Class AtomTypeList


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

      Constructors 
      Constructor Description
      AtomTypeList​(int mode)
      Creates an empty AtomTypeList, which must be populated by multiply calling processMolecule() and finally calling finalizeProcessMolecules() once.
      AtomTypeList​(java.lang.String filename, int mode)
      Creates a new AtomTypeList from a given file using the given mode.
    • Constructor Detail

      • AtomTypeList

        public AtomTypeList​(int mode)
        Creates an empty AtomTypeList, which must be populated by multiply calling processMolecule() and finally calling finalizeProcessMolecules() once.
        Parameters:
        mode -
      • AtomTypeList

        public AtomTypeList​(java.lang.String filename,
                            int mode)
                     throws java.lang.Exception
        Creates a new AtomTypeList from a given file using the given mode. If the the filename references a .typ file, then the mode is checked, whether it matches the file's content. If the the filename references a compound file, then the molecules are parsed and a new AtomTypeList is created reflecting the all contained atom types.
        Parameters:
        filename - either .typ file or a .dwar or .sdf compound file
        mode -
        Throws:
        java.lang.Exception
    • Method Detail

      • finalizeProcessMolecules

        public void finalizeProcessMolecules()
      • calculateProbabilities

        public void calculateProbabilities()
      • writeTypeFile

        public void writeTypeFile​(java.lang.String filename)
      • writeTextFile

        public void writeTextFile​(java.lang.String textfilename,
                                  int mode)
        Writes this AtomTypeList into a TAB-delimited text file in human readable form. Atom type frequency and all properties making up an atom type are written into separate columns.
        Parameters:
        textfilename -
        mode -
      • getAtomTypeList

        public java.util.TreeMap<java.lang.Long,​java.lang.Integer> getAtomTypeList()
      • processMolecule

        public void processMolecule​(StereoMolecule mol,
                                    java.util.TreeSet<java.lang.String> moleculeCache)
        Parameters:
        mol -
        moleculeCache -
      • getCountFromType

        public int getCountFromType​(long type)
      • getProbabilityFromType

        public double getProbabilityFromType​(long type)
      • getRingSizeAdjust

        public float getRingSizeAdjust​(int ringSize)