Class GroupAsa

  • All Implemented Interfaces:
    java.io.Serializable

    public class GroupAsa
    extends java.lang.Object
    implements java.io.Serializable
    A class to store the results of ASA calculations, it can hold ASA values per atom present in Group
    Author:
    duarte_j
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      GroupAsa​(Group g)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addAtomAsaC​(double asa)  
      void addAtomAsaU​(double asa)  
      java.lang.Object clone()  
      double getAsaC()
      Returns the ASA of the residue in the complexed state
      double getAsaU()
      Returns the ASA of the residue in the uncomplexed state
      java.util.List<java.lang.Double> getAtomAsaCs()  
      java.util.List<java.lang.Double> getAtomAsaUs()  
      double getBsa()
      Returns the BSA value for this group, i.e.
      double getBsaToAsaRatio()
      Returns the bsa/asa(uncomplexed) ratio, i.e.
      Group getGroup()  
      double getRelativeAsaC()
      Returns the relative (complexed) ASA, i.e.
      double getRelativeAsaU()
      Returns the relative (uncomplexed) ASA, i.e.
      void setAsaC​(double asaC)  
      void setAsaU​(double asaU)  
      void setAtomAsaCs​(java.util.List<java.lang.Double> atomAsaCs)  
      void setAtomAsaUs​(java.util.List<java.lang.Double> atomAsaUs)  
      • Methods inherited from class java.lang.Object

        equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • GroupAsa

        public GroupAsa​(Group g)
    • Method Detail

      • getGroup

        public Group getGroup()
      • getAsaU

        public double getAsaU()
        Returns the ASA of the residue in the uncomplexed state
        Returns:
      • setAsaU

        public void setAsaU​(double asaU)
      • getAsaC

        public double getAsaC()
        Returns the ASA of the residue in the complexed state
        Returns:
      • setAsaC

        public void setAsaC​(double asaC)
      • addAtomAsaU

        public void addAtomAsaU​(double asa)
      • addAtomAsaC

        public void addAtomAsaC​(double asa)
      • getAtomAsaUs

        public java.util.List<java.lang.Double> getAtomAsaUs()
      • setAtomAsaUs

        public void setAtomAsaUs​(java.util.List<java.lang.Double> atomAsaUs)
      • getAtomAsaCs

        public java.util.List<java.lang.Double> getAtomAsaCs()
      • setAtomAsaCs

        public void setAtomAsaCs​(java.util.List<java.lang.Double> atomAsaCs)
      • getBsa

        public double getBsa()
        Returns the BSA value for this group, i.e. the difference between ASA uncomplexed and ASA complexed
        Returns:
      • getBsaToAsaRatio

        public double getBsaToAsaRatio()
        Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation
        Returns:
      • getRelativeAsaU

        public double getRelativeAsaU()
        Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
        Returns:
      • getRelativeAsaC

        public double getRelativeAsaC()
        Returns the relative (complexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
        Returns:
      • clone

        public java.lang.Object clone()
        Overrides:
        clone in class java.lang.Object