• RE: what is the meaning of centroid in subsearch?

    That is correct: the centroid would lie equidistant between the two carbon atoms.

    However, please note that the indexing is from zero, so you would actually want something like...

    sub1 = ccdc.search.SMARTSSubstructure('CC')
    searcher.add_centroid('CENT1', (sub1, 0), (sub1, 1))
  • RE: what is the meaning of centroid in subsearch?

    A centroid is an object located at the geometric centre of two or more atoms. There is a description with illustration in the Conquest User Guide and Tutorial document (Section 4.4.2: Defining Geometric Objects) that might make it clearer.

    The definition uses a substructure object, here defined using a SMARTS, and atom indices with that substructure to identify the set of atoms for which a centroid object is required.

    Thus, CENT1 in this example is the centroid of two of the nitrogen atoms in a guanidinium group. If instead you wanted the centroid of these two nitrogens plus the carbon, you would use...

    searcher.add_centroid('CENT1', (sub1, 1), ( (sub1, 2), (sub1, 3))

    Hope this helps.