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See:
Description
Interface Summary | |
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AminoAcid |
A Group that represents an AminoAcid. |
Atom | A simple interface for an Atom. |
Chain | Defines the interface for a Chain. |
Group | This is the data structure for a single Group of atoms. |
PDBRecord | An interface implemented by all classes that represent PDB records |
Structure | Interface for a structure object. |
Class Summary | |
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AminoAcidImpl | AminoAcid inherits most from Hetatom. |
AtomImpl | Implementation of an Atom of a PDB file. |
AtomIterator | an iterator over all atoms of a structure / group. |
Author | Describes author attributes for author information in a PDB file. |
Bond | Simple bond - it's just an edge/vertex for two Atom nodes. |
Calc | utility operations on Atoms, AminoAcids, etc. |
ChainImpl | A Chain in a PDB file. |
Compound | Created by IntelliJ IDEA. |
DBRef | A class to represent database cross references. |
GroupIterator | An iterator over all groups of a structure. |
GroupType | contains only the static declaration of which types of Groups are available |
HetatomImpl | Generic Implementation of a Group interface. |
JournalArticle | PDB-specific |
Mutator | A class that can change one amino acid to another. |
NucleotideImpl | A nucleotide group is almost the same as a Hetatm group. |
PDBCrystallographicInfo | A class to hold crystallographic information about a PDB structure. |
PDBHeader | A class that contains PDB Header information. |
PDBStatus | Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure. |
ResidueNumber | Everything that is needed to uniquely describe a residue position |
Site | Holds the data of sites presented in PDB files. |
SSBond | A simple bean to store disulfid bridge information, the SSBOND records in the PDB files. |
StandardAminoAcid | A class that provides a set of standard amino acids. |
StructureImpl | Implementation of a PDB Structure. |
StructureTools | A class that provides some tool methods. |
SVDSuperimposer | A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class... |
Enum Summary | |
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BondType | Work in progress - NOT final! |
Element | Element is an enumeration of the elements of the periodic table. |
ElementType | ElementType is an enumeration of the types of elements found in the periodic table. |
PDBStatus.Status | Represents the status of PDB IDs. |
Exception Summary | |
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StructureException | An exception during the parsing of a PDB file. |
UnknownPdbAminoAcidException | An exception for use during translating amino acids in a PDB file. |
Interfaces and classes for protein structure (PDB).
Structure | Chain | Group | AtomLearn more how to work with groups.
For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure
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