Greg Landrum 42eecc664d Integrate Coordgen (#1708) ...

* first pass, does not yet actually work

* pass2, same problems

* pass2, same problems

* another test

* new tests; bugfix

* move the code out to a header

* add a double bond example

* enable auto-downloads of the code

* move the function to its own namespace

* first pass at a basic python wrapper

* change coordgen commit used

* try supporting bond stereo; does not currently work

* cis/trans seems to now work.

* first pass at templates; needs testing

* use the fixed flag too

* need mol align

* expand test

* initial pass at python wrapper for template

* simplify tests

* add an option to directly use a substructure match for alignment

* scaling

* add #define

* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages

* return the conformer id from addCoords

* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.

* add some debugging options for a bit

* add alignment step to testing when using non-fixed coords

* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working

* make coordgen the default when it is available

* make sure things continue to work when coordgen is disabled

* get windows builds working

* mods to get this building on windows.
something is screwy with the fileParsersTest1

* no need to generate coords for the 1K C string

* fix java wrappers

* works on linux

* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled

* docs

* extend forceRDKit applicability

* switch coordgen version

* try using templates

* try to get the template dir finding reasonably robust w.r.t. conda install

* continuing to iterate on the way the template file is installed

* fix a problem caused by the merge

* remove test that should never have been checked in

* update expected results for cartridge tests

* switch back to using the RDKit as the default coordinate generator

2018-02-15 05:36:03 +01:00

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