The present SMIRKY implementation takes ten input files which allow users more customized control of probabilities while sampling. Three of these files are similar to SMARTY inputs: a file with initial fragment types (that is SMIRKS strings) defining a hierarchical chemical perception tree; a file containing molecules to be typed in the course of scoring the direct chemical perception tree; and a SMIRNOFF file which provides the reference fragment types for use in scoring. As in SMARTY, any of the initial fragment types that do not match any fragments are removed, creating a working set of fragment types for the MC algorithm. The next five files provide the atom, bond, and decorator types: OR atom types; OR and AND decorators for atoms; OR bond types; and AND decorators for bonds (Section 2.3.1). Each decorator file includes a column for the odds of proposing a given decorator in the course of the MC sampling. The final category of files allows the user to specify the odds of picking a certain atom or bond in a fragment that will be changed during the move. There are two files in this category -one for atoms and one for bonds. There are two columns in this format, one specifying if the move is to an indexed, alpha or beta atom or bond using the SMIRKS index number or the key words "alpha" or "beta." Then the second column is used to set the odds. For example, in a torsion, a user might want to make it more likely to make changes to the outside atoms (1 and 4) than to the inside atoms (2 and 3). The SMIRKS pattern (middle) represents a bond parameter "-" (gray) between two labeled atoms -a carbon (light blue) or nitrogen (light blue) atom and a hydrogen atom (light red). In this figure, we show two matches for this SMIRKS pattern on the top structure. The matches are highlighted in light blue (atom 1) and light red (atom 2) circles on the substructure (top). In the ChemicalEnvironment representation, at bottom, atom 1 (light blue rectangle), there are two ORtypes '''#6X3H2" with a carbon atom base "#6" and OR decorators "['X3, 'H2']", corresponding to a connectivity of three and a total hydrogen count of one and "#7X2H1" with nitrogen atom base "#7" and OR decorators "['X2, 'H1']" (light green). The AND decorators for the atom 1 are "['A', '+0']" (light green) corresponding to an aliphatic atom with a zero charge. In SMIRKS strings, the high precedence "and" operator is given by a semi-colon ";", so the bond described by this pattern is one between a carbon atom with connectivity three and hydrogen count two or a nitrogen atom with connectivity two and hydrogen count one that is also aliphatic with zero charge.