org.biojava.bio.structure
Class HetatomImpl

java.lang.Object
  extended by org.biojava.bio.structure.HetatomImpl
All Implemented Interfaces:
Group
Direct Known Subclasses:
AminoAcidImpl, NucleotideImpl

public class HetatomImpl
extends java.lang.Object
implements Group

Generic Implementation of a Group interface. AminoAcidImpl and NucleotideImpl are closely related classes.

Since:
1.4
Version:
%I% %G%
Author:
Andreas Prlic, Horvath Tamas
See Also:
AminoAcidImpl, NucleotideImpl

Field Summary
static java.lang.String type
          this is a "hetatm".
 
Constructor Summary
HetatomImpl()
           
 
Method Summary
 void addAtom(Atom atom)
          add an atom to this group.
 void clearAtoms()
          remove all atoms
 java.lang.Object clone()
          returns and identical copy of this Group object .
 Atom getAtom(int position)
          return an atom by its position in the internal List.
 Atom getAtom(java.lang.String name)
          get an atom throws StructureException if atom not found.
 java.util.List getAtoms()
          get all atoms of this group .
 Chain getParent()
          Returns the parent Chain of the Group
 java.lang.String getPDBCode()
          Returns the PDBCode.
 java.lang.String getPDBName()
          Returns the PDBName.
 java.util.Map getProperties()
          return properties.
 java.lang.Object getProperty(java.lang.String key)
          get a single property .
 java.lang.String getType()
          Returns the type value.
 boolean has3D()
          returns true or false, depending if this group has 3D coordinates or not.
 boolean hasAminoAtoms()
          calculate if a groups has all atoms required for an amino acid this allows to include chemically modified amino acids that are labeled hetatoms into some computations ...
 boolean hasAtom(java.lang.String name)
          test is an Atom with name is existing.
 java.util.Iterator iterator()
          return an AtomIterator.
 void setParent(Chain parent)
          Set the back-reference (to its parent Chain)
 void setPDBCode(java.lang.String pdb)
          set the PDB code.
 void setPDBFlag(boolean flag)
          flag if group has 3D data.
 void setPDBName(java.lang.String s)
          set three character name of Group .
 void setProperties(java.util.Map props)
          properties of this amino acid.
 void setProperty(java.lang.String key, java.lang.Object value)
          set a single property .
 int size()
          getnumber of atoms.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

type

public static final java.lang.String type
this is a "hetatm".

See Also:
Constant Field Values
Constructor Detail

HetatomImpl

public HetatomImpl()
Method Detail

has3D

public boolean has3D()
returns true or false, depending if this group has 3D coordinates or not.

Specified by:
has3D in interface Group
Returns:
true if Group has 3D coordinates

setPDBFlag

public void setPDBFlag(boolean flag)
flag if group has 3D data.

Specified by:
setPDBFlag in interface Group
Parameters:
flag - true to set flag that this Group has 3D coordinates

getPDBCode

public java.lang.String getPDBCode()
Returns the PDBCode.

Specified by:
getPDBCode in interface Group
Returns:
a String representing the PDBCode value
See Also:
setPDBCode(java.lang.String)

setPDBCode

public void setPDBCode(java.lang.String pdb)
set the PDB code.

Specified by:
setPDBCode in interface Group
Parameters:
pdb - a String specifying the PDBCode value
See Also:
getPDBCode()

setPDBName

public void setPDBName(java.lang.String s)
                throws PDBParseException
set three character name of Group .

Specified by:
setPDBName in interface Group
Parameters:
s - a String specifying the PDBName value
Throws:
PDBParseException - ...
See Also:
getPDBName()

getPDBName

public java.lang.String getPDBName()
Returns the PDBName.

Specified by:
getPDBName in interface Group
Returns:
a String representing the PDBName value
See Also:
setPDBName(java.lang.String)

addAtom

public void addAtom(Atom atom)
add an atom to this group.

