Class IDCodeParser

    • Constructor Detail

      • IDCodeParser

        public IDCodeParser()
        This default constructor creates molecules guaranteed to have 2D-atom-coordinates. If 2D-coordinates are not supplied with the idcode, or if supplied coordinates are 3D, then new 2D-coordinates are created on the fly.
      • IDCodeParser

        public IDCodeParser​(boolean ensure2DCoordinates)
        Parameters:
        ensure2DCoordinates - If TRUE and no coordinates are passed with the idcode, then the parser generates atom coordinates of any molecule and assigns up/down bonds reflecting given atom parities. Generating coordinates is potentially error prone, such that providing original coordinates, where available, should be the preferred option.
        WARNING: If FALSE: In this case stereo parities are taken directly from the idcode, missing explicitly 'unknown' parities, because they are not part of the idcode. Without atom coordinates up/down bonds cannot be assigned. If further processing relies on up/down bond stereo information or needs to distinguish parities 'none' from 'unknown', (e.g. idcode creation, checking for stereo centers, calculating the skeletonSpheres descriptor), or if you are not exactly sure, what to do, then use the constructor IDCodeParser(true). If you supply encoded 3D-coordinates, then use IDCodeParser(false).