Package 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	Description
PDBCrystallographicInfo()

Method Summary

Modifier and Type	Method	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.
boolean	isNonStandardCoordFrameConvention()	Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect.
boolean	isNonStandardSg()	Whether this structure has a non-standard space group not supported by Biojava.
void	setCrystalCell(CrystalCell cell)	Set the crystal cell
void	setNcsOperators(javax.vecmath.Matrix4d[] ncsOperators)	Set the NCS operators.
void	setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention)	Set the non-standard coordinate frame convention field
void	setNonStandardSg(boolean nonStandardSg)	Set the non-standard space group field
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 -

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 -

isNonStandardSg

public boolean isNonStandardSg()

Whether this structure has a non-standard space group not supported by Biojava. If this is true getSpaceGroup() will be null.

Since:

4.2.5

setNonStandardSg

public void setNonStandardSg(boolean nonStandardSg)

Set the non-standard space group field

Parameters:

nonStandardSg -

Since:

4.2.5

isNonStandardCoordFrameConvention

public boolean isNonStandardCoordFrameConvention()

Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect. There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will be remediated in the future. For more info see: https://github.com/eppic-team/owl/issues/4

Since:

4.2.5

setNonStandardCoordFrameConvention

public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention)

Set the non-standard coordinate frame convention field

Parameters:

nonStandardCoordFrameConvention -

Since:

4.2.5

toString

public String toString()

Overrides:

toString in class Object