Class SmilesParser


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

      Constructors 
      Constructor Description
      SmilesParser()  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static void main​(java.lang.String[] args)  
      void parse​(StereoMolecule mol, byte[] smiles)  
      void parse​(StereoMolecule mol, byte[] smiles, boolean createCoordinates, boolean readStereoFeatures)  
      void parse​(StereoMolecule mol, byte[] smiles, int position, int endIndex)  
      void parse​(StereoMolecule mol, byte[] smiles, int position, int endIndex, boolean createCoordinates, boolean readStereoFeatures)  
      void parse​(StereoMolecule mol, java.lang.String smiles)
      Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
      Reaction parseReaction​(byte[] smiles)  
      • Methods inherited from class java.lang.Object

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

      • SmilesParser

        public SmilesParser()
    • Method Detail

      • parseReaction

        public Reaction parseReaction​(byte[] smiles)
                               throws java.lang.Exception
        Throws:
        java.lang.Exception
      • parse

        public void parse​(StereoMolecule mol,
                          java.lang.String smiles)
                   throws java.lang.Exception
        Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
        Parameters:
        mol -
        smiles -
        Throws:
        java.lang.Exception
      • parse

        public void parse​(StereoMolecule mol,
                          byte[] smiles)
                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • parse

        public void parse​(StereoMolecule mol,
                          byte[] smiles,
                          int position,
                          int endIndex)
                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • parse

        public void parse​(StereoMolecule mol,
                          byte[] smiles,
                          boolean createCoordinates,
                          boolean readStereoFeatures)
                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • parse

        public void parse​(StereoMolecule mol,
                          byte[] smiles,
                          int position,
                          int endIndex,
                          boolean createCoordinates,
                          boolean readStereoFeatures)
                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • main

        public static void main​(java.lang.String[] args)