Package ambit2.core.io

Package class diagram 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.