org.rcsb.mmtf.dataholders

Class Entity

java.lang.Object

org.rcsb.mmtf.dataholders.Entity

All Implemented Interfaces:

Serializable

public class Entity
extends Object
implements Serializable

Entity level data store. An Entity is defined as each of the distinct molecules present in a PDB structure. It can be of type polymer, non-polymer, macrolide or water.

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Entity()

Method Summary

Modifier and Type	Method and Description
int[]	getChainIndexList() Get a list of integers specifying the indices of the chains related to this entity.
String	getDescription() Get the description of the entity.
String	getSequence() Get the sequence of the entity.
String	getType() The type of this Entity, one of: polymer, non-polymer, macrolide or water.
void	setChainIndexList(int[] chainIndexList) Set a list of integers specifying the indices of the chains related to this entity.
void	setDescription(String description) Set the description of this entity.
void	setSequence(String entitySequence) Set the sequence of the entity.
void	setType(String type) Set the type of the entity, one of: polymer, non-polymer, macrolide or water.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Entity

public Entity()

Method Detail

getDescription

public String getDescription()

Get the description of the entity.

Returns:

a strign describing the entity, e.g. The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.

setDescription

public void setDescription(String description)

Set the description of this entity.

Parameters:

description - the string describing the entity.

getType

public String getType()

The type of this Entity, one of: polymer, non-polymer, macrolide or water.

Returns:

the type of entity as a string.

setType

public void setType(String type)

Set the type of the entity, one of: polymer, non-polymer, macrolide or water.

Parameters:

type - the string defining the type of entity.

getChainIndexList

public int[] getChainIndexList()

Get a list of integers specifying the indices of the chains related to this entity.

Returns:

a list of integers - specifying the indices of the chains related to this entity.

setChainIndexList

public void setChainIndexList(int[] chainIndexList)

Set a list of integers specifying the indices of the chains related to this entity.

Parameters:

chainIndexList - a list of integers - specifying the indices of the chains related to this entity.

getSequence

public String getSequence()

Get the sequence of the entity.

Returns:

the entity sequence as a string

setSequence

public void setSequence(String entitySequence)

Set the sequence of the entity.

Parameters:

entitySequence - the entity sequence as a string.