* SHARED-12256: Add test and change function.
* SHARED-12256: Update to only wrapping changes.
* SHARED-12256: Parameterize tests.
* SHARED-12256: GetPropIfPresent changes.
* Revert "SHARED-12256: GetPropIfPresent changes."
This reverts commit f598f8c161.
* SHARED-12256: Make default the keyword in the boost wrappings.
* SHARED-12256: Overload function instead of using a sentinel.
* SHARED-12256: Extend GetProp changes.
* SHARED-12256: Add entry point for tests and fix tests.
* Trim spaces from RDProp strings to simulate reading from SDFiles
* Update documentation
* Use the correct doc strings
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* Speed up GetProp Python keyerrors
A common pattern _in Python_ for checking for the presence or
absence of a key is:
try:
return mol.GetProp('mykey')
except KeyError:
return None
Shockingly, this is really slow with boost python objects! I was
recently profiling a workflow and 90% of the time or more was
spent in failed GetProp calls (mostly on bonds, some on atoms
or mols).
I sped up the workflow by protecting the calls using HasProp. But
I think this is a silly trap we've set for our users.
The problem comes because boost::python uses a C++ exception to
indicate that there is already a Python exception set. In C++,
exceptions are slow - they require unrolling a stack. In Python,
exceptions are about the same speed as any other control flow!
This commit speeds up GetProp failures by circumventing the
boost throw_exception_already_set() mechanism.
In my testing, this speeds up failed GetProp substantially:
* Factor of 1000x on Mac
* Factor of 40x on Linux
* Update typed GetXXXProp to bypass boost exceptions
Based on PR #8372
Updates the typed GetIntProp, GetDoubleProp, etc to bypass C++
exceptions in access. This speeds up missing key errors
significantly - for instance, calling mol. GetIntProp with a
missing prop 100,000 times:
Before: 28s
After: 0.05s
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Optimize GetPropsFromDict, use tags for conversion, not the try and fail technique
* Autoconvert strings to ints and bools if possible
* Add autoConvert option to GetPropsAsDict default=true
* Update Code/GraphMol/Wrap/props.hpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* change autoConvert to autoConvertStrings, add failed datatype conversion notices
* Fix Invariant usage
* Fix namespace for string
* Add GetProp(key, autoConvert) to allow for converting only what you want
* Make TestSetProps private
* Get _TestSetProps from rdmolops
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Fixes#2450
adds `hasOwningMol()` to the public API for Bond and Atom
* add to other classes;
add to python wrappers
* get the smiles generation partially working
* changes in response to review
* add cis and trans to bond stereo
* compiles, does not work
* tests all pass
* Whitespace cleanup to recent changes.
* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS
* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.
E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.
* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.
* verify substructure matching works
* Adding Bond::setStereoAtoms to C++ Bond class.
This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.
* Wrap Bond::SetStereoAtoms into python with a new type of test case.
* docs
* Adds RDAny (smaller generic holder) Updates all used dictionaries
This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.
* Removes code duplication
* Converts CHECK_INVARIANT to TEST_ASSERT
* Fixes DoubleTag issue
* Adds Bool to DoubleMagic implementation
* Removes reference to property pickler
