Class ChUtils

Given a structure or a chmmol, return the "smallest set of smallest rings" as determined by Canvas. Either st or chmmol must be provided. If both are provided, chmmol will be used.

Parameters:

• st (schrodinger.structure.Structure) - A chemical structure
• chmmol (schrodinger.canvas.ChmMol) - A chemical structure
• use_st_numbering (bool) - If True, add one to chmmol atom numbers
• stereo (canvas.ChmMmctAdaptor stereo option) - Stereo option for conversion of st to chmmol, if no chmmol is provided

Returns: list of lists

List containing the atom numbers of the determined sssr rings

Evaluate SMARTS patterns using the Canvas libraries.  Returns 
a sorted list of tuples, the tuples being the atom-index
 sequences constituting the matches.

Create R-group st's from a template st and its from-to pairs.

template_st contains a template structure; template_from_tos is a sequence of from-to atom-index pairs defining the R groups.

Return a list of triplet tuples: (st, from, to), where st is a gzipped BLOB and from and to are integer atom numbers for the pendant from-to on the R-group st. The first triplet tuple is for R1, the second for R2, and so on.

Each st is created from the template file as follows: Break the from-to bond; extract the peripheral fragment into its own st; add H; label the the added H with s_cgch_attachment='y'.

Given an st with some terminal atoms bearing a non-empty 's_cgch_attachment', return a list of From-To atom-index pairs, where the labeled atoms are the To's and their attached atoms are the coresponding Froms. If my_from_index is not None, only return pairs for the specified my_from_index.

Return attachment atoms for st; if possible_linker is True, then just return linker attachments if it's a linker. This is determined by the presence of an 's_cgch_attachment' on the To atom.