This is useful for installations where pg_config is renamed to not
collide with the system default pg_config name.
We should drop 'find_package(PostgreSQL REQUIRED)' statement in
future because that's supposed to find PostgreSQL client library
to build against, not PostgreSQL server. It might happen that
PostgreSQL server on the system is of different version than libpq
(Debian), but in future it will be problematic also on Fedora
(rhbz#1618698).
See also: https://gitlab.kitware.com/cmake/cmake/issues/17223
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* 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
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
* handle the heavy-atom degree queries differently
* Fixes#1563
* add a test for the heavy atom degree option
* Support (and test) adjustHeavyDegree in the cartridge too.
* test results
* switch from using `[D0]` to `[*]` to ensure single atom fragments are correctly handled in the pattern fingerprint;
Fixes#1496
* update expected reaction similarity results
* fix compatibility with PostgreSQL 9.2
* get tests working on pgsql92; the Makefile does not currently work
* simplify 9.2 handling
* seems to work on 9.6 and 9.2 now
* first pass at RWMol::replaceBond()
* get ready for the changes
* rename some options
add bond options (not doing anything with them yet)
update tests to reflect new options
* backup
* re-enable the rest of the tests
* a bit of header cleanup
* Fixes#1106
* First pass, basics.
Still need tests and handling of parameters.
* initial pass at including JSON parsing of options (not complete)
* handle errors while parsing json instead of just crashing the server
* updated (and working) JSON configuration
* first drawing tests
* document the new function
* it helps to save before committing
* - this should fix the problem with "Inchi" being hardcoded into PostgreSQL
* - moved the InChI check code out of the main CMakeLists.txt
into FindInchi.cmake
* refactored Bfp indexing and similarity search
* update CMakeLists.txt
* catch (and fix) inconsistent options around building static libs
* differentiate the data structures in inner and leaf pages
* code cleanup and some additional comments
* version bump
* fix renaming of cache function
* minor cleanup
* add -DUSE_BUILTIN_POPCOUNT to ${POPCOUNTFLAGS}
In Fedora land, format-security GCC warnings are treated as errors
so the build would fail like this:
In file included from /usr/include/pgsql/server/postgres.h:48:0,
from rdkit.h:40,
from mol_op.c:33:
mol_op.c:339:19: error: format not a string literal and no format arguments [-Werror=format-security]
elog(WARNING, t);
^
* backup commit
* Change the names and meanings of MolOps::AdjustQueryWhichFlags
What was there before was not flexible enough and was extremely confusing. This should clear that up.
NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been
widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties()
remains the same.
* adjust to the new AdjustQueryWhichFlags
* add mol_adjust_query_properties tests to the cartridge
configuration parameter" errors on Windows with PostgreSQL 9.1
- added a dummy RDKit cartridge function call at the beginning of the
reaction.sql test to avoid "unrecognized configuration parameter" errors
with PostgreSQL 9.1
- modified reaction.out to reflect the change in reaction.sql
CMakeLists.txt
- fixed a bug in Code/PgSQL/rdkit/rdkit_gist.c which did not cause
issues with PostgreSQL 9.5 on Windows, but does with earlier PostgreSQL
versions
- removed an unnecessary conditional compilation clause from
Code/PgSQL/rdkit/rdkit.h as PostgreSQL 8.x is not supported anymore
