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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:
HetatomImpl
,
AminoAcidImpl
,
NucleotideImpl
Method Summary | |
---|---|
void |
addAltLoc(Group g)
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 from this group. |
Object |
clone()
returns and identical copy of this Group object . |
List<Group> |
getAltLocs()
Get the list of alternate locations. |
Atom |
getAtom(int position)
Get at atom by position. |
Atom |
getAtom(String name)
Get an atom. |
Atom |
getAtomByPDBname(String pdbName)
Get an atom by the full PDB name e.g. |
List<Atom> |
getAtoms()
Get list of atoms. |
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. |
Chain |
getParent()
Deprecated. replaced by getChain() |
String |
getPDBCode()
Deprecated. replaced by getResidueNumber() |
String |
getPDBName()
Get the PDB 3 character name for this group. |
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()
get Type of group, e.g. |
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. |
boolean |
hasAtom(String name)
Teturns flag whether a particular atom is existing within this group . |
Iterator<Atom> |
iterator()
get an Atom Iterator. |
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 |
setParent(Chain parent)
Deprecated. |
void |
setPDBCode(String pdbcode)
Deprecated. replaced by setResidueNumber(ResidueNumber) |
void |
setPDBFlag(boolean flag)
flag if group has 3D data . |
void |
setPDBName(String s)
Set the PDB 3 letter name for this group. |
void |
setProperties(Map<String,Object> properties)
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 residueNumber,
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. |
Method Detail |
---|
@Deprecated String getPDBCode()
getResidueNumber()
setPDBCode(java.lang.String)
@Deprecated void setPDBCode(String pdbcode)
setResidueNumber(ResidueNumber)
pdbcode
- a String specifying the PDBCode valuegetPDBCode()
int size()
boolean has3D()
void setPDBFlag(boolean flag)
flag
- true to set flag that this Group has 3D coordinatesString getType()
void addAtom(Atom atom)
atom
- an Atom objectList<Atom> getAtoms()
setAtoms(List)
void setAtoms(List<Atom> atoms)
atoms
- a list of atomsAtom
void clearAtoms()
Atom getAtom(String name) throws StructureException
name
- a String
StructureException
- if atom not found.Atom getAtomByPDBname(String pdbName) throws StructureException
pdbName
- a String
StructureException
- ...Atom getAtom(int position) throws StructureException
position
- an int
StructureException
- if not atom at this positionboolean hasAtom(String name)
name
- a String ...
String getPDBName()
setPDBName(java.lang.String)
void setPDBName(String s) throws PDBParseException
s
- a String specifying the PDBName value
PDBParseException
- ...getPDBName()
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
getType()
void setProperties(Map<String,Object> properties)
properties
- a Map object specifying the properties valuegetProperties()
Map<String,Object> getProperties()
setProperties(java.util.Map)
void setProperty(String key, Object value)
key
- a Stringvalue
- an ObjectgetProperty(java.lang.String)
Object getProperty(String key)
key
- a String
setProperty(java.lang.String, java.lang.Object)
Iterator<Atom> iterator()
Object clone()
@Deprecated void setParent(Chain parent)
parent
- the parent ChainsetChain(Chain)
,
getChain()
@Deprecated Chain getParent()
getChain()
setChain(Chain)
void setChain(Chain chain)
chain
- the parent ChaingetChain()
Chain getChain()
setChain(Chain)
ResidueNumber getResidueNumber()
ResidueNumber
void setResidueNumber(ResidueNumber residueNumber)
residueNumber
- the PDB residueNumbervoid setResidueNumber(String chainId, Integer residueNumber, Character iCode)
chainId
- residueNumber
- iCode
- String getChainId()
void setChemComp(ChemComp cc)
cc
- the chemical componentChemComp getChemComp()
boolean hasAltLoc()
List<Group> getAltLocs()
void addAltLoc(Group g)
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