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Allow identification of chemistry problems (#2587)

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* add AtomValenceException

* refactor a bit and add KekulizeException

* add copy ctor and copy() method

* add detectChemistryProblems

* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts

* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.

* cleanup and finish the python wrappers for the new exceptions

* make sure things are truly polymorphic

* wrap shared_ptrs of the new exception types

* expose DetectChemistryProblems()

* get the java wrappers building again

* transfer those changes to the c# wrapper

* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue

* response to review
This commit is contained in:
Greg Landrum
2019-08-28 14:15:55 -07:00
committed by GitHub
parent 574caeba57
commit 253f172353
15 changed files with 555 additions and 77 deletions
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4
Code/JavaWrappers/gmwrapper/GraphMolJava.i
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@@ -130,6 +130,10 @@ typedef unsigned long long int uintmax_t;
%shared_ptr(RDKit::QueryBond)
%shared_ptr(RDKit::QueryOps)
%shared_ptr(RDKit::MolSanitizeException)
%shared_ptr(RDKit::AtomSanitizeException)
%shared_ptr(RDKit::AtomValenceException)
%shared_ptr(RDKit::AtomKekulizeException)
%shared_ptr(RDKit::KekulizeException)
%shared_ptr(RDKit::SmilesParseException)
%shared_ptr(RDKit::MolPicklerException)
%shared_ptr(RDKit::RingInfo)