Uses of Class
org.episteme.natural.biology.Protein

Packages that use Protein

Package	Description
org.episteme.natural.biology.loaders
org.episteme.natural.biology.loaders.biopax	BioPAX loader for biological pathways and networks.
org.episteme.natural.biology.loaders.pdbml	PDBML loader for Protein Data Bank macromolecular structures.

Uses of Protein in org.episteme.natural.biology.loaders

Subclasses with type arguments of type Protein in org.episteme.natural.biology.loaders

Modifier and Type	Class	Description
class	PDBReader	Protein Data Bank (PDB) loader and exporter.
class	PDBWriter	Writer for PDB files.

Methods in org.episteme.natural.biology.loaders that return Protein

Modifier and Type	Method	Description
protected Protein	PDBReader.loadFromSource(String path)
static Protein	PDBParser.parse(String pdbContent, String pdbId)	Parses PDB content into a Protein object.

Methods in org.episteme.natural.biology.loaders that return types with arguments of type Protein

Modifier and Type	Method	Description
Class<Protein>	PDBReader.getResourceType()
Class<Protein>	PDBWriter.getResourceType()

Methods in org.episteme.natural.biology.loaders with parameters of type Protein

Modifier and Type	Method	Description
void	PDBWriter.save(Protein protein, String destination)

Uses of Protein in org.episteme.natural.biology.loaders.biopax

Methods in org.episteme.natural.biology.loaders.biopax that return Protein

Modifier and Type	Method	Description
Protein	BioPAXBridge.convertProtein(BioPAXPhysicalEntity entity)	Converts BioPAX protein to Episteme Protein.

Uses of Protein in org.episteme.natural.biology.loaders.pdbml

Methods in org.episteme.natural.biology.loaders.pdbml that return Protein

Modifier and Type	Method	Description
Protein	PDBMLBridge.toProtein(PDBMLStructure pdbModel)	Converts PDBML structure to Episteme Protein.