public class HetatomImpl extends Object implements Group
AminoAcidImpl
,
NucleotideImpl
Constructor and Description |
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HetatomImpl() |
Modifier and Type | Method and Description |
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void |
addAtom(Atom atom)
add an atom to this group.
|
void |
clearAtoms()
remove all atoms
|
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(String name)
get an atom throws StructureException if atom not found.
|
List<Atom> |
getAtoms()
get all atoms of this group .
|
long |
getId()
the Hibernate database ID
|
Chain |
getParent()
Returns the parent Chain of the Group
|
String |
getPDBCode()
Returns the PDBCode.
|
String |
getPDBName()
Returns the PDBName.
|
Map<String,Object> |
getProperties()
return properties.
|
Object |
getProperty(String key)
get a single property .
|
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(String name)
test is an Atom with name is existing.
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Iterator<Atom> |
iterator()
return an AtomIterator.
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void |
setAtoms(List<Atom> atoms)
set the atoms of this group
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void |
setId(long id)
the Hibernate database ID
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void |
setParent(Chain parent)
Set the back-reference (to its parent Chain)
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void |
setPDBCode(String pdb)
set the PDB code.
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void |
setPDBFlag(boolean flag)
flag if group has 3D data.
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void |
setPDBName(String s)
set three character name of Group .
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void |
setProperties(Map<String,Object> props)
properties of this amino acid.
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void |
setProperty(String key,
Object value)
set a single property .
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int |
size()
getnumber of atoms.
|
String |
toString() |
public static final String type
public boolean has3D()
public void setPDBFlag(boolean flag)
setPDBFlag
in interface Group
flag
- true to set flag that this Group has 3D coordinatespublic String getPDBCode()
getPDBCode
in interface Group
setPDBCode(java.lang.String)
public void setPDBCode(String pdb)
setPDBCode
in interface Group
pdb
- a String specifying the PDBCode valuegetPDBCode()
public void setPDBName(String s) throws PDBParseException
setPDBName
in interface Group
s
- a String specifying the PDBName valuePDBParseException
- ...getPDBName()
public String getPDBName()
getPDBName
in interface Group
setPDBName(java.lang.String)
public void addAtom(Atom atom)
public void clearAtoms()
clearAtoms
in interface Group
public int size()
public List<Atom> getAtoms()
getAtoms
in interface Group
Group.setAtoms(List)
public Atom getAtom(String name) throws StructureException
getAtom
in interface Group
name
- a StringStructureException
- ...public Atom getAtom(int position) throws StructureException
getAtom
in interface Group
position
- an intStructureException
- ...public boolean hasAtom(String name)
public String getType()
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(Map<String,Object> props)
setProperties
in interface Group
props
- a Map object specifying the properties valuegetProperties()
public Map<String,Object> getProperties()
getProperties
in interface Group
setProperties(java.util.Map<java.lang.String, java.lang.Object>)
public void setProperty(String key, Object value)
setProperty
in interface Group
key
- a Stringvalue
- an ObjectgetProperties()
,
getProperty(java.lang.String)
public Object getProperty(String key)
getProperty
in interface Group
key
- a StringsetProperty(java.lang.String, java.lang.Object)
,
setProperties(java.util.Map<java.lang.String, java.lang.Object>)
public Object clone()
public void setParent(Chain parent)
setParent
in interface Group
parent
- the parent ChainGroup.getParent()
public Chain getParent()
getParent
in interface Group
Group.setParent(Chain)
public long getId()
public void setId(long id)
id
- the hibernate id