|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.structure.HetatomImpl
public class HetatomImpl
Generic Implementation of a Group interface. AminoAcidImpl and NucleotideImpl are closely related classes.
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 |
---|
public static final java.lang.String type
Constructor Detail |
---|
public HetatomImpl()
Method Detail |
---|
public boolean has3D()
has3D
in interface Group
public void setPDBFlag(boolean flag)
setPDBFlag
in interface Group
flag
- true to set flag that this Group has 3D coordinatespublic java.lang.String getPDBCode()
getPDBCode
in interface Group
setPDBCode(java.lang.String)
public void setPDBCode(java.lang.String pdb)
setPDBCode
in interface Group
pdb
- a String specifying the PDBCode valuegetPDBCode()
public void setPDBName(java.lang.String s) throws PDBParseException
setPDBName
in interface Group
s
- a String specifying the PDBName value
PDBParseException
- ...getPDBName()
public java.lang.String getPDBName()
getPDBName
in interface Group
setPDBName(java.lang.String)
public void addAtom(Atom atom)
addAtom
in interface Group
atom
- an Atom objectpublic void clearAtoms()
clearAtoms
in interface Group
public int size()
size
in interface Group
public java.util.List getAtoms()
getAtoms
in interface Group
public Atom getAtom(java.lang.String name) throws StructureException
getAtom
in interface Group
name
- a String
StructureException
- ...public Atom getAtom(int position) throws StructureException
getAtom
in interface Group
position
- an int
StructureException
- ...public boolean hasAtom(java.lang.String name)
hasAtom
in interface Group
name
- a String ...
public java.lang.String getType()
getType
in interface Group
public java.lang.String toString()
toString
in class java.lang.Object
public boolean hasAminoAtoms()
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
hasAminoAtoms
in interface Group
getType()
public void setProperties(java.util.Map props)
setProperties
in interface Group
props
- a Map object specifying the properties valuegetProperties()
public java.util.Map getProperties()
getProperties
in interface Group
setProperties(java.util.Map)
public void setProperty(java.lang.String key, java.lang.Object value)
setProperty
in interface Group
key
- a Stringvalue
- an ObjectgetProperties()
,
getProperty(java.lang.String)
public java.lang.Object getProperty(java.lang.String key)
getProperty
in interface Group
key
- a String
setProperty(java.lang.String, java.lang.Object)
,
setProperties(java.util.Map)
public java.util.Iterator iterator()
iterator
in interface Group
public java.lang.Object clone()
clone
in interface Group
clone
in class java.lang.Object
public void setParent(Chain parent)
setParent
in interface Group
parent
- the parent Chainpublic Chain getParent()
getParent
in interface Group
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |