Story: I have a PDB I want to read into RDKit. It has a disulfide bond
between two cysteines ~400 residues apart. This creates a very large
ring. RDKit throws an error because the number of found rings is less
than the expected number of rings. The ring wasn't found because RDKit
thought all "smallest" rings should be 256 or smaller.
Now, as long as your ring is UINT_MAX aka 4,294,967,295 or smaller, life
is beautiful. I hope no one has a ring bigger than 4 billion atoms.
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%)
The original version using products of primes broke down for proteins (or things with
large numbers of atoms) since collisions were quite possible.
Switched to using a hashing scheme; collisions are also possible here, but are even
less likely.
