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* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference to only use part of a scaffold - adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match - adds allowRGroups parameter to enable using a scaffold bearing R groups as reference * changes in response to review * added comments * fixes failing doctest * - reverted change committed accidentally - fixed get_sss_json for the case where R groups are not included in the match - added tests for the return value of generate_aligned_coords * Documented the value returned by GenerateDepictionMatching2DStructure (Python) * changes in response to review * - changes in response to review - fixed sortMatchesByDegreeOfCoreSubstitution that was not working - added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch - added C++ and Pyhon unit tests for the above * added missing variable initialization Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>