Class ChainClusterer
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.ChainClusterer
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public class ChainClusterer extends java.lang.Object
Wraps a sequence clustering with structural information
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Constructor Summary
Constructors Constructor Description ChainClusterer(java.util.List<SequenceAlignmentCluster> seqClusters)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<javax.vecmath.Point3d[]>
getCalphaCoordinates()
java.util.List<Atom[]>
getCalphaTraces()
java.util.List<java.lang.String>
getChainIds()
java.util.List<java.lang.Integer>
getFolds()
Get valid symmetry order for this stoichiometry.java.util.List<java.lang.Double>
getMaxSequenceIdentity()
java.util.List<java.lang.Double>
getMinSequenceIdentity()
java.util.List<java.lang.Integer>
getModelNumbers()
java.util.List<java.lang.Boolean>
getPseudoStoichiometry()
java.util.List<SequenceAlignmentCluster>
getSequenceAlignmentClusters()
int
getSequenceClusterCount()
java.util.List<java.lang.Integer>
getSequenceClusterIds()
java.lang.String
getStoichiometry()
static java.util.List<java.lang.Integer>
getValidFolds(java.util.List<java.lang.Integer> stoichiometry)
Find valid symmetry orders for a given stoichiometry.java.lang.String
toString()
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Constructor Detail
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ChainClusterer
public ChainClusterer(java.util.List<SequenceAlignmentCluster> seqClusters)
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Method Detail
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getCalphaCoordinates
public java.util.List<javax.vecmath.Point3d[]> getCalphaCoordinates()
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getCalphaTraces
public java.util.List<Atom[]> getCalphaTraces()
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getChainIds
public java.util.List<java.lang.String> getChainIds()
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getModelNumbers
public java.util.List<java.lang.Integer> getModelNumbers()
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getStoichiometry
public java.lang.String getStoichiometry()
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getFolds
public java.util.List<java.lang.Integer> getFolds()
Get valid symmetry order for this stoichiometry.- Returns:
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getValidFolds
public static java.util.List<java.lang.Integer> getValidFolds(java.util.List<java.lang.Integer> stoichiometry)
Find valid symmetry orders for a given stoichiometry. For instance, an A6B4 protein would give [1,2] because (A6B4)1 and (A3B2)2 are valid decompositions.- Parameters:
stoichiometry
- List giving the number of copies in each chain cluster- Returns:
- The common factors of the stoichiometry
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getSequenceClusterIds
public java.util.List<java.lang.Integer> getSequenceClusterIds()
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getSequenceClusterCount
public int getSequenceClusterCount()
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getSequenceAlignmentClusters
public java.util.List<SequenceAlignmentCluster> getSequenceAlignmentClusters()
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getPseudoStoichiometry
public java.util.List<java.lang.Boolean> getPseudoStoichiometry()
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getMinSequenceIdentity
public java.util.List<java.lang.Double> getMinSequenceIdentity()
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getMaxSequenceIdentity
public java.util.List<java.lang.Double> getMaxSequenceIdentity()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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