.biojava.nbio.structure

Class PDBCrystallographicInfo

java.lang.Object

org.biojava.nbio.structure.PDBCrystallographicInfo

All Implemented Interfaces:

Serializable

public class PDBCrystallographicInfo
extends Object
implements Serializable

A class to hold crystallographic information about a PDB structure.

Author:

Peter Rose, duarte_j

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PDBCrystallographicInfo()

Method Summary

Modifier and Type	Method and Description
float	getA()
float	getAlpha()
float	getB()
float	getBeta()
float	getC()
CrystalCell	getCrystalCell() Return the crystal cell
float	getGamma()
javax.vecmath.Matrix4d[]	getNcsOperators() Get the NCS operators.
SpaceGroup	getSpaceGroup() Get the SpaceGroup
javax.vecmath.Matrix4d[]	getTransformationsOrthonormal() Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis.
int	getZ() Deprecated. As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()
void	setCrystalCell(CrystalCell cell) Set the crystal cell
void	setNcsOperators(javax.vecmath.Matrix4d[] ncsOperators) Set the NCS operators.
void	setSpaceGroup(SpaceGroup spaceGroup) Set the SpaceGroup
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBCrystallographicInfo

public PDBCrystallographicInfo()

Method Detail

getA

public float getA()

Returns:

the unit cell parameter a

getB

public float getB()

Returns:

the unit cell parameter b

getC

public float getC()

Returns:

the unit cell parameter c

getAlpha

public float getAlpha()

Returns:

the unit cell parameter alpha (degrees)

getBeta

public float getBeta()

Returns:

the unit cell parameter beta (degrees)

getGamma

public float getGamma()

Returns:

the unit cell parameter gamma (degrees)

getCrystalCell

public CrystalCell getCrystalCell()

Return the crystal cell

Returns:

setCrystalCell

public void setCrystalCell(CrystalCell cell)

Set the crystal cell

Parameters:

cell -

getSpaceGroup

public SpaceGroup getSpaceGroup()

Get the SpaceGroup

Returns:

the spaceGroup

setSpaceGroup

public void setSpaceGroup(SpaceGroup spaceGroup)

Set the SpaceGroup

Parameters:

spaceGroup -

getZ

@Deprecated
public int getZ()

Deprecated. As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()

Return the z, i.e. the multiplicity of the space group times the number of chains in asymmetric unit

Returns:

0

getTransformationsOrthonormal

public javax.vecmath.Matrix4d[] getTransformationsOrthonormal()

Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis. Using PDB axes convention (NCODE=1).

Returns:

an array of size SpaceGroup.getNumOperators()

getNcsOperators

public javax.vecmath.Matrix4d[] getNcsOperators()

Get the NCS operators. Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.

Returns:

the operators or null if no operators present

setNcsOperators

public void setNcsOperators(javax.vecmath.Matrix4d[] ncsOperators)

Set the NCS operators. Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.

Parameters:

ncsOperators -

toString

public String toString()

Overrides:

toString in class Object