Class Site

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Site>, PDBRecord

    public class Site
    extends java.lang.Object
    implements PDBRecord, java.io.Serializable, java.lang.Comparable<Site>
    Holds the data of sites presented in PDB files.
    Example from the PDB flatfile:
            SITE     1 AC1  3 GLY A  65  CYS A  67  HOH A 180
            SITE     1 AC2 10 HIS C  37  ALA C  39  THR C 152  LEU C 153
            SITE     2 AC2 10 HIS D  37  ALA D  39  THR D 152  LEU D 153
            SITE     3 AC2 10 SER D 154  GOL D 172
            
    Author:
    Amr AL-Hossary, Jules Jacobsen
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      Site()  
      Site​(java.lang.String siteID, java.util.List<Group> groups)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int compareTo​(Site other)  
      boolean equals​(java.lang.Object obj)  
      java.lang.String getDescription()
      gets the REMARK 800 description of the site
      java.lang.String getEvCode()
      gets the REMARK 800 EVIDENCE CODE for the site.
      java.util.List<Group> getGroups()  
      java.lang.String getSiteID()  
      int hashCode()  
      java.lang.String remark800toPDB()
      Provides REMARK 800 section pertaining to the site as a string.
      void remark800toPDB​(java.lang.StringBuffer stringBuffer)
      Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.
      void setDescription​(java.lang.String description)
      sets the REMARK 800 description of the site
      void setEvCode​(java.lang.String evCode)
      sets the REMARK 800 EVIDENCE CODE for the site.
      void setGroups​(java.util.List<Group> residues)  
      void setSiteID​(java.lang.String siteID)  
      java.lang.String toPDB()
      Returns a PDB file like representation of this record.
      void toPDB​(java.lang.StringBuffer buf)
      Appends a PDB file like representation of this record to the provided StringBuffer.
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • Site

        public Site()
      • Site

        public Site​(java.lang.String siteID,
                    java.util.List<Group> groups)
    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toPDB

        public java.lang.String toPDB()
        Description copied from interface: PDBRecord
        Returns a PDB file like representation of this record.
        Specified by:
        toPDB in interface PDBRecord
        Returns:
        a String providing a PDB file like representation of the record.
      • toPDB

        public void toPDB​(java.lang.StringBuffer buf)
        Description copied from interface: PDBRecord
        Appends a PDB file like representation of this record to the provided StringBuffer.
        Specified by:
        toPDB in interface PDBRecord
      • remark800toPDB

        public void remark800toPDB​(java.lang.StringBuffer stringBuffer)
        Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided. For example in pdb 1a4w: REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
        Parameters:
        stringBuffer -
      • remark800toPDB

        public java.lang.String remark800toPDB()
        Provides REMARK 800 section pertaining to the site as a string. For example in pdb 1a4w: REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
      • setSiteID

        public void setSiteID​(java.lang.String siteID)
        Parameters:
        siteID - the siteID to set e.g. CAT, AC1, AC2...
      • getSiteID

        public java.lang.String getSiteID()
        Returns:
        the siteID e.g. CAT, AC1, AC2...
      • getGroups

        public java.util.List<Group> getGroups()
        Returns:
        the groups
      • setGroups

        public void setGroups​(java.util.List<Group> residues)
        Parameters:
        residues - the groups to set
      • getDescription

        public java.lang.String getDescription()
        gets the REMARK 800 description of the site
        Returns:
        description
      • setDescription

        public void setDescription​(java.lang.String description)
        sets the REMARK 800 description of the site
      • getEvCode

        public java.lang.String getEvCode()
        gets the REMARK 800 EVIDENCE CODE for the site.
        Returns:
        evidence code
      • setEvCode

        public void setEvCode​(java.lang.String evCode)
        sets the REMARK 800 EVIDENCE CODE for the site.
      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • compareTo

        public int compareTo​(Site other)
        Specified by:
        compareTo in interface java.lang.Comparable<Site>