public class Subunits
extends java.lang.Object
Constructor and Description |
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Subunits(java.util.List<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.
|
Modifier and Type | Method and Description |
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boolean |
contains(Subunits subunits) |
int |
getCalphaCount() |
java.util.List<Point3d> |
getCenters() |
Point3d |
getCentroid() |
java.util.List<java.lang.String> |
getChainIds() |
java.util.List<java.lang.Integer> |
getFolds() |
int |
getLargestSubunit() |
Point3d |
getLowerBound() |
double |
getMaxSequenceIdentity() |
double |
getMinSequenceIdentity() |
java.util.List<java.lang.Integer> |
getModelNumbers() |
MomentsOfInertia |
getMomentsOfInertia() |
int |
getNucleicAcidChainCount() |
java.util.List<Point3d> |
getOriginalCenters() |
java.util.List<java.lang.Integer> |
getSequenceClusterIds() |
java.lang.String |
getStoichiometry() |
int |
getSubunitCount() |
java.util.List<Point3d[]> |
getTraces() |
java.util.List<Vector3d> |
getUnitVectors() |
Point3d |
getUpperBound() |
boolean |
isPseudoStoichiometric() |
boolean |
isPseudoSymmetric() |
boolean |
overlaps(Subunits subunits) |
void |
setNucleicAcidChainCount(int nucleicAcidChainCount) |
void |
setPseudoSymmetric(boolean pseudoSymmetric) |
public Subunits(java.util.List<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)
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 subunitpublic java.util.List<Point3d[]> getTraces()
public int getSubunitCount()
public java.util.List<java.lang.Integer> getSequenceClusterIds()
public boolean isPseudoStoichiometric()
public boolean isPseudoSymmetric()
public void setPseudoSymmetric(boolean pseudoSymmetric)
public double getMinSequenceIdentity()
public double getMaxSequenceIdentity()
public java.util.List<java.lang.String> getChainIds()
public java.util.List<java.lang.Integer> getModelNumbers()
public java.util.List<java.lang.Integer> getFolds()
public java.lang.String getStoichiometry()
public int getCalphaCount()
public int getLargestSubunit()
public java.util.List<Point3d> getCenters()
public java.util.List<Vector3d> getUnitVectors()
public java.util.List<Point3d> getOriginalCenters()
public Point3d getCentroid()
public MomentsOfInertia getMomentsOfInertia()
public int getNucleicAcidChainCount()
public void setNucleicAcidChainCount(int nucleicAcidChainCount)
nucleicAcidChainCount
- the nucleicAcidChainCount to setpublic boolean overlaps(Subunits subunits)
public boolean contains(Subunits subunits)
public Point3d getLowerBound()
public Point3d getUpperBound()