* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to review
* Issue #2108: Read Enhanced Stereochemistry from Python
This wraps enhanced stereochemistry data for an ROMol for use
in Python and includes a test that demonstrates access.
* Adds test for potential memory management problems
(also fixes incorrect class name and bad docstring)
* Corrected file reading idiom and object lifetime test logic
* initial pass at pickling reaction properties
* move more of the property handling functions to props.hpp
Wouldn't be bad to rename these at some point.
* add reaction properties to python wrappers
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* add test
* update that test
* add python version of a test
* add some preconditions before dereferencing pointers
* make data members of AtomIterators private (not sure why these were ever made public)
* Fixes#1366
* switch to using std::runtime_error
* switch python tests too
* move the tests from the C++ side to be on the python side.
This will be more useful in a later pull request I'm working on that
exposes QueryBonds to Python. Though it is usable without QueryBonds
as well, so submitting this for now.
* 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
- added threading support to the ResonanceMolSupplier-enabled
SubstructMatch() and relevant tests
- modified/removed some code in O3AAlignMolecules.cpp which doesn't
seem necessary anymore
- modified Code/GraphMol/CMakeLists.txt to allow building
on Windows
RWMol becomes a replacement for EditableMol.
It has the EditableMol interface in addition
to the ROMol interface. In the future this
may or may not grow the RWMol C++ interface.
Conflicts:
Code/GraphMol/Wrap/rough_test.py
