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java.lang.Objectbelka.mol.Assembly
public abstract class Assembly
Abstract class describing behavior of an assembly. Assembly is the group of atoms, for example residue or nucleotide.
Constructor Summary | |
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Assembly()
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Method Summary | |
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abstract boolean |
addAtom(Atom atom)
Adds atom to the end of atom list of the current assembly. |
abstract boolean |
addBond(Bond bond)
Adds peptide/phosphodiester bond. |
abstract Atom |
atomList()
Returns list of atoms. |
abstract Bond[] |
bondArray()
Returns array of peptide/phosphodiester bonds. |
abstract Chain |
chain()
Returns a chain the assembly belongs to. |
abstract int |
countAtoms()
Returns number of atoms in the assembly. |
abstract int |
countBonds()
Returns number of peptide/phosphodiester bonds for the assembly. |
static Assembly |
create(Compound comp)
Static method to create a new assembly. |
static Assembly |
createGap()
Static method to create a new assembly representing gap. |
abstract void |
disassemble()
Disassembles assembly into null pointers to help garbage collector to free memory. |
abstract Assembly |
extractAfter()
Extracts the assembly following the current one from the list. |
abstract Assembly |
extractBefore()
Extracts the assembly preceeding the current one from the list. |
static int |
getAlignedAttribute()
Returns flag attribute of aligned assemblies. |
abstract Atom |
getCAAtom()
Returns C-alpha atom or null if it is not found. |
abstract Compound |
getCompound()
Returns assembly's compound. |
static int |
getGroupAttribute(int group_id)
Returns flag attribute for assemblies in particular group. |
abstract int |
getGroupId()
Returns group id or 0 if assembly is not assigned to any group. |
static int |
getHelix3Attribute()
Returns flag attribute for residues in 3,10-helices. |
static int |
getHelix4Attribute()
Returns flag attribute for residues in 4-helices. |
static int |
getHelix5Attribute()
Returns flag attribute for residues in 5-helices. |
static int |
getHelixAttribute()
Returns flag attribute for residues in helices. |
abstract char |
getICode()
Returns assembly's icode. |
abstract char |
getLetterName()
Returns assembly's one letter name. |
abstract Atom |
getMainAtom()
Returns the main atom (CA for proteins and sugar P for nucleotides) in assembly or null if such atom can't be found. |
abstract String |
getName()
Returns assembly's name. |
static int |
getRegularAttribute()
Returns flag attribute for residues in any secondary structure elements. |
abstract int |
getSerialNum()
Returns assembly's serial number. |
static int |
getSheetAttribute()
Returns flag attribute for residues in sheets. |
static int |
getTurnAttribute()
Returns flag attribute for residues in turn. |
abstract boolean |
hasAttribute(int att)
Returns true if the provide attribute matches to the attributes of the assembly. |
abstract boolean |
insertAfter(Assembly newAssembly)
Inserts an assembly after the current one. |
abstract boolean |
insertBefore(Assembly newAssembly)
Inserts an assembly before the current one. |
abstract boolean |
isAligned()
Returns true if assemblies is aligned, false otherwise. |
abstract boolean |
isConnectedTo(Assembly s)
Returns true if assemblies are connected by peptide/phosphodiester bonds, false otherwise. |
abstract boolean |
isGap()
Returns true if the assembly represents gap. |
abstract Assembly |
next()
Returns next assembly in list. |
abstract Assembly |
prev()
Returns previous assembly in list. |
abstract void |
selectAllAtoms(boolean val)
Select or deselect all atoms in a assembly. |
abstract void |
setAligned(boolean val)
Sets assembly's alignment attribute. |
abstract boolean |
setChain(Chain chain)
Sets a chain the assembly belongs to. |
abstract boolean |
setGroupId(int groupId)
Sets group id for the assembly. |
abstract void |
setICode(char icode)
Sets assembly's icode. |
abstract void |
setSerialNum(int serial)
Sets assembly's serial number. |
abstract String |
toString()
Returns string representation of the assembly. |
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 Assembly()
Method Detail |
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public static Assembly create(Compound comp)
comp
- assembly's chemical compound.
public static Assembly createGap()
public abstract void disassemble()
public abstract boolean isGap()
public abstract Assembly next()
public abstract Assembly prev()
public abstract boolean insertAfter(Assembly newAssembly)
newAssembly
- assembly to insert.
public abstract boolean insertBefore(Assembly newAssembly)
newAssembly
- assembly to insert.
public abstract Assembly extractAfter()
public abstract Assembly extractBefore()
public abstract Atom atomList()
public abstract boolean addAtom(Atom atom)
atom
- atom to add.
public abstract boolean addBond(Bond bond)
bond
- bond to add.
public abstract int countBonds()
public abstract Bond[] bondArray()
public abstract boolean isConnectedTo(Assembly s)
public abstract Chain chain()
public abstract boolean setChain(Chain chain)
chain
- chain to set.
public abstract Compound getCompound()
public abstract String getName()
public abstract char getLetterName()
public abstract int getSerialNum()
public abstract void setSerialNum(int serial)
serial
- assembly's serial number.public abstract char getICode()
public abstract void setICode(char icode)
icode
- assembly's icode.public abstract Atom getCAAtom()
public abstract Atom getMainAtom()
public abstract int countAtoms()
public abstract void selectAllAtoms(boolean val)
val
- if true -- select all atoms, if false -- deselect.public static int getAlignedAttribute()
public static int getHelixAttribute()
public static int getHelix3Attribute()
public static int getHelix4Attribute()
public static int getHelix5Attribute()
public static int getSheetAttribute()
public static int getTurnAttribute()
public static int getRegularAttribute()
public static int getGroupAttribute(int group_id)
public abstract boolean isAligned()
public abstract void setAligned(boolean val)
val
- assembly's alignment attribute.public abstract int getGroupId()
public abstract boolean setGroupId(int groupId)
public abstract boolean hasAttribute(int att)
public abstract String toString()
toString
in class Object
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