Uses of Interface org.biojava.bio.structure.Group (BioJava-1.5-beta API)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## Uses of Interface
org.biojava.bio.structure.Group

Packages that use Group
org.biojava.bio.structure | Interfaces and classes for protein structure (PDB).

Uses of Group in org.biojava.bio.structure

Subinterfaces of Group in org.biojava.bio.structure
`interface` | `AminoAcid` AminoAcid inherits most from Hetatom.

Classes in org.biojava.bio.structure that implement Group
`class` | `AminoAcidImpl` AminoAcid inherits most from Hetatom.
`class` | `HetatomImpl` Generic Implementation of a Group interface.
`class` | `NucleotideImpl` A nucleotide group is almost the same as a Hetatm group.

Methods in org.biojava.bio.structure that return Group
`Group` | `StructureImpl.findGroup(String chainName, String pdbResnum)`
`Group` | `Structure.findGroup(String chainId, String pdbResnum)` request a particular group from a structure.
`Group` | `StructureImpl.findGroup(String chainId, String pdbResnum, int modelnr)`
`Group` | `Structure.findGroup(String chainId, String pdbResnum, int modelnr)` request a particular group from a structure.
`Group` | `Chain.getGroup(int position)` return the amino acid at position X.
`Group` | `ChainImpl.getGroup(int position)` return the amino acid at position .
`Group` | `Chain.getGroupByPDB(String pdbresnum)` get a group by its PDB residue numbering.
`Group` | `ChainImpl.getGroupByPDB(String pdbresnum)`
`Group[]` | `Chain.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` get all groups that are located between two PDB residue numbers
`Group[]` | `ChainImpl.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)`
`Group` | `Atom.getParent()` Returns the parent Group of the Atom returns null if the referenced object is not Group
`Group` | `AtomImpl.getParent()`

Methods in org.biojava.bio.structure with parameters of type Group
`void` | `Chain.addGroup(Group group)` add a group to this chain.
`void` | `ChainImpl.addGroup(Group group)`
`static void` | `Calc.rotate(Group group, double[][] rotationmatrix)` rotate a structure .
`static void` | `Calc.rotate(Group group, Matrix m)` rotate a group object
`void` | `Atom.setParent(Group parent)` Sets the back-reference to its parent Group
`void` | `AtomImpl.setParent(Group parent)`
`static void` | `Calc.shift(Group group, Atom a)` shift a Group with a vector.

Constructors in org.biojava.bio.structure with parameters of type Group
`AtomIterator(Group g)` Constructs an AtomIterator object.
`StructureImpl(Group g)` construct a Structure object that only contains a single group

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES