* add a test (currently fails, of course)
* backup, not really working
* Fixes#1240
* a bit more parameter tweaking to get some more structures to embed
* backup
* Fixes#1387
this passes the bug tests, but needs the full tests run
* all tests pass
* remove some droppings left from an earlier attempt at a fix
* remove some additional printing
* cleanup
* Start of GettingStartedInC++ documentation.
* Changed GettingStartedInC++ from rst to markdown format. Added some more text.
* Added Working with Molecules to GettingStartedInC++
* Expanded on behaviour of Kekulize wrt clearing aromatic flags on atoms and bonds.
* Added section Modifying Molecules.
* More plodding progress.
* A load more documentation.
* Undid change to global CMakeLists.txt
* Minor editing of docs.
* Changed examples so they use RDBASE to find test data rather than relative
path.
* Fixed use of -std=c++ in CMakeLists.txt. Extra waffling about memory.
* Modifications to examples and documentation as requested.
* Couple of minor changes.
* Change to example11.cpp and associated text in docs.
* add test
* update that test
* add python version of a test
* add some preconditions before dereferencing pointers
* make data members of AtomIterators private (not sure why these were ever made public)
* Fixes#1366
* switch to using std::runtime_error
* switch python tests too
* move the tests from the C++ side to be on the python side.
* add test
* update that test
* add python version of a test
* add some preconditions before dereferencing pointers
* make data members of AtomIterators private (not sure why these were ever made public)
* Fixes#1366
* switch to using std::runtime_error
* switch python tests too
* Fixes exceptions to use correct functionName
* Deprecates ChemDrawAdjustParams name sciquest integration/eln searching
doesn’t map to this behavior. renamed MatchOnlyAtRgroupAdjustParams
* Python wrapper for deprecated API
* fixHs now is more intelligent about merging hs.
The only cases where hs can’t be merged is if they are mapped
to a non hydrogen in the product.
* Updates deprecated ChemDrawAdjustParams
* Fixes#1338;
cmake files still need to be updated
* all tests now pass
* a bit of reworking about how bare Hs are handled
* more perversity
* update cmake files for those changes
* test atom map too
* clean up the header a bit
clang-format
* clang-format
* add test for #1286
* backup
* fixes the specific failure, but needs more looking
* add an additional test
* update the inchi code to explicitly include queue
* fix a typo identified during the review
* fix a possible infinite loop in cxsmiles parser
* support atom values from cxsmiles
this also adds proper handling of escaped characters in cxsmiles text
* add atom props
a bit of refactoring too
* very basics of charge checking in
* add the new parameters to the python wrapper. more testing please
* Additional testing.
* update which unittest methods are used
* Adds FragmentMol with minCuts specified
* Adds ability to cut by bond indices as opposed to smarts patterns
* Fixed API (remove maxBondCuts when bonds are sent in)
* Adds bond api test
* Fixes docs
* Small doc change
* Removes cstdint
* Adds ValueError minor bond retrieval optimization
* Removes fragMolHelper4
* Tests ValueError
* py3 fix
* add cis and trans to bond stereo
* compiles, does not work
* tests all pass
* Whitespace cleanup to recent changes.
* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS
* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.
E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.
* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.
* verify substructure matching works
* Adding Bond::setStereoAtoms to C++ Bond class.
This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.
* Wrap Bond::SetStereoAtoms into python with a new type of test case.
* docs
* add a SmilesParserParams object to prepare for this
* add a SmilesParserParams object to prepare for this
* add tests for the SmilesParseParmas
* support name parsing, should it be the default?
* rename CXNSmiles to CXSmiles;
add a spirit parser for CXSmiles coordinate that is at least syntax correct
* abandon boost::spirit for now; crude atom token parser
* support params in smiles parser (not tested, may not build)
* can read coords and atom labels along with mol names; crude, but works
* read coordinate bonds
* remove some compiler warnings with VS2015
* remove a bunch of compiler warnings on windows
* remove more warnings on windows
* remove more warnings on windows
* backup commit: first pass at parsing query features
* radical spec parsing
* handle attachment points using atom mapping
* switch to a named property for atom labels
* fix handling of the "A" atom query
* add functions to construct A and Q queries (needs more work)
* fix a problem created while cleaning up warnings earlier
* add some additional convenience functions for making generic atoms.
Still need M and to recognize these while writing CXSMILES
* add M queries; update some tests
* fix a linux compile problem
* get the cxsmiles stuff working in python; basic testing
* support "M" in CXSMILES
* Fixes#1271
* add a comment or two
* fix single-atom molecules too
* add a test for grid drawing too
* simplification of the special cases; no need to make things so complex
* fix for calculation of prinicipal moments of inertia
* fix a typo
update expected values
* PMI and NPR tests working
* cleanup some of the other descriptors and tests
* Test against Moments.py descriptors
* add new tests from Brian
* remove some warnings
* - optimization to UFF and MMFF forcefields
* - further optimizations (memset, factoring unnecessary in-loop
initialization out of the loop, replacing if clause with pre-increment)
* - fixed a couple of stylistic glitches
* - the torsionSmarts parameter in addTorsions() is now a const std::string&
* - implemented the DefaultTorsionBondSmarts singleton using boost::call_once()
