Class SDFWriter

All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class SDFWriter extends DefaultChemObjectWriter
Writes MDL SD files ([Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]). A MDL SD file contains one or more molecules, complemented by properties.
Source code:
main
IO options:
NameQuestionDefault
WriteAromaticBondTypesShould aromatic bonds be written as bond type 4?false
WriteMajorIsotopesWrite atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C)true
writePropertiesShould molecule properties be written as non-structural datatrue
WriteQueryFormatValenciesShould valencies be written in the MDL Query format? (deprecated)false
TruncateLongDataTruncate long data files >200 charactersfalse
ProgramNameProgram name to write at the top of the molfile header, should be exactly 8 characters longCDK
ForceWriteAs2DCoordinatesShould coordinates always be written as 2D?false
WriteDefaultPropertiesWrite trailing zero's on atom/bond property blocks even if they're not used.true
writeV3000Write all records as V3000false
Belongs to CDK module:
io
Keywords:
file format, MDL SD file
  • Field Details

  • Constructor Details

    • SDFWriter

      public SDFWriter(BufferedWriter wtr)
      Create an SDfile writer that will output directly to the provided buffered writer.
      Parameters:
      wtr - writer
    • SDFWriter

      public SDFWriter(Writer wtr)
      Create an SDfile writer, the provided writer is buffered if it's not an instance of BufferedWriter. For flush control etc please create with BufferedWriter.
      Parameters:
      wtr - writer
    • SDFWriter

      public SDFWriter(OutputStream output)
      Create an SDfile writer, the provided output stream is wrapped in a UTF-8 buffered writer.
      Parameters:
      output - out stream
    • SDFWriter

      public SDFWriter()
    • SDFWriter

      public SDFWriter(Writer out, Set<String> propertiesToWrite)
      Constructs a new SDFWriter that writes to the given Writer.
      Parameters:
      out - The Writer to write to
    • SDFWriter

      public SDFWriter(OutputStream output, Set<String> propertiesToWrite)
      Constructs a new SdfWriter that can write to a given OutputStream.
      Parameters:
      output - The OutputStream to write to
    • SDFWriter

      public SDFWriter(Set<String> propertiesToWrite)
      Writes SD-File to a String including the given properties
  • Method Details