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public interface Group
This is the datastructure for a single Group of atoms. A protein sequence (Chain in PDB file) is represented as a list of this kind of objects. Groups can be of type "amino","hetatm","nucleotide". There are corresponding classes for each of this type which implement interface Group.
HetatomImpl
,
AminoAcidImpl
,
NucleotideImpl
Method Summary | |
---|---|
void |
addAtom(Atom atom)
add an atom to this group. |
void |
clearAtoms()
remove all atoms from this group |
java.lang.Object |
clone()
returns and identical copy of this Group object . |
Atom |
getAtom(int position)
get at atom by position. |
Atom |
getAtom(java.lang.String name)
get an atom throws StructureException if atom not found. |
java.util.List |
getAtoms()
get list of atoms. |
Chain |
getParent()
Returns the parent Chain of the Group |
java.lang.String |
getPDBCode()
return the PDBcode (residue number) of this group. |
java.lang.String |
getPDBName()
set the PDB 3 character name for this group. |
java.util.Map |
getProperties()
return properties. |
java.lang.Object |
getProperty(java.lang.String key)
get a single property . |
java.lang.String |
getType()
get Type of group, e.g. |
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. |
boolean |
hasAtom(java.lang.String name)
returns flag whether a particular atom is existing within this group . |
java.util.Iterator |
iterator()
get an Atom Iterator. |
void |
setParent(Chain parent)
Set the back-reference (to its parent Chain) |
void |
setPDBCode(java.lang.String pdbcode)
Specifies the PDBCode value. |
void |
setPDBFlag(boolean flag)
flag if group has 3D data . |
void |
setPDBName(java.lang.String s)
get the PDB 3 character name for this group. |
void |
setProperties(java.util.Map properties)
properties of this amino acid. |
void |
setProperty(java.lang.String key,
java.lang.Object value)
set a single property . |
int |
size()
getnumber of atoms. |
Method Detail |
---|
java.lang.String getPDBCode()
setPDBCode(java.lang.String)
void setPDBCode(java.lang.String pdbcode)
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 coordinatesjava.lang.String getType()
void addAtom(Atom atom)
atom
- an Atom objectjava.util.List getAtoms()
void clearAtoms()
Atom getAtom(java.lang.String name) throws StructureException
name
- a String
StructureException
- ...Atom getAtom(int position) throws StructureException
position
- an int
StructureException
- ...boolean hasAtom(java.lang.String name)
name
- a String ...
java.lang.String getPDBName()
setPDBName(java.lang.String)
void setPDBName(java.lang.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(java.util.Map properties)
properties
- a Map object specifying the properties valuegetProperties()
java.util.Map getProperties()
setProperties(java.util.Map)
void setProperty(java.lang.String key, java.lang.Object value)
key
- a Stringvalue
- an ObjectgetProperty(java.lang.String)
java.lang.Object getProperty(java.lang.String key)
key
- a String
setProperty(java.lang.String, java.lang.Object)
java.util.Iterator iterator()
java.lang.Object clone()
void setParent(Chain parent)
parent
- a WeakReference to the parent ChainChain getParent()
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