Paolo Tosco 19c9a3905c Enhanced generateDepictionMatching2DStructure functionality (#3811) ...

* - 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>

2021-02-24 05:37:31 +01:00

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