* Move DetectAtomStereoChemistry to Molops::assignChiralTypesFromBondDirs
DetectAtomStereoChemistry in MolFileStereochem is more broadly
useful. Additionally, it was not named very clearly for what
it was actually doing.
* Wraps assignChiralTypesFromBondDirs for use in Python
Makes assignChiralTypesFromBondDirs available in Python
and adds a test demonstrating that availability.
* Move RDBoostStreams to RDStreams
* RDBoostStreams->RDStreams
* RDBoostStreams->RDStreams
* Wrap SWIG (with Java test)
* Fix missing declaration
* Use the file that already exists
* Revert to original version
* Revert to CXSMiles version
* Update boost version
* Remove redundant code
* Add zlib
* check for win32
* FileParsers now builds static on windows
* added a set of test files for SGroups.
Many thanks to Gerd Blanke for providing these
* Partial version of the wrapper
Definitely needs more work
* add some properties
* basic SGroup property change test
* not working; backup commit
* disable writing for now
* add ClearMolSGroups() function
* review response: add a couple missing methods
* remove spaces from filenames
* update filename in test
* changes in response to review
* add operator== to SGroups
* solve lifetime problems with a vector_indexing_suite
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* first crude pass
* fix a deprecation
* change naming scheme, support bools
* add standalone function
* add a default value for missings
* support long lines
* stupid typo
* make operator[] work
* revisit missing value handling
* modify missing value handling
* switch to an alternate scheme for specifying missing values
* clang-format
* First pass at property list parser
still needs more tests
* add test for processMolPropertyLists
* get this working as part of the ForwardSDMolSupplier
* first pass at python wrappers and tests
* clang-format run
* add creation of property lists at the mol level
* wrap long lines on output
* remove PoC implementation
* fix python wrappers
* remove out-of-date reference to the Python PoC
* changes in response to review
* Fixes#2277
* changes in response to review
the big one is to move the PXA parser into the normal mol file parsing
* move the PXA changes to the writer as well
* SCN actually only needs 7 characters
* add test
* fixes in response to review
* handle blanks (instead of zeros) in the counts line.
The ctfile.pdf doc says we should do this
* Make the SGroup reader more robust w.r.t. bad data
The current behavior leads to uncaught exceptions when a line is too short.
This should clear that up so that we always throw the usual FileParseException
* make error messages a bit easier to read
* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
* Fixes#2225
* A bit of extra cleanup
* forgotten file
* Make this thread safe and add support for v3K mol blocks
* add the file
* update expected results
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* does not yet really work
* tests pass
* store the info about the attachment points in case we want to use it later.
* add a couple more tests; changes in response to review
* Fix 2D/3D interpretation of V2000 ctabs
* Remove debugging statements
* Apply fix to V3000 molblock
* Add 3D pretending to be 2D test case
* Fix for review comments.
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* add SVG parsing to python
re-enable the moldraw2d tests
* A couple of fixes connected to #2029
* handle problems parsing atom/bond SMILES
* wrap the whole thing in the <metadata> tag
* patch a memory allocation problem in the maeparser v1.0.0 (#2044)
* add atoms
* add bonds
* backup
* Fixes#2029
* Get metadata working for drawMolecules()
* add to python wrapper
const correctness
* also connected to #2029: make sure bond direction also ends up in the output
* initial version of an SVG->ROMol parser
this is in the wrong place, but I wanted to make sure it actually works
* move svg parser to a more reasonable location
there is still some work to be done here
* add conformer parsing
* Fixes#1929
* add a tests to make sure bogus template directories work
* add a combined atomic number + aromaticity query operation to speed up SMARTS matches
Still needs to be recognized by the SMARTS writer, serialization, and no doubt a few other places.
* add a combined query for the single/aromatic bond query that shows up in SMARTS
* Stop using a dead pointer in the when parsing Marvin SMARTS in a CTAB
* At this point all tests pass on windows
* debugging info back in
* update the bison output
* Add initial Maestro format Supplier using maeparser library
Right now it's carrying over very limited information, more to come. Initially:
* 3D Coordinates
* Bonds with order
* Atom charges
* Structure title
* Greg's code review suggestions
Put MaeMolSupplier behind the coordgen flag. Added Python wrapper. Made other small
changes.
* Fix wrapping of MaeMolSupplier.cpp
* More code review feedback response
Also fixed an issue where exception during iteration locks up iterator
Remaining items:
* Bug where for i in MaeMolSupplier() works, but suppl = MaeMolSupplier
segfaults on OSX
* Add Python Unit tests
* Get build working with Coordgen flag turned off
* Fix memory bug, add Python unit tests
* Get rid of dead code in test
* Ifdef forward definitions for Maestro file reader
* This makes assignStereochemistry cleanIt=True not remove CIS/TRANS
bond stereo chemistry that was manually added as described in issue #1614.
Incorrect CIS/TRANS stereochemistry will still be removed by
'cleanIt=true' if symmetry is detected. However, this symmetry
detection doesn't work in more complex pseudo-stereo chemistry cases:
bond stereo that depends on other bond stereo to break symmetry; and
bond stereo that depends on other atom stereo centers to break
symmetry. Test cases for these cases have been added ifdef'd in based
on USE_NEW_STEREOCHEMISTRY.
However, getting USE_NEW_STEREOCHEMISTRY to work in a copacetic way is
not trivial, I tried a little bit here to no avail. I'm leaving the
test cases checked in as they should be useful when we decide to make
the plunge into using Canon::chiralRankMolAtoms for symmetry detection
instead of the CIP ranks.
So this fixes at least the glaring issue of STEREOCIS and STEREOTRANS
being incorrectly removed by 'cleanIt=true' when it is indeed valid
stereo. The checks made for symmetry are rudimentary, but don't feel
complete.
* add another test; make what's being tested explicit
* test smiles generation and function when Hs have been added
* add a test that fails
* I think that it's ok to remove this
* backup
* At this point all tests pass.
Bond wedging is now handled even if sanitization is turned off when mol files are read
* adjust to code changes
* fix a couple problems caused by rebase
* update docs
* boost::thread mostly gone... still need to get rid of once
everything compiles
* replace boost::call_once
* remove link-time dependency on boost::thread
* first pass at using async
* switch to using async everywhere
