Package org.biojava.nbio.structure

Class Site

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Site>, PDBRecord
    public class Site
extends java.lang.Object
implements PDBRecord, 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>