* Trim spaces from RDProp strings to simulate reading from SDFiles
* Update documentation
* Use the correct doc strings
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* - avoid code duplication through a templated function
- enable switching off boolean flags via JSON and not just on as before
* ran clang-format
* change in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fist pass at CDX support
* Enable CDX support for reading (also) in the CDXMLParser API
* Add cdxml test files
* Update swig wrappers for CDXMLFormat and Parameters
* Add constructor to ChemDrawParserParams
* Add Java SWIG support for ChemDraw
* Add chemdraw define to rdconfig
* Add missing chemdraw deps
* Remove direct expat link
* Fix Java linkages for ChemDraw
* Remove bad merge code
* Remove bad merge code
* Fix csharp builds
* Add sniffer for the ChemDraw DataStream
* Include filesystem
* Fix test on windows
* Add more CDX tests
* Ensure streams are open in binary mode to support CDX on windows
* Fix text to show that a Block is the text input, not a file
* Fix CSharp test
* Disable CDX tests when not building chemdraw
* Turn back on chemdraw
* Response to review
* Turn off chemdraw support for the limited external test
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* Adds a df_forceStop to stop readers and writers, clears out queues on destructor
* Propery implement close function, requires protected closeStreams
* changes from greg's version
* close() needs to be called in the derived destructors
* Close the writers before the reader to avoid deadlock
* Don't process trailing new lines
* Don't accept pushes if the queue is done
* Add mutex protecting d_threadCounter, remove unneeded forceStop checks
* Update Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add comment for the d_threadCounterMutex unlock
---------
Co-authored-by: = <=>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Parsing SCSR
* add scsrol to mol
* removed bad include file
* loosen distGeom test slightly
* add wrap test for SCSRMol
* Add test for scsr in python
* tests added for scsr and strict parsing removed
* remove extra stuff
* More fully specified use of SCSRMol for PR CI build
* Added flags for SCSR expansion to not include any leaving groups
* Added MolFromScsrParams to Wrap for python
* added SCSRMol destructor
* Added two tests for RNA macromols, and fixed a bug they revealed
* Added new tests abd expected files
* changes as per PR review
* SCSR Chnages for leaving groups
* fixed testScsr.py
* hydrogen bond treatment
* in SCSR expand, allow Hbond to be autoatically detected
* changes as per code review
* Adding new test file
* chages for SCSR contructors, destructors for CI build
* fixed pyton for SCSR hydrogen bond modes, and added tests
* Added new test files
* fixed edge case for SCSR
* fix checksum for inchi
* consistent capitalization of SCSR throughout
* switch to enum class
* make things shorter
* simplify
* get rid of the ATTCHORD class
* New section for SCSR in RDKit_book
* addeed section to RDKit_Book
* SCSRMol is no longer exposed in Python
* fix leak in MolFromSCSRFile()
light refactoring
* expose MolFromSCSRFile() to python
make the MolFromSCSR functions work with default args
a bit more testing
* removed C++ access to SCSRMol
* CXMsiles now ouputs hbonds, fix to template matching, and a few other things
* Addl fix for bad aromaticity in Hbond rings
* Test files needed
* Test files needed
* try to fix a CI build errors
* CI error fix
* Added missing test file
* CMake version - for CI build
* remove full file compoarison from macromol test file
* accidental change to debug restored to release
* Code review changes
* As per PR review
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* Implements #8222 adds react_idx (index of reactant) to product atoms
* Remove react_idx from mol enumerator products
* Response to review, add test to ensure product only atoms aren't tagged
* Reenable tests
* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Properly cleanup Dict::Pair when serializing HasPropWithQueryValue
* Make sure pickling doesn't change original molecule
* Fix bad cut and paste
* Add PairHolder utility class for memory management of non Dict Dict::Pairs, fix mem leak in pickler
* Edit comment to force a rebuild
* Ignore PairHolder from Java/Swig builds
* Ignore PairHolder API from swig
* Reponses to review
* Add backward incompatible change
* Make release note a bullet point
* - moved SMILES and RGroupDecomp JSON parsers to their own translation units
- added missing DLL export decorators that had been previously forgotten
- changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON
to replace enum parameters with the underlying types
- updated ReleaseNotes.md
* make sure cxSmilesFields is only updated if the JSON string contains keys
belonging to the CXSmilesFields enum
* added missing copyright notices
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* test changes
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* Merge branch 'master' into pr/specialQueries
* changes from previous PR
* Iclude false chiral
* rigorous enhnced stereo canoncalization
* Added more tests and clenup
* removed commented out code
* corrected init of SmilesWriteParams
* added MolFileStereoChem.h to the header files
* Renamed Rxn parser to MrvBlockToChemicalReaction
* To make catch2 work, and match the checksum
* Fixed Structchecker errors
* fix CI for DetermineBonds catch test
* error in catch_test for CI
* Allow custom smileWriteParams in GetMolLayers
* misnamed entry point
* ReactionFromMrvString change name
* remove adding writeParams to GetMolLayers
* make rigorous enhanced stereo the default, and fix tests
* only one abs group no longer needs Rigorous Enhanced treatment
* changed string_view to string in catch test
* Canonicalize Enhnaced Stereo only resturne unique smiles
* Now allows or and and groups together
* internal routines inside detail scope
* fix test error
* changed string back to string_view and fixed a CHECK
* Fixes for PR review tests
* Fix RDKit_Book.rst failure on build test
* fix xqm sql test
* updated expected files for cxsmiles_test
* Fixed removal of atom attrs
* Fixed tests after merge of master
* More efficient version of Stereo Groups Canonicalization
* Fixes for ctests
* removed debug code
* readded cipLabel test
* fix generalizedSubstruct/catch_tests.cpp error
* hueristics to improve speed
* Rationaized control of abs groups
* removed unused routine
* added rigorous stereo group treatment to test
* some suggested changes
* Changes per PR review and removed some changes to smiles
* Fixed CI errors
* changes per PR review
* more PR review vhanges and cleanup
* Fixed PSql PKL change
* changes as per PR review
* Restored error type for bad mols for canonicalizeStereoGroups and added a test
* Merge master and fix test in MolDraw2D
* Fix for randomize test error and other PR review comments
* Removed unsued variable to fix mac CI
* do not force aromatization in canonicalizeStereoGroups
* changes as per PR review
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Code/GraphMol/Depictor/RDDepictor.h
- fixed typo in docstring
Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
- added a missing const; formatting changes
Code/GraphMol/RGroupDecomposition/RGroupData.cpp, Code/GraphMol/RGroupDecomposition/RGroupData.h
- moved the code which merges disconnected R groups sharing the same attachment point into a single combined molecule to a private method, RGroupData::mergeIntoCombinedMol(). The method also includes logic to merge atom and bond highlights, if present.
- modernized a for loop
- isMolHydrogen is now a static function since it does not actually require any instance data
- implemented three static function to return the R group, Core and Mol labels, respectively
Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecomp.h
- implemented two private methods, RGroupDecomposition::labelAtomBondIndices() and RGroupDecomposition::setTargetAtomBondIndices(). The first method tags all atoms and bonds in the target molecule such that they can be tracked following core removal by RDKit::replaceCore(). The second method sets common_properties::_rgroupTargetAtoms and common_properties::_rgroupTargetBonds properties on core and R groups. These are vectors of atom and bond indices in the target molecule corresponding to core and R group atom/bonds, respectively, and can be used for color-coding the target molecule according to the R group decomposition it was subjected to, similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp
- formatting changes and for loop modernization
Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h
- implemented updateRGroupDecompositionParametersFromJSON()
- added includeTargetMolInResults boolean parameter
Code/GraphMol/RGroupDecomposition/RGroupMatch.h
- implemented RGroupMatch::setTargetMoleculeForHighlights() and RGroupMatch::getTargetMoleculeForHighlights() methods to, respectively set and get the target molecule where R group decomposition can be color-coded with highlights. This molecule includes the explicit H atoms corresponding to extracted R groups, if any.
