public class HetatomImpl extends java.lang.Object implements Group, java.io.Serializable
AminoAcidImpl
,
NucleotideImpl
,
Serialized FormModifier and Type | Field and Description |
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protected java.util.List<Atom> |
atoms |
protected boolean |
pdb_flag |
protected java.lang.String |
pdb_name |
protected ResidueNumber |
residueNumber |
static java.lang.String |
type
this is a "hetatm".
|
Constructor and Description |
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HetatomImpl() |
Modifier and Type | Method and Description |
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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
|
java.lang.Object |
clone()
returns and identical copy of this Group object .
|
Group |
getAltLocGroup(java.lang.Character altLoc)
Gets the alternate location group to this group that has the alt-loc character code passed.
|
java.util.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(java.lang.String name)
get an atom throws StructureException if atom not found.
|
Atom |
getAtomByPDBname(java.lang.String name)
Get an atom by the full PDB name e.g.
|
java.util.List<Atom> |
getAtoms()
get all atoms of this group .
|
Chain |
getChain()
Returns the parent Chain of the Group.
|
java.lang.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
|
java.lang.String |
getPDBCode()
Deprecated.
replaced by #getSeqNum
|
java.lang.String |
getPDBName()
Returns the PDBName.
|
java.util.Map<java.lang.String,java.lang.Object> |
getProperties()
return properties.
|
java.lang.Object |
getProperty(java.lang.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.
|
java.lang.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(java.lang.String fullName)
test is an Atom with name is existing.
|
boolean |
isWater()
Determines if this group is water.
|
java.util.Iterator<Atom> |
iterator()
return an AtomIterator.
|
void |
setAtoms(java.util.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(java.lang.String pdb_code)
Deprecated.
replaced by
setResidueNumber(ResidueNumber) |
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<java.lang.String,java.lang.Object> props)
properties of this amino acid.
|
void |
setProperty(java.lang.String key,
java.lang.Object value)
set a single property .
|
void |
setResidueNumber(ResidueNumber residueNumber)
sets the ResidueNumber for this Group
|
void |
setResidueNumber(java.lang.String chainId,
java.lang.Integer resNum,
java.lang.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.
|
java.lang.String |
toString() |
void |
trimToSize()
attempts to reduce the memory imprint of this group by trimming
all internal Collection objects to the required size.
|
public static final java.lang.String type
protected boolean pdb_flag
protected java.lang.String pdb_name
protected ResidueNumber residueNumber
protected java.util.List<Atom> atoms
public boolean has3D()
public void setPDBFlag(boolean flag)
setPDBFlag
in interface Group
flag
- true to set flag that this Group has 3D coordinates@Deprecated public java.lang.String getPDBCode()
getPDBCode
in interface Group
setPDBCode(java.lang.String)
@Deprecated public void setPDBCode(java.lang.String pdb_code)
setResidueNumber(ResidueNumber)
setPDBCode
in interface Group
pdb_code
- 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 valuePDBParseException
- ...getPDBName()
public java.lang.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 java.util.List<Atom> getAtoms()
getAtoms
in interface Group
Group.setAtoms(List)
public void setAtoms(java.util.List<Atom> atoms)
public Atom getAtom(java.lang.String name) throws StructureException
getAtom
in interface Group
name
- a StringStructureException
- ...public Atom getAtomByPDBname(java.lang.String name) throws StructureException
getAtomByPDBname
in interface Group
name
- a StringStructureException
- ...public Atom getAtom(int position) throws StructureException
getAtom
in interface Group
position
- an intStructureException
- ...public boolean hasAtom(java.lang.String fullName)
public java.lang.String getType()
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 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(java.util.Map<java.lang.String,java.lang.Object> props)
setProperties
in interface Group
props
- a Map object specifying the properties valuegetProperties()
public java.util.Map<java.lang.String,java.lang.Object> getProperties()
getProperties
in interface Group
setProperties(java.util.Map<java.lang.String, java.lang.Object>)
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 StringsetProperty(java.lang.String, java.lang.Object)
,
setProperties(java.util.Map<java.lang.String, java.lang.Object>)
public java.util.Iterator<Atom> iterator()
public java.lang.Object clone()
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 java.lang.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(java.lang.String chainId, java.lang.Integer resNum, java.lang.Character iCode)
Group
setResidueNumber
in interface Group
public boolean hasAltLoc()
Group
public java.util.List<Group> getAltLocs()
Group
getAltLocs
in interface Group
public Group getAltLocGroup(java.lang.Character altLoc)
Group
getAltLocGroup
in interface Group
altLoc
- the alternate location code of the group desiredpublic void addAltLoc(Group group)
Group
public boolean isWater()
Group
public void trimToSize()
trimToSize
in interface Group