* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* 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
* Allow Atoms to be copyied in Python.
The dunder copy method is the idiomatic way to support
making copies in Python. Includes a test to make sure that
copied atoms are usable.
* Use RWMol in Code/GraphMol/Wrap/rough_test.py
Co-Authored-By: d-b-w <dan.nealschneider@schrodinger.com>
* Allow access to an atom's copy constructor in Python
* 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
* Expose SetQuery to python
* Add a default for maximum products generated by a reaction (maxProducts=1000)
* Add better documentation for test that used to raise exception
* properly import rdqueries
* Add more options to GetAtomSmiles() to control output.
The most important one here is that you can now directly control whether or not isomeric SMILES is generated.
Expand the python interface so that we have more control over Atom.GetSmarts()
* make the use of isomeric atomic smiles explicit (since we can)
* start release notes for 2018.09.1
* python formatting
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
* Adds Atom atom map and rlabel apis
* Moves RLabels to their own namespace, adds other properties.
* Removes namespaces, liberally adds Atom to function names.
* move detail::computedPropName to RDKit::detail::computedPropName
* 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
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