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
- use a std::unique_ptr to store the pointer to the C++ RGroupDecomposition instance
- fixed typos in docstrings
Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
- formatting changes
Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp
- do not use deprecated constant
Code/MinimalLib/CMakeLists.txt
- added RDK_BUILD_MINIMAL_LIB_RGROUPDECOMP CMake flag to optionally expose R group decomposition functionality into MinimalLib
Code/MinimalLib/common.h
- added makeDummiesQueries flag to mol_from_input() (defaults to false)
- implemented parse_highlight_multi_colors() function to parse multi-color atom and bond highlights
- enable multi-color atom and bond highlighting
Code/MinimalLib/demo/rgd_demo.html
- added HTML page showcasing the multi-color highlights similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/MinimalLib/jswrapper.cpp
- removed checks for non-nullness of d_mol as d_mol cannot be directly accessed anymore
- replaced all instances of d_mol with get()
- implemented support for multi-color atom and bond highlights
- implemented optional support for R group decomposition
- added JSMol::copy() convenience method with same functionality as get_mol_copy() to duplicate a molecule
Code/MinimalLib/minilib.cpp, Code/MinimalLib/minilib.h
- replaced all occurrences of d_mol with get(), as d_mol is now private
- removed all occurrences of assert(d_mol) as non-nullness is checked at construction time and whenever get() is called
- JSMol is now split into two subbclasses, JSMolUnique and JSMolShared, which both inherit from the JSMol base class. JSMolUnique can be constructed from a RWMol* (as the old JSMol), while JSMolShared can be constructed from a ROMOL_SPTR. This avoids unnecessary copies when wrapping a ROMOL_SPTR (e.g., from subtructure library, JSMolList or R group decomposition) into a JSMol to pass it to JS. This also avoids that modifications done in the JS layer on a molecule stored in a MolList (e.g., adding a property) are not persisted because they are carried out on a volatile copy of the molecule rather than on the actual molecule.
Code/MinimalLib/tests/tests.js
- added a test for pesistence of modifications made to JSSharedMol
- added tests for RGD
- added test for JSMol::copy()
Code/RDGeneral/RDValue.h
- removed trailing comma from vector properties such that they can be deserialized as syntactically correct JSON
Code/RDGeneral/types.cpp, Code/RDGeneral/types.h
- added _rgroupTargetAtoms and _rgroupTargetBonds common_properties
* Code/GraphMol/Depictor/RDDepictor.h
- fixed typo in docstring
Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
- added a missing const; formatting changes
Code/GraphMol/RGroupDecomposition/RGroupData.cpp, Code/GraphMol/RGroupDecomposition/RGroupData.h
- moved the code which merges disconnected R groups sharing the same attachment point into a single combined molecule to a private method, RGroupData::mergeIntoCombinedMol(). The method also includes logic to merge atom and bond highlights, if present.
- modernized a for loop
- isMolHydrogen is now a static function since it does not actually require any instance data
- implemented three static function to return the R group, Core and Mol labels, respectively
Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecomp.h
- implemented two private methods, RGroupDecomposition::labelAtomBondIndices() and RGroupDecomposition::setTargetAtomBondIndices(). The first method tags all atoms and bonds in the target molecule such that they can be tracked following core removal by RDKit::replaceCore(). The second method sets common_properties::_rgroupTargetAtoms and common_properties::_rgroupTargetBonds properties on core and R groups. These are vectors of atom and bond indices in the target molecule corresponding to core and R group atom/bonds, respectively, and can be used for color-coding the target molecule according to the R group decomposition it was subjected to, similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp
- formatting changes and for loop modernization
Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h
- implemented updateRGroupDecompositionParametersFromJSON()
- added includeTargetMolInResults boolean parameter
Code/GraphMol/RGroupDecomposition/RGroupMatch.h
- implemented RGroupMatch::setTargetMoleculeForHighlights() and RGroupMatch::getTargetMoleculeForHighlights() methods to, respectively set and get the target molecule where R group decomposition can be color-coded with highlights. This molecule includes the explicit H atoms corresponding to extracted R groups, if any.
