Class Subunits
- java.lang.Object
-
- org.biojava.nbio.structure.symmetry.core.Subunits
-
public class Subunits extends java.lang.Object
A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.- Author:
- Peter Rose
-
-
Constructor Summary
Constructors Constructor Description Subunits(java.util.List<javax.vecmath.Point3d[]> caCoords, java.util.List<java.lang.Integer> sequenceClusterIds, java.util.List<java.lang.Boolean> pseudoStoichiometry, java.util.List<java.lang.Double> minSequenceIdentity, java.util.List<java.lang.Double> maxSequenceIdentity, java.util.List<java.lang.Integer> folds, java.util.List<java.lang.String> chainIds, java.util.List<java.lang.Integer> modelNumbers)
All inputs should contain one element per subunit.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
contains(Subunits subunits)
int
getCalphaCount()
java.util.List<javax.vecmath.Point3d>
getCenters()
javax.vecmath.Point3d
getCentroid()
java.util.List<java.lang.String>
getChainIds()
java.util.List<java.lang.Integer>
getFolds()
int
getLargestSubunit()
javax.vecmath.Point3d
getLowerBound()
double
getMaxSequenceIdentity()
double
getMinSequenceIdentity()
java.util.List<java.lang.Integer>
getModelNumbers()
MomentsOfInertia
getMomentsOfInertia()
int
getNucleicAcidChainCount()
java.util.List<javax.vecmath.Point3d>
getOriginalCenters()
java.util.List<java.lang.Integer>
getSequenceClusterIds()
java.lang.String
getStoichiometry()
int
getSubunitCount()
java.util.List<javax.vecmath.Point3d[]>
getTraces()
java.util.List<javax.vecmath.Vector3d>
getUnitVectors()
javax.vecmath.Point3d
getUpperBound()
boolean
isPseudoStoichiometric()
boolean
isPseudoSymmetric()
boolean
overlaps(Subunits subunits)
void
setNucleicAcidChainCount(int nucleicAcidChainCount)
void
setPseudoSymmetric(boolean pseudoSymmetric)
-
-
-
Constructor Detail
-
Subunits
public Subunits(java.util.List<javax.vecmath.Point3d[]> caCoords, java.util.List<java.lang.Integer> sequenceClusterIds, java.util.List<java.lang.Boolean> pseudoStoichiometry, java.util.List<java.lang.Double> minSequenceIdentity, java.util.List<java.lang.Double> maxSequenceIdentity, java.util.List<java.lang.Integer> folds, java.util.List<java.lang.String> chainIds, java.util.List<java.lang.Integer> modelNumbers)
All inputs should contain one element per subunit.- Parameters:
caCoords
- CA coordinates of all subunitssequenceClusterIds
- ID of the cluster that each subunit belongs topseudoStoichiometry
- Whether pseudosymmetry was used when clustering the subunitminSequenceIdentity
- Minimum sequence identity to other cluster membersmaxSequenceIdentity
- Maximum sequence identity to other cluster membersfolds
- Valid symmetry orders for this stoichiometrychainIds
- Chain ID for the subunitmodelNumbers
- Model number for the subunit
-
-
Method Detail
-
getTraces
public java.util.List<javax.vecmath.Point3d[]> getTraces()
-
getSubunitCount
public int getSubunitCount()
-
getSequenceClusterIds
public java.util.List<java.lang.Integer> getSequenceClusterIds()
-
isPseudoStoichiometric
public boolean isPseudoStoichiometric()
-
isPseudoSymmetric
public boolean isPseudoSymmetric()
-
setPseudoSymmetric
public void setPseudoSymmetric(boolean pseudoSymmetric)
-
getMinSequenceIdentity
public double getMinSequenceIdentity()
-
getMaxSequenceIdentity
public double getMaxSequenceIdentity()
-
getChainIds
public java.util.List<java.lang.String> getChainIds()
-
getModelNumbers
public java.util.List<java.lang.Integer> getModelNumbers()
-
getFolds
public java.util.List<java.lang.Integer> getFolds()
-
getStoichiometry
public java.lang.String getStoichiometry()
-
getCalphaCount
public int getCalphaCount()
-
getLargestSubunit
public int getLargestSubunit()
-
getCenters
public java.util.List<javax.vecmath.Point3d> getCenters()
-
getUnitVectors
public java.util.List<javax.vecmath.Vector3d> getUnitVectors()
-
getOriginalCenters
public java.util.List<javax.vecmath.Point3d> getOriginalCenters()
-
getCentroid
public javax.vecmath.Point3d getCentroid()
-
getMomentsOfInertia
public MomentsOfInertia getMomentsOfInertia()
-
getNucleicAcidChainCount
public int getNucleicAcidChainCount()
- Returns:
- the nucleicAcidChainCount
-
setNucleicAcidChainCount
public void setNucleicAcidChainCount(int nucleicAcidChainCount)
- Parameters:
nucleicAcidChainCount
- the nucleicAcidChainCount to set
-
overlaps
public boolean overlaps(Subunits subunits)
-
contains
public boolean contains(Subunits subunits)
-
getLowerBound
public javax.vecmath.Point3d getLowerBound()
-
getUpperBound
public javax.vecmath.Point3d getUpperBound()
-
-