Class ChiralityAtom

    • Constructor Detail

      • ChiralityAtom

        public ChiralityAtom​(IChemObjectBuilder builder)
        Deprecated.
        Creates a new instance
    • Method Detail

      • getDegree

        public int getDegree()
        Deprecated.
      • setDegree

        public void setDegree​(int degree)
        Deprecated.
      • isUnspecified

        public boolean isUnspecified()
        Deprecated.
      • setUnspecified

        public void setUnspecified​(boolean unspecified)
        Deprecated.
      • isClockwise

        public boolean isClockwise()
        Deprecated.
      • setClockwise

        public void setClockwise​(boolean clockwise)
        Deprecated.
      • matches

        public boolean matches​(IAtom atom)
        Deprecated.
        Description copied from class: QueryAtom
        Returns true of the given atom matches this IQueryAtom.
        Specified by:
        matches in interface IQueryAtom
        Overrides:
        matches in class SMARTSAtom
        Parameters:
        atom - IAtom to match against
        Returns:
        true, if this IQueryAtom matches the given IAtom
      • chiralityMatches

        public boolean chiralityMatches​(IAtom target,
                                        int tParity,
                                        int permParity)
        Deprecated.
        Check if the atom-based chirality of the target matches. This check is done post-matching and should only be checked on atoms which are know to have already been matched (SMARTSAtom.matches(IAtom). Currently the only atom-based chirality allowed is tetrahedral stereo- chemistry. The
        Overrides:
        chiralityMatches in class SMARTSAtom
        Parameters:
        target - the matched target (required to verify 'OR' conditions)
        tParity - the parity (winding) of the target centre, 0=unspecified, 1=clockwise and -1=anticlockwise
        permParity - permutation parity of the query neighbors (will be multiplied by the query parity)