Package ambit2.core.io

Input output support.

See: Description

Interface Summary

Interface	Description
ICompoundImageTools
IInputState	Status of the input reader.
IOutputState	Status of the output writer.
IRawReader<T>

Class Summary

Class	Description
ArffWriter
DelimitedFileFormat	File format for delimited files
DelimitedFileReader
DelimitedFileWriter	Writes delimited files
ECHAPreregistrationListReader	Reads preregistration list in XML format as in http://apps.echa.europa.eu/preregistered/prsDownload.aspx
FileInputState	Use FileInputState.getReader(InputStream, String) to get a reader of the right type.
FileOutputState	Use FileOutputState.getWriter(OutputStream, String) to get a writer of the right type.
FileState	This is to be able to verify if a file has changed since it has been last processed by FileBatchProcessing
FilesWithHeaderWriter
FileWithHeaderWriter
FilteredMDLReader
I5ReaderSimple	IUCLID5 .i5d files support http://iuclid.eu/ Reads ReferenceSubstances only.
InteractiveIteratingMDLReader	A descendant of IteratingMDLReader able to ask for type of each SDF property
IteratingChemObjectReaderWrapper	A wrapper for DefaultChemObjectReader.
IteratingDelimitedFileReader	Iterating reader for delimited files.
IteratingDelimitedFileReaderComplexHeader<COLUMN>
IteratingFileReader	A wrapper for all file readers.
IteratingFilesWithHeaderReader<COLUMN>
IteratingFolderReader<T,ItemReader extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader>
IteratingMolFolderReader
IteratingXLSReader	Reads XLS files.
MDLReader	Reads a molecule from the original MDL MOL or SDF file .
MolPropertiesIOSetting	An IOSetting descendant to provide means for transforming property names.
MultiNewlineFilterReader
PDFWriter	Exporting set of structures as PDF file.
QuotedTokenizer	The QuotedTokenizer class is used to break a string into simple tokens or quoted tokens.
RawIteratingCSVReader	CSV parser implemented using CSVParser
RawIteratingFolderReader
RawIteratingMOLReader
RawIteratingReader<T>
RawIteratingSDFReader
RawIteratingWrapper<R extends org.openscience.cdk.io.iterator.IIteratingChemObjectReader>
SDFBrokenLineTerminationConverter
SGroupMDL2000Helper	Helper for MDL SGroups
SimpleIOListener
StringArrayHeader<CATEGORIES>
ToxcastAssayReader	ToxCast assay data are TXT tab delimited files. Lines starting with # are comments. The column SOURCE_NAME_SID contains DSSTOX_RID (DSSTOX record ID) , prependend with "DSSTOX_" string, e.g.
ToxcastFileFormat	Toxcast Assay files are tab delimited files
ToXMLReaderSimple
XLSFileFormat	Microsoft Excel XLS file format.
XLSFileWriter
ZipReader<OPTIONS>

Enum Summary

Enum	Description
ECHAPreregistrationListReader.echa_tags
FileState._FILE_TYPE
I5ReaderSimple.i5_refs_attr
I5ReaderSimple.i5_tags
RawIteratingFolderReader.FileNameMode
SGroupMDL2000Helper.SGROUP_CONNECTIVITY
SGroupMDL2000Helper.SGROUP_LINE
SGroupMDL2000Helper.SGROUP_POLYMER_TYPE
SGroupMDL2000Helper.SGROUP_TYPE
ToXMLReaderSimple.toxml_attributes
ToXMLReaderSimple.toxml_names
ToXMLReaderSimple.toxml_quantity_types
ToXMLReaderSimple.toxml_tags
ToXMLReaderSimple.toxml_tags_level1	toxml.xsd 3.0.8

Package ambit2.core.io Description

Input output support. This is mainly an extension of The CDK io package in order to support .CSV and .TXT files.

CSV files and tab delimited .TXT files can be read/written by MS Excel :)

A column with "SMILES" heading is mandatory for CSV/TXT files in order the structure to be read. All other fields are optional, will be read as molecule properties and displayed as such.