PIP.Core
Class Assembly

java.lang.Object
  PIP.Core.Assembly

All Implemented Interfaces:

java.io.Serializable, MSDID

public class Assembly
extends java.lang.Object
implements MSDID, java.io.Serializable

This is a PQS generated biological unit. A PDB Entry can contain one or more Assemblies.

See Also:

Serialized Form

Constructor Summary

Assembly(int id)

Method Summary

void	addChain(Chain ch)
void	addDomain(Domain d)
int	getAssemblySerial()
Chain	getChain(char chainCodeOneLetter)
Chain	getChain(int chainId)
Chain	getChain(java.lang.String chainCode)
java.util.List<Chain>	getChains()
java.util.List<DomainInteraction>	getDomainInteractions()
java.util.List<DomainInteraction>	getDomainInteractions(java.lang.Class familyClass)
java.util.List<DomainInteraction>	getDomainInteractionsWithRNAAndXPacking()
java.util.List<DomainInteraction>	getDomainInteractionsWithRNAAndXPacking(java.lang.Class familyClass)
java.util.List<Domain>	getDomains()
java.util.List<Domain>	getDomains(java.lang.Class familyClass)
java.util.List<Domain>	getDomainsIncludingThoseWithNucAcids()
java.util.List<Domain>	getDomainsIncludingThoseWithNucAcids(java.lang.Class familyClass)
Entry	getEntry()
java.util.List<DomainInteraction>	getInteractions()
java.util.List<DomainInteraction>	getInteractions(java.lang.Class familyClass)
int	getMSDID()
boolean	isCrystalPacking() Kim Henrick decided to include assemblies which are due to crystal packing according to PQS but may have interesting properties.
void	setChains(java.util.List<Chain> chains)
void	setCrystalPacking(boolean crystalPacking)
void	setDomainInteractions(java.util.List<DomainInteraction> domainInteractions)
void	setEntry(Entry entry)
void	setMSDID(int id)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Assembly

public Assembly(int id)

Method Detail

getInteractions

public java.util.List<DomainInteraction> getInteractions()

Returns:

all domain interaction observed within the Assembly

getInteractions

public java.util.List<DomainInteraction> getInteractions(java.lang.Class familyClass)

Parameters:

familyClass - e.g. Scop.class, Pfam.class or Cath.Class

Returns:

the interactions of the familyClass

setChains

public void setChains(java.util.List<Chain> chains)

isCrystalPacking

public boolean isCrystalPacking()

Kim Henrick decided to include assemblies which are due to crystal packing according to PQS but may have interesting properties. Most of the time only use assemblies where crystalPacking is false otherwise you will be using non valid assemblies.

Returns:

true if the Assembly is considered by PQS to be a non biologically relevant Assembly.

setCrystalPacking

public void setCrystalPacking(boolean crystalPacking)

Parameters:

crystalPacking - should be true if the Assembly is non biologically relevant

getEntry

public Entry getEntry()

setEntry

public void setEntry(Entry entry)

getAssemblySerial

public int getAssemblySerial()

Returns:

the position of the Assembly in its Entry list of Assemblies

getChain

public Chain getChain(java.lang.String chainCode)

Parameters:

chainCode -

Returns:

the chain which has the chainCode passed in

getChain

public Chain getChain(int chainId)

Parameters:

chainId -

Returns:

the chain which has the chainId passed in

getChain

public Chain getChain(char chainCodeOneLetter)

addChain

public void addChain(Chain ch)

getChains

public java.util.List<Chain> getChains()

getDomains

public java.util.List<Domain> getDomains()

getDomainsIncludingThoseWithNucAcids

public java.util.List<Domain> getDomainsIncludingThoseWithNucAcids()

addDomain

public void addDomain(Domain d)

getDomains

public java.util.List<Domain> getDomains(java.lang.Class familyClass)

getDomainsIncludingThoseWithNucAcids

public java.util.List<Domain> getDomainsIncludingThoseWithNucAcids(java.lang.Class familyClass)

Parameters:

familyClass -

Returns:

A list of all the domains within the assmebly for a given family Class including domains which contain nucleic acids.

getDomainInteractions

public java.util.List<DomainInteraction> getDomainInteractions()

getDomainInteractions

public java.util.List<DomainInteraction> getDomainInteractions(java.lang.Class familyClass)

getDomainInteractionsWithRNAAndXPacking

public java.util.List<DomainInteraction> getDomainInteractionsWithRNAAndXPacking()

getDomainInteractionsWithRNAAndXPacking

public java.util.List<DomainInteraction> getDomainInteractionsWithRNAAndXPacking(java.lang.Class familyClass)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getMSDID

public int getMSDID()

Specified by:

getMSDID in interface MSDID

setMSDID

public void setMSDID(int id)

Specified by:

setMSDID in interface MSDID

setDomainInteractions

public void setDomainInteractions(java.util.List<DomainInteraction> domainInteractions)