|
|||||||||
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
,
Serialized FormField Summary | |
---|---|
protected List<Atom> |
atoms
|
protected boolean |
pdb_flag
|
protected String |
pdb_name
|
protected ResidueNumber |
residueNumber
|
static String |
type
this is a "hetatm". |
Constructor Summary | |
---|---|
HetatomImpl()
|
Method Summary | |
---|---|
void |
addAltLoc(Group group)
Add a group that is an alternate location for this group. |
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 . |
List<Group> |
getAltLocs()
Get the list of alternate locations. |
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. |
Atom |
getAtomByPDBname(String name)
Get an atom by the full PDB name e.g. |
List<Atom> |
getAtoms()
get all atoms of this group . |
Chain |
getChain()
Returns the parent Chain of the Group. |
String |
getChainId()
Utility method for returning the chainId of the Group or null if no Chain has been set. |
ChemComp |
getChemComp()
Get the chemical component that closer describes this group. |
long |
getId()
the Hibernate database ID |
Chain |
getParent()
Returns the parent Chain of the Group |
String |
getPDBCode()
Deprecated. replaced by #getSeqNum |
String |
getPDBName()
Returns the PDBName. |
Map<String,Object> |
getProperties()
return properties. |
Object |
getProperty(String key)
get a single property . |
ResidueNumber |
getResidueNumber()
returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group. |
String |
getType()
Returns the type value. |
boolean |
has3D()
returns true or false, depending if this group has 3D coordinates or not. |
boolean |
hasAltLoc()
Test if this group has alternate locations. |
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 fullName)
test is an Atom with name is existing. |
Iterator<Atom> |
iterator()
return an AtomIterator. |
void |
setAtoms(List<Atom> atoms)
set the atoms of this group |
void |
setChain(Chain chain)
Sets the back-reference to its parent Chain. |
void |
setChemComp(ChemComp cc)
Set the Chemical Component that closer describes this group. |
void |
setId(long id)
the Hibernate database ID |
void |
setParent(Chain parent)
Set the back-reference (to its parent Chain) |
void |
setPDBCode(String pdb_code)
Deprecated. replaced by setResidueNumber(ResidueNumber) |
void |
setPDBFlag(boolean flag)
flag if group has 3D data. |
void |
setPDBName(String s)
set three character name of Group . |
void |
setProperties(Map<String,Object> props)
properties of this amino acid. |
void |
setProperty(String key,
Object value)
set a single property . |
void |
setResidueNumber(ResidueNumber residueNumber)
sets the ResidueNumber for this Group |
void |
setResidueNumber(String chainId,
Integer resNum,
Character iCode)
Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet. |
int |
size()
getnumber of atoms. |
String |
toString()
|
Methods inherited from class java.lang.Object |
---|
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
public static final String type
protected boolean pdb_flag
protected String pdb_name
protected ResidueNumber residueNumber
protected List<Atom> atoms
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 coordinates@Deprecated public String getPDBCode()
getPDBCode
in interface Group
setPDBCode(java.lang.String)
@Deprecated public void setPDBCode(String pdb_code)
setResidueNumber(ResidueNumber)
setPDBCode
in interface Group
pdb_code
- a String specifying the PDBCode valuegetPDBCode()
public void setPDBName(String s) throws PDBParseException
setPDBName
in interface Group
s
- a String specifying the PDBName value
PDBParseException
- ...getPDBName()
public 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 List<Atom> getAtoms()
getAtoms
in interface Group
Group.setAtoms(List)
public void setAtoms(List<Atom> atoms)
setAtoms
in interface Group
atoms
- a list of atomsAtom
public Atom getAtom(String name) throws StructureException
getAtom
in interface Group
name
- a String
StructureException
- ...public Atom getAtomByPDBname(String name) throws StructureException
getAtomByPDBname
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(String fullName)
hasAtom
in interface Group
fullName
- a String ...
public String getType()
getType
in interface Group
public String toString()
toString
in class 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 parent 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)
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 String
setProperty(java.lang.String, java.lang.Object)
,
setProperties(java.util.Map)
public Iterator<Atom> iterator()
iterator
in interface Group
public Object clone()
clone
in interface Group
clone
in class Object
public void setParent(Chain parent)
setParent
in interface Group
parent
- the parent ChainGroup.setChain(Chain)
,
Group.getChain()
public Chain getParent()
getParent
in interface Group
Group.setChain(Chain)
public long getId()
public void setId(long id)
id
- the hibernate idpublic ChemComp getChemComp()
Group
getChemComp
in interface Group
public void setChemComp(ChemComp cc)
Group
setChemComp
in interface Group
cc
- the chemical componentpublic void setChain(Chain chain)
setChain
in interface Group
chain
- the parent ChainGroup.getChain()
public Chain getChain()
getChain
in interface Group
Group.setChain(Chain)
public String getChainId()
getChainId
in interface Group
public ResidueNumber getResidueNumber()
getResidueNumber
in interface Group
ResidueNumber
public void setResidueNumber(ResidueNumber residueNumber)
Group
setResidueNumber
in interface Group
residueNumber
- the PDB residueNumberpublic void setResidueNumber(String chainId, Integer resNum, Character iCode)
Group
setResidueNumber
in interface Group
public boolean hasAltLoc()
Group
hasAltLoc
in interface Group
public List<Group> getAltLocs()
Group
getAltLocs
in interface Group
public void addAltLoc(Group group)
Group
addAltLoc
in interface Group
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |