Class FileUtilities


  • public class FileUtilities
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      FileUtilities()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void buildSdfFromTSV​(java.lang.String tsvFileName)  
      static int countUniqueCompounds​(java.lang.String sdfFileName)  
      static void divideSdfFile​(java.lang.String sdfFileName, int limit)  
      static org.openscience.cdk.interfaces.IAtomContainerSet parseSdf​(java.lang.String sdfFileName)  
      static org.openscience.cdk.interfaces.IAtomContainerSet parseSdfAndAddTitles​(java.lang.String sdfFileName, org.openscience.cdk.inchi.InChIGeneratorFactory igf)  
      static void saveAtomContainerSetToCSV​(org.openscience.cdk.interfaces.IAtomContainerSet products, java.lang.String outputFileName)  
      static void saveAtomContainerSetToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers, java.lang.String outputFileName)  
      static java.lang.String saveAtomContainersToString​(org.openscience.cdk.interfaces.IAtomContainerSet containers)  
      static java.lang.String saveAtomContainerToString​(org.openscience.cdk.interfaces.IAtomContainer container)  
      • Methods inherited from class java.lang.Object

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

      • FileUtilities

        public FileUtilities()
    • Method Detail

      • parseSdf

        public static org.openscience.cdk.interfaces.IAtomContainerSet parseSdf​(java.lang.String sdfFileName)
                                                                         throws java.io.IOException
        Throws:
        java.io.IOException
      • parseSdfAndAddTitles

        public static org.openscience.cdk.interfaces.IAtomContainerSet parseSdfAndAddTitles​(java.lang.String sdfFileName,
                                                                                            org.openscience.cdk.inchi.InChIGeneratorFactory igf)
                                                                                     throws org.openscience.cdk.exception.CDKException,
                                                                                            java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • countUniqueCompounds

        public static int countUniqueCompounds​(java.lang.String sdfFileName)
                                        throws org.openscience.cdk.exception.CDKException,
                                               java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • divideSdfFile

        public static void divideSdfFile​(java.lang.String sdfFileName,
                                         int limit)
                                  throws org.openscience.cdk.exception.CDKException,
                                         java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • buildSdfFromTSV

        public static void buildSdfFromTSV​(java.lang.String tsvFileName)
                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • saveAtomContainerSetToCSV

        public static void saveAtomContainerSetToCSV​(org.openscience.cdk.interfaces.IAtomContainerSet products,
                                                     java.lang.String outputFileName)
                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • saveAtomContainerSetToSDF

        public static void saveAtomContainerSetToSDF​(org.openscience.cdk.interfaces.IAtomContainerSet containers,
                                                     java.lang.String outputFileName)
                                              throws org.openscience.cdk.exception.CDKException,
                                                     java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • saveAtomContainersToString

        public static java.lang.String saveAtomContainersToString​(org.openscience.cdk.interfaces.IAtomContainerSet containers)
                                                           throws org.openscience.cdk.exception.CDKException,
                                                                  java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException
      • saveAtomContainerToString

        public static java.lang.String saveAtomContainerToString​(org.openscience.cdk.interfaces.IAtomContainer container)
                                                          throws org.openscience.cdk.exception.CDKException,
                                                                 java.io.IOException
        Throws:
        org.openscience.cdk.exception.CDKException
        java.io.IOException