Package org.biojava.nbio.structure
Class PDBCrystallographicInfo
- java.lang.Object
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- org.biojava.nbio.structure.PDBCrystallographicInfo
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- 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
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Constructor Summary
Constructors Constructor Description PDBCrystallographicInfo()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description float
getA()
float
getAlpha()
float
getB()
float
getBeta()
float
getC()
CrystalCell
getCrystalCell()
Return the crystal cellfloat
getGamma()
javax.vecmath.Matrix4d[]
getNcsOperators()
Get the NCS operators.SpaceGroup
getSpaceGroup()
Get the SpaceGroupjavax.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 cellvoid
setNcsOperators(javax.vecmath.Matrix4d[] ncsOperators)
Set the NCS operators.void
setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention)
Set the non-standard coordinate frame convention fieldvoid
setNonStandardSg(boolean nonStandardSg)
Set the non-standard space group fieldvoid
setSpaceGroup(SpaceGroup spaceGroup)
Set the SpaceGroupString
toString()
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Constructor Detail
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PDBCrystallographicInfo
public PDBCrystallographicInfo()
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Method Detail
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getA
public float getA()
- Returns:
- the unit cell parameter a
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getB
public float getB()
- Returns:
- the unit cell parameter b
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getC
public float getC()
- Returns:
- the unit cell parameter c
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getAlpha
public float getAlpha()
- Returns:
- the unit cell parameter alpha (degrees)
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getBeta
public float getBeta()
- Returns:
- the unit cell parameter beta (degrees)
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getGamma
public float getGamma()
- Returns:
- the unit cell parameter gamma (degrees)
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getCrystalCell
public CrystalCell getCrystalCell()
Return the crystal cell- Returns:
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setCrystalCell
public void setCrystalCell(CrystalCell cell)
Set the crystal cell- Parameters:
cell
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getSpaceGroup
public SpaceGroup getSpaceGroup()
Get the SpaceGroup- Returns:
- the spaceGroup
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setSpaceGroup
public void setSpaceGroup(SpaceGroup spaceGroup)
Set the SpaceGroup- Parameters:
spaceGroup
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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()
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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
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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
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isNonStandardSg
public boolean isNonStandardSg()
Whether this structure has a non-standard space group not supported by Biojava. If this is truegetSpaceGroup()
will be null.- Since:
- 4.2.5
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setNonStandardSg
public void setNonStandardSg(boolean nonStandardSg)
Set the non-standard space group field- Parameters:
nonStandardSg
-- Since:
- 4.2.5
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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
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setNonStandardCoordFrameConvention
public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention)
Set the non-standard coordinate frame convention field- Parameters:
nonStandardCoordFrameConvention
-- Since:
- 4.2.5
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