org.biojava.bio.structure
Interface Group

All Known Subinterfaces:
AminoAcid
All Known Implementing Classes:
AminoAcidImpl, HetatomImpl, NucleotideImpl

public interface Group

This is the data structure for a single Group of atoms. A protein sequence (Chain in PDB file) is represented as a list of Groups. There are 3 types of Groups:

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

Method Summary
 void addAtom(Atom atom)
          add an atom to this group.
 void clearAtoms()
          Remove all atoms from this group.
 java.lang.Object clone()
          returns and identical copy of this Group object .
 Atom getAtom(int position)
          Get at atom by position.
 Atom getAtom(java.lang.String name)
          Get an atom.
 java.util.List<Atom> getAtoms()
          Get list of atoms.
 Chain getParent()
          Returns the parent Chain of the Group.
 java.lang.String getPDBCode()
          Return the PDBcode (residue number + insertion code ) of this group.
 java.lang.String getPDBName()
          Get the PDB 3 character name for this group.
 java.util.Map<java.lang.String,java.lang.Object> getProperties()
          return properties.
 java.lang.Object getProperty(java.lang.String key)
          get a single property .
 java.lang.String getType()
          get Type of group, e.g.
 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.
 boolean hasAtom(java.lang.String name)
          Teturns flag whether a particular atom is existing within this group .
 java.util.Iterator<Atom> iterator()
          get an Atom Iterator.
 void setAtoms(java.util.List<Atom> atoms)
          Set the atoms of this group.
 void setParent(Chain parent)
          Set the back-reference (to its parent Chain).
 void setPDBCode(java.lang.String pdbcode)
          Specifies the PDBCode (residue number + insertion code) value.
 void setPDBFlag(boolean flag)
          flag if group has 3D data .
 void setPDBName(java.lang.String s)
          Set the PDB 3 letter name for this group.
 void setProperties(java.util.Map<java.lang.String,java.lang.Object> properties)
          properties of this amino acid.
 void setProperty(java.lang.String key, java.lang.Object value)
          set a single property .
 int size()
          getnumber of atoms.
 

Method Detail

getPDBCode

java.lang.String getPDBCode()
Return the PDBcode (residue number + insertion code ) of this group. The residue number is treated as a String for the following reasons: Every amino acid in a PDB file is identified uniquely by 3 things: The chain ID, the residue number and the insertion code. To make sure one does not forget about the insertion code, in BJ it is appended to the residue number. To add to this, residue numbers can be negative, non-consecutive and also non-sequential. As such it is often easiest, to treat them as public identifiers and within your own code work with the internal atom or group positions...

Returns:
a String representing the PDBCode value
See Also:
setPDBCode(java.lang.String)

setPDBCode

void setPDBCode(java.lang.String pdbcode)
Specifies the PDBCode (residue number + insertion code) value.

Parameters:
pdbcode - a String specifying the PDBCode value
See Also:
getPDBCode()

size

int size()
getnumber of atoms.

Returns:
number of atoms of this Group

has3D

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

Returns:
true if Group has 3D coordinates

setPDBFlag

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

Parameters:
flag - true to set flag that this Group has 3D coordinates

getType

java.lang.String getType()
get Type of group, e.g. amino, hetatom, nucleotide.

Returns:
a String representing the type value

addAtom

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

Parameters:
atom - an Atom object

getAtoms

java.util.List<Atom> getAtoms()
Get list of atoms.

Returns:
an List object representing the atoms
See Also:
setAtoms(List)

setAtoms

void setAtoms(java.util.List<Atom> atoms)
Set the atoms of this group.

Parameters:
atoms - a list of atoms
See Also:
Atom

clearAtoms

void clearAtoms()
Remove all atoms from this group.


getAtom

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

Parameters:
name - a String
Returns:
an Atom object
Throws:
StructureException - if atom not found.

getAtom

Atom getAtom(int position)
             throws StructureException
Get at atom by position.

Parameters:
position - an int
Returns:
an Atom object
Throws:
StructureException - if not atom at this position

hasAtom

boolean hasAtom(java.lang.String name)
Teturns flag whether a particular atom is existing within this group .

Parameters:
name - a String ...
Returns:
true if Atom with name is existing within this group

getPDBName

java.lang.String getPDBName()
Get the PDB 3 character name for this group. (e.g. ALA)

Returns:
a String representing the PDBName value
See Also:
setPDBName(java.lang.String)

setPDBName

void setPDBName(java.lang.String s)
                throws PDBParseException
Set the PDB 3 letter name for this group. (e.g. ALA)

Parameters:
s - a String specifying the PDBName value
Throws:
PDBParseException - ...
See Also:
getPDBName()

hasAminoAtoms

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
     

Returns:
true if all Atoms required for an AminoAcid are available (N, CA, C, O, CB)
See Also:
getType()

setProperties

void setProperties(java.util.Map<java.lang.String,java.lang.Object> properties)
properties of this amino acid. currerntly available properties. are: phi psi

Parameters:
properties - a Map object specifying the properties value
See Also:
getProperties()

getProperties

java.util.Map<java.lang.String,java.lang.Object> getProperties()
return properties.

Returns:
a HashMap object representing the properties value
See Also:
setProperties(java.util.Map)

setProperty

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

Parameters:
key - a String
value - an Object
See Also:
getProperty(java.lang.String)

getProperty

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

Parameters:
key - a String
Returns:
an Object
See Also:
setProperty(java.lang.String, java.lang.Object)

iterator

java.util.Iterator<Atom> iterator()
get an Atom Iterator.

Returns:
an Iterator object

clone

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

Returns:
and identical copy of this Group object

setParent

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

Parameters:
parent - the parent Chain
See Also:
getParent()

getParent

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

Returns:
Chain the Chain object that contains the Group
See Also:
setParent(Chain)