Class QuatSymmetryResults
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
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public class QuatSymmetryResults extends Object
Holds the results of quaternary symmetry perception obtained withQuatSymmetryDetector
.- Author:
- Peter Rose, Aleix Lafita
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Constructor Summary
Constructors Constructor Description QuatSymmetryResults(Stoichiometry stoichiometry, HelixLayers helixLayers, SymmetryPerceptionMethod method)
Constructor for roto-translational symmetries.QuatSymmetryResults(Stoichiometry stoichiometry, RotationGroup rotationGroup, SymmetryPerceptionMethod method)
Constructor for rotational symmetries.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description HelixLayers
getHelixLayers()
SymmetryPerceptionMethod
getMethod()
RotationGroup
getRotationGroup()
QuatSymmetryScores
getScores()
Stoichiometry
getStoichiometry()
Structure
getStructure()
List<SubunitCluster>
getSubunitClusters()
Returns the List of SubunitCluster used to calculate symmetry.int
getSubunitCount()
Return the number of Subunits involved in the symmetry.List<Subunit>
getSubunits()
Returns the List of Subunits used to calculate symmetry.String
getSymmetry()
boolean
isLocal()
A local result means that only a subset of the original Subunits was used for symmetry determination.boolean
isPseudoStoichiometric()
boolean
isSupersededBy(QuatSymmetryResults other)
Determine if this symmetry result is a subset of the other Symmetry result.void
setStructure(Structure structure)
String
toString()
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Constructor Detail
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QuatSymmetryResults
public QuatSymmetryResults(Stoichiometry stoichiometry, RotationGroup rotationGroup, SymmetryPerceptionMethod method)
Constructor for rotational symmetries.- Parameters:
stoichiometry
- Stoichiometry used to calculate symmetryrotationGroup
-method
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QuatSymmetryResults
public QuatSymmetryResults(Stoichiometry stoichiometry, HelixLayers helixLayers, SymmetryPerceptionMethod method)
Constructor for roto-translational symmetries.- Parameters:
stoichiometry
- Stoichiometry used to calculate symmetryhelixLayers
-method
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Method Detail
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isSupersededBy
public boolean isSupersededBy(QuatSymmetryResults other)
Determine if this symmetry result is a subset of the other Symmetry result. Checks the following conditions: - 'Other' includes all subunits of 'this'. - 'Other' has the same or higher order than 'this'. Special treatment for the helical symmetry: - 'Other' includes all subunits of 'this'. - 'this' may be Cn, as well as H Note that isSupersededBy establishes a partial order, i.e. for some symmetries A and B, neither A.isSupersededBy(B) nor B.isSupersededBy(A) may be true.- Parameters:
other
- QuatSymmetryResults- Returns:
- true if other supersedes this, false otherwise
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getSubunitClusters
public List<SubunitCluster> getSubunitClusters()
Returns the List of SubunitCluster used to calculate symmetry.- Returns:
- an unmodifiable view of the original List
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getSubunits
public List<Subunit> getSubunits()
Returns the List of Subunits used to calculate symmetry.- Returns:
- an unmodifiable view of the List
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getSubunitCount
public int getSubunitCount()
Return the number of Subunits involved in the symmetry.- Returns:
- the number of Subunits
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getRotationGroup
public RotationGroup getRotationGroup()
- Returns:
- rotation group (point group) information representing rotational quaternary symmetry.
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getHelixLayers
public HelixLayers getHelixLayers()
- Returns:
- helix layers (layer lines) as a list of helices that describe a helical structure.
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getMethod
public SymmetryPerceptionMethod getMethod()
- Returns:
- the method used for symmetry perception.
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getSymmetry
public String getSymmetry()
- Returns:
- the symmetry group symbol. For point groups returns the point group symbol and for helical symmetry returns "H".
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getScores
public QuatSymmetryScores getScores()
- Returns:
- the quaternary scores as an object
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getStoichiometry
public Stoichiometry getStoichiometry()
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isPseudoStoichiometric
public boolean isPseudoStoichiometric()
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isLocal
public boolean isLocal()
A local result means that only a subset of the original Subunits was used for symmetry determination.- Returns:
- true if local result, false otherwise
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getStructure
public Structure getStructure()
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setStructure
public void setStructure(Structure structure)
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