Package org.biojava.nbio.structure
Class Site
- java.lang.Object
-
- org.biojava.nbio.structure.Site
-
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
-
-
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 sitejava.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 sitevoid
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()
-
-
-
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 classjava.lang.Object
-
toPDB
public java.lang.String toPDB()
Description copied from interface:PDBRecord
Returns a PDB file like representation of this 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.
-
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 classjava.lang.Object
-
hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
-
-