Class MolfileParser


  • public class MolfileParser
    extends java.lang.Object
    • Field Detail

      • debug

        public static boolean debug
    • Constructor Detail

      • MolfileParser

        public MolfileParser()
        Constructor of a MolFileParser, which will mirror Y,Z coordinates
      • MolfileParser

        public MolfileParser​(int mode)
    • Method Detail

      • getHandleHydrogenMap

        public int[] getHandleHydrogenMap()
        If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP
        Returns:
      • setAssumeChiralTrue

        public void setAssumeChiralTrue​(boolean b)
        Some software exports mol/sd-files with an unset chiral flag despite the original molecule is a pure enantiomer. This method allows the MolfileParser to override the molfile's chiral flag for such cases.
        Parameters:
        b -
      • isChiralFlagSet

        public boolean isChiralFlagSet()
        Returns:
        whether the previous molfile's chiral flag was set
      • isV3000

        public boolean isV3000()
        Returns:
        whether the previous molfile was a V3000
      • parse

        public boolean parse​(StereoMolecule mol,
                             java.io.File file)
      • parse

        public boolean parse​(StereoMolecule mol,
                             java.lang.String molFile)
      • parse

        public boolean parse​(StereoMolecule mol,
                             java.lang.StringBuffer molFile)
      • parse

        public boolean parse​(StereoMolecule m,
                             java.io.BufferedReader rd)
      • getCompactMolecule

        public StereoMolecule getCompactMolecule​(java.lang.String molFile)
      • getCompactMolecule

        public StereoMolecule getCompactMolecule​(java.io.BufferedReader reader)
      • getCompactMolecule

        public StereoMolecule getCompactMolecule​(java.io.File file)