enumeration is only carried out when the user asks for a structure
or when the user explicitly request that calling the enumerate()
member function. This makes object creation fast and enables
calling getNumConjGrps(), getBondConjGrpIdx() and getAtomConjGrpIdx()
member function without incurring in the cost of necessarily
enumerating resonance structures
- fixed some int/unsigned int inconsistencies
- now bonds and atoms with do not belong to conjugated groups
get a -1 index
- added a few Python wrappers
- added a few tests
- removed unused variables from Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp
- fixed ResonanceMolSupplier Java wrappers which were really broken
- 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
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
* remove some debugging info
* move classes from .h to .cpp
* SWIG wrappers
* improve resonance structure sorting for degenerate resonance
structures
I will do all of the above ASAP
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
smarts queries run faster (like vector bindings). Though there is an addition to the smarts parser
exposed here, I do not recommend using it in client code.
