Class QuatSymmetryResults
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
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public class QuatSymmetryResults extends java.lang.Object
Holds the results of quaternary symmetry perception.- Author:
- Peter Rose
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Constructor Summary
Constructors Constructor Description QuatSymmetryResults(Subunits subunits, HelixLayers helixLayers, java.lang.String method)
QuatSymmetryResults(Subunits subunits, RotationGroup rotationGroup, java.lang.String method)
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description double
getAverageTraceRmsd()
Deprecated.usegetScores()
instead.double
getAverageTraceTmScoreMin()
Deprecated.usegetScores()
instead.HelixLayers
getHelixLayers()
java.lang.String
getMethod()
Returns name of method used for symmetry perception.int
getNucleicAcidChainCount()
RotationGroup
getRotationGroup()
Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)QuatSymmetryScores
getScores()
double
getSequenceIdentityThreshold()
Subunits
getSubunits()
Returns protein subunit information that was used to determine symmetry informationjava.lang.String
getSymmetry()
Returns the symmetry group.boolean
isLocal()
Return trueboolean
isPreferredResult()
void
setLocal(boolean local)
void
setPreferredResult(boolean preferredResult)
void
setSequenceIdentityThreshold(double sequenceIdentityThreshold)
java.lang.String
toString()
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Constructor Detail
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QuatSymmetryResults
public QuatSymmetryResults(Subunits subunits, RotationGroup rotationGroup, java.lang.String method)
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QuatSymmetryResults
public QuatSymmetryResults(Subunits subunits, HelixLayers helixLayers, java.lang.String method)
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Method Detail
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getSubunits
public Subunits getSubunits()
Returns protein subunit information that was used to determine symmetry information- Returns:
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getRotationGroup
public RotationGroup getRotationGroup()
Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)- Returns:
- rotation group
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getHelixLayers
public HelixLayers getHelixLayers()
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getMethod
public java.lang.String getMethod()
Returns name of method used for symmetry perception.- Returns:
- method
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getSymmetry
public java.lang.String getSymmetry()
Returns the symmetry group. For point groups returns the point group symbol and for helical symmetry returns "H".- Returns:
- symmetry symbol
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getScores
public QuatSymmetryScores getScores()
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getAverageTraceRmsd
@Deprecated public double getAverageTraceRmsd()
Deprecated.usegetScores()
instead.Returns the average Calpha trace RMSD for all symmetry operations- Returns:
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getAverageTraceTmScoreMin
@Deprecated public double getAverageTraceTmScoreMin()
Deprecated.usegetScores()
instead.Returns the average Calpha trace Tm for all symmetry operations- Returns:
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getNucleicAcidChainCount
public int getNucleicAcidChainCount()
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getSequenceIdentityThreshold
public double getSequenceIdentityThreshold()
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setSequenceIdentityThreshold
public void setSequenceIdentityThreshold(double sequenceIdentityThreshold)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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isLocal
public boolean isLocal()
Return true- Returns:
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setLocal
public void setLocal(boolean local)
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isPreferredResult
public boolean isPreferredResult()
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setPreferredResult
public void setPreferredResult(boolean preferredResult)
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