Uses of Class
org.biojava.nbio.structure.EntityInfo

Packages that use EntityInfo

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of EntityInfo in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return EntityInfo

Modifier and Type	Method and Description
EntityInfo	StructureImpl.getCompoundById(int molId) Request a particular entity by its entity id (mol id in legacy PDB format)
EntityInfo	Structure.getCompoundById(int entityId) Deprecated. use Structure.getEntityById(int) instead
EntityInfo	StructureImpl.getEntityById(int entityId) Request a particular entity by its entity id (mol id in legacy PDB format)
EntityInfo	Structure.getEntityById(int entityId) Request a particular entity by its entity id (mol id in legacy PDB format)
EntityInfo	Chain.getEntityInfo() Returns the EntityInfo for this chain.
EntityInfo	ChainImpl.getEntityInfo() Returns the EntityInfo for this chain.

Methods in org.biojava.nbio.structure that return types with arguments of type EntityInfo

Modifier and Type	Method and Description
List<EntityInfo>	StructureImpl.getEntityInfos() Get all the EntityInfo for this Structure.
List<EntityInfo>	Structure.getEntityInfos() Get all the EntityInfo for this Structure.

Methods in org.biojava.nbio.structure with parameters of type EntityInfo

Modifier and Type	Method and Description
void	StructureImpl.addEntityInfo(EntityInfo entityInfo) Add an EntityInfo to this Structure
void	Structure.addEntityInfo(EntityInfo entityInfo) Add an EntityInfo to this Structure
void	Chain.setEntityInfo(EntityInfo entityInfo) Sets the Entity information
void	ChainImpl.setEntityInfo(EntityInfo mol) Sets the Entity information

Method parameters in org.biojava.nbio.structure with type arguments of type EntityInfo

Modifier and Type	Method and Description
void	StructureImpl.setEntityInfos(List<EntityInfo> molList) Set the EntityInfo
void	Structure.setEntityInfos(List<EntityInfo> molList) Set the EntityInfo

Constructors in org.biojava.nbio.structure with parameters of type EntityInfo

Constructor and Description
EntityInfo(EntityInfo c) Constructs a new EntityInfo copying all data from the given one but not setting the Chains

Uses of EntityInfo in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact that return types with arguments of type EntityInfo

Modifier and Type	Method and Description
Pair<EntityInfo>	StructureInterface.getParentCompounds() Finds the parent compounds by looking up the references of first atom of each side of this interface

Uses of EntityInfo in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return types with arguments of type EntityInfo

Modifier and Type	Method and Description
static List<EntityInfo>	EntityFinder.findPolyEntities(List<List<Chain>> polyModels) Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.

Method parameters in org.biojava.nbio.structure.io with type arguments of type EntityInfo

Modifier and Type	Method and Description
static void	EntityFinder.createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels, List<List<Chain>> waterModels, List<EntityInfo> entities) Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.