Class SmirksTransform

    • Method Detail

      • setPrepare

        public SmirksTransform setPrepare​(boolean doPrep)
        Sets whether the molecule should be "prepared" for a SMIRKS transform, including set ring flags and perceiving aromaticity. The main reason to skip preparation (via SmartsPattern.prepare(IAtomContainer)) is if it has already been done, for example when matching multiple SMIRKS transforms.
        Parameters:
        doPrep - whether preparation should be done
        Returns:
        self for inline calling
      • apply

        public Iterable<IAtomContainer> apply​(IAtomContainer mol,
                                              Transform.Mode mode)
        Description copied from class: Transform
        Apply the transform to the provided molecule and obtain the results of applying the transform. The original molecule is NOT modified.
        Overrides:
        apply in class Transform
        Parameters:
        mol - the molecule to transform
        mode - how to transform the molecule
        Returns:
        an iterable which may be empty or contain copies of the molecule transformed
      • apply

        public boolean apply​(IAtomContainer mol)
        Description copied from class: Transform
        Applies the exclusive transform to the provided molecule modifying it as required.
        Overrides:
        apply in class Transform
        Parameters:
        mol - the molecule to modify
        Returns:
        the molecule was modified or not