Files
rdkit/Code/GraphMol
Brian Kelley fa89438358 Dev/reaction enumeration (#1111)
* Adds C++ Enumeration Engine to the RDKit

* Adds Sanitization helpers, wrappers and tests

* Clang format

* Remove unused enumerationStateOnly flag

* Fixes docStrings to current API

* Adds doc strings

* Removes RGroupPosition, adds getPosition to EnumerationBase

* Fixes readability.

* Adds EnumerateLibraryBase::reset and getReaction

* Added getReagents method to EnumerateLibrary

* Make the tests have the same naming

* Need to save the initial state for resetting.

* Stupid case-insensitive file systems

* Moves ResetState to EnumerateLibraryBase

* Adds removeNonmatchingReagents helper

* Renames currentPosition to getPosition

* Adds Enumeration Toolkit tutorial

* Fixes Python3 serialization and enumerators

* Verified to run on python2 and 3

* Fixes integer issues on windows

* The number of enumeration should be unsigned.

* Adds deserialization constructor

* Moves boost_serialization to the end

* Deprecates Clone in favor of copy

* Update tests to use copy.copy not Clone

* Move RGROUPS and BBS into an EnumerationTypes namespace

* Make sure old pickles work

* Adds pickle for backwards compatibility

* Moves to uint64_t from size_t for public api

* Whups, accidentally used the binary archiver.

* Commits boost 1.55 serialization

* Makes serialization turnoffable Like Filter Catalog

* Fixes tests when serialization not available.  Adds more enumeration strategy tests

* Fixes a syntax error on some versions of python

* Fixes sanitizeRxn to actually make proper RGroup atoms

* Updates SanitizeRXN python API

* Updates Enumeration API to a parameter class - fixes reagent removal

* Adds a mess of tests

* Change stats to return a string.

* Exposes EvenPairSamplingStrategy Stats to python

* Fixes a crash bug in SanitizeRxn

* Adds better testing of the even pair sampling

* Fixes namespace

* One more try to fix gcc

* Enum classes are c++11 and a microsoft extension.

* Fix typo

* Fixes np.median for python3

* Fixes atom iterators

* Adds virtual tags to derived virtual functions (for clarity)

* Fixes size comparison issues

* Adds doc string

* Small cleanup (has no effect since flags aren’t used)

* fixes crash bug on windows

* get the tests working on windows

* Updates tutorial

* Adds Glare implementation to Contrib
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