Uses of Interface
org.openscience.cdk.interfaces.IBioPolymer

Packages that use IBioPolymer

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.interfaces
org.openscience.cdk.protein
org.openscience.cdk.protein.data
org.openscience.cdk.silent
org.openscience.cdk.tools

Uses of IBioPolymer in org.openscience.cdk

Classes in org.openscience.cdk that implement IBioPolymer

Modifier and Type	Class and Description
class	BioPolymer A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.

Methods in org.openscience.cdk that return IBioPolymer

Modifier and Type	Method and Description
IBioPolymer	BioPolymer.clone()

Uses of IBioPolymer in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IBioPolymer

Modifier and Type	Class and Description
class	DebugBioPolymer Debugging data class.
class	DebugPDBPolymer Debugging data class.

Methods in org.openscience.cdk.debug that return IBioPolymer

Modifier and Type	Method and Description
IBioPolymer	DebugBioPolymer.clone() Clones this AtomContainer object and its content.

Uses of IBioPolymer in org.openscience.cdk.interfaces

Subinterfaces of IBioPolymer in org.openscience.cdk.interfaces

Modifier and Type	Interface and Description
interface	IPDBPolymer A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.

Methods in org.openscience.cdk.interfaces that return IBioPolymer

Modifier and Type	Method and Description
IBioPolymer	IBioPolymer.clone() Returns a deep clone of this IChemObject.

Uses of IBioPolymer in org.openscience.cdk.protein

Methods in org.openscience.cdk.protein that return IBioPolymer

Modifier and Type	Method and Description
IBioPolymer	ProteinPocketFinder.getProtein()

Methods in org.openscience.cdk.protein with parameters of type IBioPolymer

Modifier and Type	Method and Description
void	ProteinPocketFinder.setProtein(IBioPolymer protein)

Constructors in org.openscience.cdk.protein with parameters of type IBioPolymer

Constructor and Description
ProteinPocketFinder(IBioPolymer protein, double[][][] grid)

Uses of IBioPolymer in org.openscience.cdk.protein.data

Classes in org.openscience.cdk.protein.data that implement IBioPolymer

Modifier and Type	Class and Description
class	PDBPolymer An entry in the PDB database.

Uses of IBioPolymer in org.openscience.cdk.silent

Methods in org.openscience.cdk.silent that return IBioPolymer

Modifier and Type	Method and Description
IBioPolymer	BioPolymer.clone()

Uses of IBioPolymer in org.openscience.cdk.tools

Methods in org.openscience.cdk.tools that return IBioPolymer

Modifier and Type	Method and Description
static IBioPolymer	ProteinBuilderTool.addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo) Builds a protein by connecting a new amino acid at the C-terminus of the given strand.
static IBioPolymer	ProteinBuilderTool.addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo) Builds a protein by connecting a new amino acid at the N-terminus of the given strand.
static IBioPolymer	ProteinBuilderTool.createProtein(String sequence) Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.
static IBioPolymer	ProteinBuilderTool.createProtein(String sequence, IChemObjectBuilder builder) Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.

Methods in org.openscience.cdk.tools with parameters of type IBioPolymer

Modifier and Type	Method and Description
static IBioPolymer	ProteinBuilderTool.addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo) Builds a protein by connecting a new amino acid at the C-terminus of the given strand.
static IBioPolymer	ProteinBuilderTool.addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo) Builds a protein by connecting a new amino acid at the N-terminus of the given strand.