Uses of Class
org.biojava.nbio.structure.io.FileParsingParameters

Packages that use FileParsingParameters

Package	Description
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.cif
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.

Uses of FileParsingParameters in org.biojava.nbio.structure.align.util

Fields in org.biojava.nbio.structure.align.util declared as FileParsingParameters

Modifier and Type	Field and Description
protected FileParsingParameters	AtomCache.params

Methods in org.biojava.nbio.structure.align.util that return FileParsingParameters

Modifier and Type	Method and Description
FileParsingParameters	AtomCache.getFileParsingParams()

Methods in org.biojava.nbio.structure.align.util with parameters of type FileParsingParameters

Modifier and Type	Method and Description
void	AtomCache.setFileParsingParams(FileParsingParameters params)

Uses of FileParsingParameters in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return FileParsingParameters

Modifier and Type	Method and Description
FileParsingParameters	StructureProvider.getFileParsingParameters() Get the parameters that should be used for file parsing
FileParsingParameters	LocalPDBDirectory.getFileParsingParameters()
FileParsingParameters	PDBFileParser.getFileParsingParameters()
FileParsingParameters	SandboxStyleStructureProvider.getFileParsingParameters()

Methods in org.biojava.nbio.structure.io with parameters of type FileParsingParameters

Modifier and Type	Method and Description
void	StructureProvider.setFileParsingParameters(FileParsingParameters params) Set the parameters that should be used for file parsing
void	LocalPDBDirectory.setFileParsingParameters(FileParsingParameters params)
void	PDBFileParser.setFileParsingParameters(FileParsingParameters params)
void	SandboxStyleStructureProvider.setFileParsingParameters(FileParsingParameters params)

Constructors in org.biojava.nbio.structure.io with parameters of type FileParsingParameters

Constructor and Description
BondMaker(Structure structure, FileParsingParameters params)

Uses of FileParsingParameters in org.biojava.nbio.structure.io.cif

Methods in org.biojava.nbio.structure.io.cif with parameters of type FileParsingParameters

Modifier and Type	Method and Description
static Structure	CifFileConverter.fromCifFile(org.rcsb.cif.model.CifFile cifFile, FileParsingParameters parameters) Convert CifFile to Structure.
static Structure	CifFileConverter.fromInputStream(InputStream inputStream, FileParsingParameters parameters) Convert InputStream to Structure.
static Structure	CifFileConverter.fromPath(Path path, FileParsingParameters parameters) Read data from a file and convert to Structure.

Uses of FileParsingParameters in org.biojava.nbio.structure.io.mmcif

Methods in org.biojava.nbio.structure.io.mmcif that return FileParsingParameters

Modifier and Type	Method and Description
FileParsingParameters	MMcifConsumer.getFileParsingParameters()
FileParsingParameters	ChemCompConsumer.getFileParsingParameters()
FileParsingParameters	MetalBondConsumer.getFileParsingParameters()
FileParsingParameters	SimpleMMcifConsumer.getFileParsingParameters()

Methods in org.biojava.nbio.structure.io.mmcif with parameters of type FileParsingParameters

Modifier and Type	Method and Description
void	MMcifConsumer.setFileParsingParameters(FileParsingParameters params)
void	ChemCompConsumer.setFileParsingParameters(FileParsingParameters params)
void	MetalBondConsumer.setFileParsingParameters(FileParsingParameters params)
void	SimpleMMcifConsumer.setFileParsingParameters(FileParsingParameters params)