org.biojava.bio.structure
Class Site

java.lang.Object
  extended by org.biojava.bio.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:
Serialized Form

Constructor Summary
Site()
           
Site(String siteID, List<Group> groups)
           
 
Method Summary
 int compareTo(Site other)
           
 boolean equals(Object obj)
           
 String getDescription()
          gets the REMARK 800 description of the site
 String getEvCode()
          gets the REMARK 800 EVIDENCE CODE for the site.
 List<Group> getGroups()
           
 String getSiteID()
           
 int hashCode()
           
 String remark800toPDB()
          Provides REMARK 800 section pertaining to the site as a string.
 void remark800toPDB(StringBuffer stringBuffer)
          Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.
 void setDescription(String description)
          sets the REMARK 800 description of the site
 void setEvCode(String evCode)
          sets the REMARK 800 EVIDENCE CODE for the site.
 void setGroups(List<Group> residues)
           
 void setSiteID(String siteID)
           
 String toPDB()
          Returns a PDB file like representation of this record.
 void toPDB(StringBuffer buf)
          Appends a PDB file like representation of this record to the provided StringBuffer.
 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(String siteID,
            List<Group> groups)
Method Detail

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>