Package org.biojava.nbio.structure

Class Site

java.lang.Object
org.biojava.nbio.structure.Site
All Implemented Interfaces:
Serializable, Comparable<Site>, PDBRecord
public class Site extends Object implements PDBRecord, Serializable, 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:

  • Constructor Details

    • Site

      public Site()

    • Site

      public Site(String siteID, List<Group> groups)

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toPDB

      public 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(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(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 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(String siteID)
      Parameters:
      siteID - the siteID to set e.g. CAT, AC1, AC2...

    • getSiteID

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

    • getGroups

      public List<Group> getGroups()
      Returns:
      the groups

    • setGroups

      public void setGroups(List<Group> residues)
      Parameters:
      residues - the groups to set

    • getDescription

      public String getDescription()
      gets the REMARK 800 description of the site
      Returns:
      description

    • setDescription

      public void setDescription(String description)
      sets the REMARK 800 description of the site

    • getEvCode

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

    • setEvCode

      public void setEvCode(String evCode)
      sets the REMARK 800 EVIDENCE CODE for the site.

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • compareTo

      public int compareTo(Site other)
      Specified by:
      compareTo in interface Comparable<Site>