* forward doIsomericSmiles
* added test for #2565
* fix for my snippet
* update test with Greg's comments
* add braces for readability to MolMatchFinalCheckFunctor
* small refactors: abstract label checking, while/size, final check
* merge loops reading order of bonds -- all tests pass
* fix chiral-lead fragments, allow frags w. degree < 3
* add new test, update old
* add test, update old
* fix (inocuous) bug with ranks assignment in MolToSmarts
* start SMARTS with first non-chiral atom
* use smart pointers in test
* reenable doIsomericSmiles
* update patch for #2594
* remove faulty fragments matching
* review tests, remove wrong flip
Before this commit, if enhanced stereochemistry information was
added to a CXSMILES string as well as other information, the
separator would be missing. This made CXSMILES written by
RDKit unreadable if enhanced stereo information was present.
* - fixes#2663 (The C++ MCS code generates ambiguous SMARTS strings)
* - fixes#2662 (C++ MCS code returns a null MCS between
methylcyclopentane and methylcyclohexane)
* Updated cartridge documentation
Made examples compatible with latest chembl (25) and most recent conda versions of rdkit (2019.03.4.0, python 3.6.9) + rdkit-postgresql (2019.03.4.0)
* updated more query results
* updated more query results
* copy in, get building, add some basic tests
* complete the testing
Except for regiosiomers, which do not work
* regioisomers work now
* backup commit; things work
* remove last of NM macros from hashfunctions.cpp
* remove last of NM macros from hashfunctions.cpp
* remove dependency on the abstraction layer
* typo
* start using namespaces
clang-format
* switch to using enums for the HashFunctions and StripTypes
* Add initial python wrapper (and tests)
* move the new hashing code to the MolHash library
still may want to revise the naming of this
* Setup deprecation of the older hashing code
* better release notes text
* change in response to review
So far, the installation instructions for Linux rely on a specific
python version in order to include numpy. Replace the hard-coded path
with a call to numpy.get_include().
* Fixes a molblock writing problem
with undervalent atoms from the organic subset
* Fixes#2649
Also ensures that allenes are not written as crossed bonds
(which does not make sense at the moment anyway)
* clang-format run
* Better resolve ties in rgroup matches
* Break ties by choosing the permutation that adds the fewest rgroups
* Update aligned cores after tie breaking\nI think this results is more optimal
* Remove unused code
* Replace count with UsedLabels
* Remove whitespace
* Remove whitespace
* Remove redundant code and error message
* Revert test
* remove debug prints
* add AtomValenceException
* refactor a bit and add KekulizeException
* add copy ctor and copy() method
* add detectChemistryProblems
* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts
* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.
* cleanup and finish the python wrappers for the new exceptions
* make sure things are truly polymorphic
* wrap shared_ptrs of the new exception types
* expose DetectChemistryProblems()
* get the java wrappers building again
* transfer those changes to the c# wrapper
* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue
* response to review
* Fix CanonicalRankAtomsInFragment API, adds includeChirality, includeIsotopes
* Add testGithub2611
* Update python doc string
* Ensure isotopes are being ignored when requested
Co-Authored-By: Greg Landrum <greg.landrum@gmail.com>
* Need to use all atoms for test
* Enable getStereoAtoms() for E/Z stereo bonds
* do not copy reactant bond directions to product & refactor
* new bond stereo mechanism
* update tests & add some more
* fix problems in E/Z getStereoAtoms()
* use make_iterator_range in Bonds.cpp
* backwards match, refactor, +1 test
* Apply suggestions from code review
Co-Authored-By: Greg Landrum <greg.landrum@gmail.com>
* Apply more suggestions, clang-format
* add comments, mixed pair stereo forwarding, tests; fix bug
* make Bond::getStereoAtoms threadsafe
* Revert "make Bond::getStereoAtoms threadsafe"
This reverts commit c5902d9dfb.
* Revert "Enable getStereoAtoms() for E/Z stereo bonds"
This reverts commit 9ef8c4d1f8.
* add back findStereoAtoms() to ReactionRunner
* add missing brace in conflict resolution
We have MolFragmentToSmiles already. But I think that when talking
about a fragment or part of a molecule, maybe SMARTS makes more
sense. If I see a SMILES string, I'll definitely think that
it should be a valid molecule, but I have no such
presumption about SMARTS.
Additionally, Schrodinger software sometimes generates SMARTS
for selection using a set of atoms picked in a GUI. It will
be useful to generate these SMARTS using RDKit.
