Uses of Interface
org.biojava.nbio.structure.Bond

Packages that use Bond

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

Uses of Bond in org.biojava.nbio.structure

Classes in org.biojava.nbio.structure that implement Bond

Modifier and Type	Class and Description
class	BondImpl A simple bond -- it stores information about two atoms as well as information about its bond order.

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

Modifier and Type	Method and Description
List<Bond>	Atom.getBonds() Get all Bonds this atom is part of.
List<Bond>	AtomImpl.getBonds() Get all Bonds this atom is part of.
List<Bond>	StructureImpl.getSSBonds() Get the list of disulfide Bonds as they have been defined in the PDB files
List<Bond>	Structure.getSSBonds() Get the list of disulfide Bonds as they have been defined in the PDB files

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

Modifier and Type	Method and Description
void	Atom.addBond(Bond bond) Add a bond
void	AtomImpl.addBond(Bond bond)
void	StructureImpl.addSSBond(Bond ssbond) Adds a single disulfide Bond to this structure
void	Structure.addSSBond(Bond ssbond) Add a single disulfide Bond to this structure

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

Modifier and Type	Method and Description
void	Atom.setBonds(List<Bond> bonds) Sets the bonds
void	AtomImpl.setBonds(List<Bond> bonds) Sets the bonds
void	StructureImpl.setSSBonds(List<Bond> ssbonds) Set the list of SSBonds for this structure
void	Structure.setSSBonds(List<Bond> ssbonds) Set the list of SSBonds for this structure

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

Methods in org.biojava.nbio.structure.io with parameters of type Bond

Modifier and Type	Method and Description
static SSBondImpl	SSBondImpl.toSsBond(Bond bond) Converts the given Bond object into a SSBondImpl.

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

Modifier and Type	Method and Description
static List<SSBondImpl>	SSBondImpl.getSsBondListFromBondList(List<Bond> bonds)