Package de.bioforscher.singa.structure.parser.pdb.structures

Interface Summary

Interface	Description
StructureParser.AdditionalLocalSourceStep	Using a local pdb installation, additional source steps might be used.
StructureParser.IdentifierStep	After selecting the source, the identifer(s) to parse can be chosen.
StructureParser.LocalSourceStep	Select a local source to parse from.
StructureParser.MultiBranchStep	Initiates the structure reduction steps for multiple structures.
StructureParser.MultiChainStep	Initiates the selection of chains, if multiple structures have been chosen.
StructureParser.SingleBranchStep	Initiates the structure reduction steps for a single structure.
StructureParser.SingleChainStep	Initiates the selection of chains, if a single structure has been chosen.
StructureSelector.AminoAcidAtomStep
StructureSelector.AtomContainerAtomStep
StructureSelector.AtomStep
StructureSelector.ChainStep
StructureSelector.NucleotideAtomStep
StructureSelector.ResidueStep
StructureSelector.SelectStep
StructureSelector.StructuralModelStep

Class Summary

Class	Description
MmtfReducer
StructureCollector	The actual processing of pdb files.
StructureParser	Parses structures in pdb format.
StructureParser.LocalPDB	This class represents a local PDB installation.
StructureParser.MultiParser	The MultiParser performs parsing of multiple structures from a single source.
StructureParser.Reducer	This class remembers what general restrictions are to be applied during the parsing.
StructureParser.SingleParser	This parser should be used if you require only a single structure.
StructureParserOptions	Options for faster or more detailed parsing.
StructureRepresentation	This class represents any AtomContainer in a pdb format, ready to be written to a file.
StructureSelector
StructureSelector.Selector
StructureWriter	A class to write Structures objects to PDB format.

Enum Summary

Enum	Description
SourceLocation	The location the files should be parsed from.
StructureParserOptions.Setting	Settings that can be passed to the Options.

Exception Summary

Exception	Description
StructureParserException	Exceptions encountered during parsing of molecular structures.