* make sure that we can build without boost iostreams or seralization
adds some "private" variables on the python side to check for these compilation flags
* get out minimal cmake version correct
* get minimallib js building
installs an up-to-date cmake
also updates the version of boost being used for the minimallib
adds extra argument to allow the repo to be specified
* framework for extended query.
serialization works
to/from text doesn't work
* first pass at getting substructure search working
basic tests
improved error handling (try not to take down the server thread!)
* add serialization to MolBundle
* we really need to pickle mol properties
* basic support for molbundle
including substructure search
* tautomer and molbundle queries to JSON
* remove debug msg
* cleanup debug
initial index steps (not tested)
* remove indexing stuff since it wasn't working
will try to come back to that
* add xqm to update script
* add c++ testing for molbundle serialization
* add serialization of molbundles to python interface
* support expanding molbundles to arrays of tautomer queries
* edge cases
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* change in response to review
* a bunch of updates
* make sure the mol props needed for XQMs are being serialized
* update update script
* fix binary string output from ExtendedQueryMols in python
* tautomer queries should serialize properties
* more testing never hurts
* combo of generic groups and generalized queries works
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Fix weird quotes?
---------
Signed-off-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* bring over XQMol.h
* bring XQMol over for a separate PR
* backup... need to move these files
* refactor
* substruct
* oops
* testing basics
* basic tests
* more test
* more testing
* add empty() method to MolBundle
* easy creation of ExtendedQueryMols
* SRU test
* reorg
* the MolEnumerator should clear out residual reaction properties
* support to/from JSON
* cleanup
* first past at python wrappers
put the new code in a namespace
* less stupid names
more tests
* undo some unnecessary changes
* remove compiler warning
* release GIL during hasSubstructMatch too
* support adjustQueryProperties
* support toggling which operations apply
Fix the tautomer tests to include a molecule which actually requires the tautomer matching