Specified by:
addAtom in interface Group
Parameters:
atom - an Atom object

clearAtoms

public void clearAtoms()
remove all atoms

Specified by:
clearAtoms in interface Group

size

public int size()
getnumber of atoms.

Specified by:
size in interface Group
Returns:
number of atoms

getAtoms

public java.util.List getAtoms()
get all atoms of this group . returns a List of all atoms in this Group

Specified by:
getAtoms in interface Group
Returns:
an List object representing the atoms value

getAtom

public Atom getAtom(java.lang.String name)
             throws StructureException
get an atom throws StructureException if atom not found.

Specified by:
getAtom in interface Group
Parameters:
name - a String
Returns:
an Atom object
Throws:
StructureException - ...

getAtom

public Atom getAtom(int position)
             throws StructureException
return an atom by its position in the internal List.

Specified by:
getAtom in interface Group
Parameters:
position - an int
Returns:
an Atom object
Throws:
StructureException - ...

hasAtom

public boolean hasAtom(java.lang.String name)
test is an Atom with name is existing.

Specified by:
hasAtom in interface Group
Parameters:
name - a String ...
Returns:
true if Atom with name is existing within this group

getType

public java.lang.String getType()
Returns the type value.

Specified by:
getType in interface Group
Returns:
a String representing the type value

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

hasAminoAtoms

public boolean hasAminoAtoms()
calculate if a groups has all atoms required for an amino acid this allows to include chemically modified amino acids that are labeled hetatoms into some computations ... the usual way to identify if a group is an amino acid is getType() !

amino atoms are : N, CA, C, O, CB GLY does not have CB (unless we would calculate some artificially

Example: 1DW9 chain A first group is a Selenomethionine, provided as HETATM, but here returns true.
     HETATM    1  N   MSE A   1      11.720  20.973   1.584  0.00  0.00           N
     HETATM    2  CA  MSE A   1      10.381  20.548   1.139  0.00  0.00           C
     HETATM    3  C   MSE A   1       9.637  20.037   2.398  0.00  0.00           C
     HETATM    4  O   MSE A   1      10.198  19.156   2.985  0.00  0.00           O
     HETATM    5  CB  MSE A   1      10.407  19.441   0.088  0.00  0.00           C
     

Specified by:
hasAminoAtoms in interface Group
Returns:
true if all Atoms required for an AminoAcid are available (N, CA, C, O, CB)
See Also:
getType()

setProperties

public void setProperties(java.util.Map props)
properties of this amino acid. currerntly available properties. are: phi psi

Specified by:
setProperties in interface Group
Parameters:
props - a Map object specifying the properties value
See Also:
getProperties()

getProperties

public java.util.Map getProperties()
return properties.

Specified by:
getProperties in interface Group
Returns:
a HashMap object representing the properties value
See Also:
setProperties(java.util.Map)

setProperty

public void setProperty(java.lang.String key,
                        java.lang.Object value)
set a single property .

Specified by:
setProperty in interface Group
Parameters:
key - a String
value - an Object
See Also:
getProperties(), getProperty(java.lang.String)

getProperty

public java.lang.Object getProperty(java.lang.String key)
get a single property .

Specified by:
getProperty in interface Group
Parameters:
key - a String
Returns:
an Object
See Also:
setProperty(java.lang.String, java.lang.Object), setProperties(java.util.Map)

iterator

public java.util.Iterator iterator()
return an AtomIterator.

Specified by:
iterator in interface Group
Returns:
an Iterator object

clone

public java.lang.Object clone()
returns and identical copy of this Group object .

Specified by:
clone in interface Group
Overrides:
clone in class java.lang.Object
Returns:
and identical copy of this Group object

setParent

public void setParent(Chain parent)
Set the back-reference (to its parent Chain)

Specified by:
setParent in interface Group
Parameters:
parent - the parent Chain

getParent

public Chain getParent()
Returns the parent Chain of the Group

Specified by:
getParent in interface Group
Returns:
Chain the Chain object that contains the Group