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

Packages that use IMonomer

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.interfaces
org.openscience.cdk.io.cml
org.openscience.cdk.libio.cml
org.openscience.cdk.protein.data
org.openscience.cdk.silent

Uses of IMonomer in org.openscience.cdk

Classes in org.openscience.cdk that implement IMonomer

Modifier and Type	Class	Description
class	AminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
class	Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.

Methods in org.openscience.cdk that return IMonomer

Modifier and Type	Method	Description
IMonomer	Monomer.clone()	Clones this IChemObject.
IMonomer	BioPolymer.getMonomer(String monName, String strandName)	Retrieves a Monomer object by specifying its name.
IMonomer	Polymer.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.
IMonomer	Strand.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.

Methods in org.openscience.cdk that return types with arguments of type IMonomer

Modifier and Type	Method	Description
Map<String,IMonomer>	Strand.getMonomers()	Returns a hashtable containing the monomers in the strand.

Methods in org.openscience.cdk with parameters of type IMonomer

Modifier and Type	Method	Description
void	BioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	Polymer.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	Strand.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specific Monomer.

Uses of IMonomer in org.openscience.cdk.debug

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

Modifier and Type	Class	Description
class	DebugAminoAcid	Debugging data class.
class	DebugMonomer	Debugging data class.
class	DebugPDBMonomer	Debugging data class.

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

Modifier and Type	Method	Description
IMonomer	DebugMonomer.clone()	Clones this IChemObject.
IMonomer	DebugBioPolymer.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.
IMonomer	DebugBioPolymer.getMonomer(String monName, String strandName)	Retrieves a Monomer object by specifying its name.
IMonomer	DebugPolymer.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.
IMonomer	DebugStrand.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.

Methods in org.openscience.cdk.debug that return types with arguments of type IMonomer

Modifier and Type	Method	Description
Map<String,IMonomer>	DebugStrand.getMonomers()	Returns a hashtable containing the monomers in the strand.

Methods in org.openscience.cdk.debug with parameters of type IMonomer

Modifier and Type	Method	Description
void	DebugBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	DebugBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	DebugPolymer.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	DebugStrand.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specific Monomer.

Uses of IMonomer in org.openscience.cdk.interfaces

Subinterfaces of IMonomer in org.openscience.cdk.interfaces

Modifier and Type	Interface	Description
interface	IAminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
interface	IPDBMonomer	Represents the idea of an protein monomer as found in PDB files.

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

Modifier and Type	Method	Description
IMonomer	IMonomer.clone()	Returns a deep clone of this IChemObject.
IMonomer	IBioPolymer.getMonomer(String monName, String strandName)	Retrieve a Monomer object by specifying its name.
IMonomer	IPolymer.getMonomer(String cName)	Retrieve a Monomer object by specifying its name.
IMonomer	IStrand.getMonomer(String cName)	Retrieve a Monomer object by specifying its name.

Methods in org.openscience.cdk.interfaces that return types with arguments of type IMonomer

Modifier and Type	Method	Description
Map<String,IMonomer>	IStrand.getMonomers()	Returns the monomers in this strand.

Methods in org.openscience.cdk.interfaces with parameters of type IMonomer

Modifier and Type	Method	Description
void	IBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	IPDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	IPolymer.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	IStrand.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specific Monomer.

Uses of IMonomer in org.openscience.cdk.io.cml

Fields in org.openscience.cdk.io.cml declared as IMonomer

Modifier and Type	Field	Description
protected IMonomer	CMLCoreModule.currentMonomer

Uses of IMonomer in org.openscience.cdk.libio.cml

Methods in org.openscience.cdk.libio.cml with parameters of type IMonomer

Modifier and Type	Method	Description
org.xmlcml.cml.element.CMLMolecule	Convertor.cdkMonomerToCMLMolecule(IMonomer monomer)

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

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

Modifier and Type	Class	Description
class	PDBMonomer	Represents the idea of an monomer as used in PDB files.

Methods in org.openscience.cdk.protein.data with parameters of type IMonomer

Modifier and Type	Method	Description
void	PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
void	PDBStrand.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.

Uses of IMonomer in org.openscience.cdk.silent

Classes in org.openscience.cdk.silent that implement IMonomer

Modifier and Type	Class	Description
class	AminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
class	Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
class	PDBMonomer	Represents the idea of an monomer as used in PDB files.

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

Modifier and Type	Method	Description
IMonomer	Monomer.clone()	Clones this IChemObject.
IMonomer	BioPolymer.getMonomer(String monName, String strandName)	Retrieves a Monomer object by specifying its name.
IMonomer	Polymer.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.
IMonomer	Strand.getMonomer(String cName)	Retrieves a Monomer object by specifying its name.

Methods in org.openscience.cdk.silent that return types with arguments of type IMonomer

Modifier and Type	Method	Description
Map<String,IMonomer>	Strand.getMonomers()	Returns a hashtable containing the monomers in the strand.

Methods in org.openscience.cdk.silent with parameters of type IMonomer

Modifier and Type	Method	Description
void	BioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	PDBPolymer.addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
void	Polymer.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	Strand.addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specific Monomer.