Class Sdf


  • public class Sdf
    extends java.lang.Object
    The Sdf class provides helper functions for dealing with the SDF file format.
    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      static interface  Sdf.OnMolecule  
    • Constructor Summary

      Constructors 
      Constructor Description
      Sdf()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Vector3[] getPositions​(java.lang.String sdfpath)
      Parses a SDF file to extract the positions of each atom.
      static void testFolder​(java.lang.String sdfbase, java.lang.String refbase, java.lang.String ext, Sdf.OnMolecule cb)
      Tests an entire pair of folders, one containing SDF files and the other containing reference files.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • Sdf

        public Sdf()
    • Method Detail

      • testFolder

        public static void testFolder​(java.lang.String sdfbase,
                                      java.lang.String refbase,
                                      java.lang.String ext,
                                      Sdf.OnMolecule cb)
        Tests an entire pair of folders, one containing SDF files and the other containing reference files. Each folder should contain either all SDF files or all reference files. There should be a corresponding reference file for each SDF file, and they should have the same name (excluding extension).
        Parameters:
        sdfbase - The base folder which contains all of the SDF files.
        refbase - The base folder which contains all of the reference files.
      • getPositions

        public static Vector3[] getPositions​(java.lang.String sdfpath)
        Parses a SDF file to extract the positions of each atom. Positions are extracted as an (X, Y, Z) Vector3 object.
        Parameters:
        sdfpath - The string path to the SDF file to be loaded.
        Returns:
        Returns an array of Vector3's which contain the X, Y, Z coordinates of each atom.