Package ambit2.core.io

Input output support.

See:
Description

Interface Summary

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

Class Summary

CompoundImageTools	Generates BufferedImage from smiles or compound.
DelimitedFileFormat	File format for delimited files
DelimitedFileReader	Reads delimited files (CSV, TXT)
DelimitedFileWriter	Writes delimited files
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
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.
IteratingFileReader	A wrapper for all file readers.
IteratingFilesWithHeaderReader
IteratingFolderReader<T,ItemReader extends IIteratingChemObjectReader>
IteratingMolFolderReader
IteratingXLSReader	Reads XLS files.
MDLReader	Reads a molecule from the original MDL MOL or SDF file {cdk.cite DAL92}.
MDLV2000ReaderExtended	Supports SGroups.
MDLWriter	Copied here from CDK source tree in order to handle the aromatic bond issue (this code writes 4 as aromatic bond code); until a proper fix is available.
MolPropertiesIOSetting	An IOSetting descendant to provide means for transforming property names.
MultiNewlineFilterReader
MyIteratingMDLReader	Copied here (with corrections)until Bug 1758372 in CDK is fixed.
PDFWriter	Exporting set of structures as PDF file.
RandomAccessReader	Random access to text files of compounds.
RandomAccessSDFReader	Random access of SDF file.
RawIteratingFolderReader
RawIteratingMOLReader
RawIteratingReader<T>
RawIteratingSDFReader
RawIteratingWrapper<R extends IIteratingChemObjectReader>
ReaderFactoryExtended
SDFBrokenLineTerminationConverter
SGroupMDL2000Helper	Helper for MDL SGroups
SimpleIOListener
XLSFileFormat	Microsoft Excel XLS file format.
XLSFileWriter

Enum Summary

SGroupMDL2000Helper.SGROUP_CONNECTIVITY
SGroupMDL2000Helper.SGROUP_LINE
SGroupMDL2000Helper.SGROUP_POLYMER_TYPE
SGroupMDL2000Helper.SGROUP_TYPE

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.