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java.lang.Objectbelka.mol.Chain
public abstract class Chain
Abstract class describing behavior of a chain. Chain is a set of molecule building blocks. It can be, for example, polypetide chain, nucleotide chain, or set of water molecules.
Constructor Summary | |
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Chain()
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Method Summary | |
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abstract boolean |
addAfter(Chain newChain)
Adds a chain after the current one. |
abstract boolean |
addAssembly(Assembly assembly)
Adds an assembly to the end of assembly list for the current chain. |
abstract boolean |
addBefore(Chain newChain)
Adds a chain before the current one. |
abstract Assembly |
assemblyList()
Returns list of assemblies. |
abstract int |
countAssemblies()
Returns number of assemblies in the chain. |
abstract int |
countAtoms()
Returns number of atoms in the chain. |
static Chain |
create(char id)
Static method to create a new chain. |
abstract void |
disassemble()
Disassembles chain into null pointers to help garbage collector to free memory. |
abstract char |
getId()
Returns chain's id. |
abstract int |
getModel()
Returns chain's model number. |
abstract String |
getSequence()
Returns sequence of the chain. |
abstract Molecule |
molecule()
Returns a molecule the chain belongs to. |
abstract Chain |
next()
Returns next chain in list. |
abstract Chain |
prev()
Returns previous chain in list. |
abstract int |
removeGaps()
Removes assemblies that are gaps from the list of assemblies. |
abstract void |
resetGroupId(int val)
Resets group id for assemblies in the chain to the specified value. |
abstract void |
selectAllAtoms(boolean val)
Select or deselect all atoms in a chain. |
abstract void |
setModel(int model)
Sets chain's model number. |
abstract boolean |
setMolecule(Molecule mol)
Sets a molecule the chain belongs to. |
String |
toString()
Returns string representation of the chain. |
abstract void |
updateAssemblyPointers()
The function updates pointers to the first and last assemblies belonging to the chain. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Chain()
Method Detail |
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public static Chain create(char id)
id
- chain's id.
public abstract void disassemble()
public abstract Chain next()
public abstract Chain prev()
public abstract boolean addAfter(Chain newChain)
newChain
- chain to add.
public abstract boolean addBefore(Chain newChain)
newChain
- chain to add.
public abstract Assembly assemblyList()
public abstract boolean addAssembly(Assembly assembly)
assembly
- assembly to add.
public abstract void updateAssemblyPointers()
public abstract int removeGaps()
public abstract Molecule molecule()
public abstract boolean setMolecule(Molecule mol)
mol
- molecule to set.
public abstract char getId()
public abstract int getModel()
public abstract void setModel(int model)
model
- chain's model number.public abstract int countAssemblies()
public abstract int countAtoms()
public abstract void selectAllAtoms(boolean val)
val
- if true -- select all atoms, if false -- deselect.public abstract String getSequence()
public abstract void resetGroupId(int val)
public String toString()
toString
in class Object
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