org.biojava.bio.structure
Class Site

java.lang.Object
  org.biojava.bio.structure.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

Site()

Site(java.lang.String siteID, java.util.List<Group> groups)

Method Summary

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>