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
- use a std::unique_ptr to store the pointer to the C++ RGroupDecomposition instance
- fixed typos in docstrings
Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
- formatting changes
Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp
- do not use deprecated constant
Code/MinimalLib/CMakeLists.txt
- added RDK_BUILD_MINIMAL_LIB_RGROUPDECOMP CMake flag to optionally expose R group decomposition functionality into MinimalLib
Code/MinimalLib/common.h
- added makeDummiesQueries flag to mol_from_input() (defaults to false)
- implemented parse_highlight_multi_colors() function to parse multi-color atom and bond highlights
- enable multi-color atom and bond highlighting
Code/MinimalLib/demo/rgd_demo.html
- added HTML page showcasing the multi-color highlights similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/MinimalLib/jswrapper.cpp
- removed checks for non-nullness of d_mol as d_mol cannot be directly accessed anymore
- replaced all instances of d_mol with get()
- implemented support for multi-color atom and bond highlights
- implemented optional support for R group decomposition
- JSMol is now split into two subbclasses, JSMol and JSMolShared, which both inherit from the JSMolBase class. While JSMol can be constructed from a RWMol* as usual, JSMolShared can be constructed from a ROMOL_SPTR. This avoids unnecessary copies when wrapping a ROMOL_SPTR (e.g., from subtructure library, JSMolList or R group decomposition) into a JSMol to pass it to JS. This also avoids that modifications done in the JS layer on a molecule stored in a MolList (e.g., adding a property) are not persisted because they are carried out on a volatile copy of the molecule rather than on the actual molecule.
- added JSMolBase::copy() convenience method with same functionality as get_mol_copy() to duplicate a molecule
Code/MinimalLib/minilib.cpp, Code/MinimalLib/minilib.h
- replaced all occurrences of d_mol with get(), as d_mol is now private
- removed all occurrences of assert(d_mol) as non-nullness is checked at construction time and whenever get() is called
Code/MinimalLib/tests/tests.js
- added a test for pesistence of modifications made to JSMolShared
- added tests for RGD
- added test for JSMolBase::copy()
Code/RDGeneral/RDValue.h
- removed trailing comma from vector properties such that they can be deserialized as syntactically correct JSON
Code/RDGeneral/types.cpp, Code/RDGeneral/types.h
- added _rgroupTargetAtoms and _rgroupTargetBonds common_properties
* added assignChiralTypesFromMolParity flag
* added test for makeDummiesQueries
* added CFFI tests
* reordered tests
* re-added piece of code that had gone accidentally lost while merging conflicts
* Removed CHECK_INVARIANT following code review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* add option to use chiral presence in atom ranking
* add findMesoCenters
* add includeChiralPresence to python wrapper
* add python wrapper for that
* backup, not working
* backup
* all tests pass
* add tests for partial coverage of stereo groups
all tests pass
* backout the cleanup operations for the initial merge
* track the meso atoms with atom properties.
this is an optimization for later.
* changes in response to review
* add MolOps::expandAttachmentPoints, along with tests
* support expandAttachmentPoints in the mol file parser
* switch the v2 stuff in the guts of the reaction parser
* add collapseAttachmentPoints()
add addAsQueries option to expandAttachmentPoints()
lots of testing
* an edge case and some cleanup
* add python wrapper for those two functions
* Update Code/GraphMol/FileParsers/FileParsers.h
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* changes in response to review
- support addCoords in expandAttachmentPoints()
- support the new attachment point stuff to/from CXSMILES
- add MolOps::details::addExplicitAttachmentPoint() and MolOps::details::isAttachmentPoint() utility functions
---------
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Compile time and runtime deprecation warnings
* Used [[deprecated]] attribute to mark deprecation on cpp side
* Used RDLog to escalate deprecation warnings to python
* deprecated non fingerprint generator fingerprint generation functions
* Address build errors
* suppress deprecation warnings in cpps and tests
* experiment with new SWIG versions in the mac azure pipeline
* More deprecation suppression
* revert mac java experiment
* Fix SWIG syntax errors
* Attempt to fix windows unit test
* Remove test because of logging behavior
* Change linux java build to SWIG 4.1
- removes the need for preprocessor interaction
* Change mac java build to SWIG 4.1
* try updating the CI buid
* lock cmake version
needed to find JNI correctly
* update compiler versions
needed for the boost
* Fix typo and unavailable version
* Fix version conflict
* update mac build
* get linux build working?
---------
Co-authored-by: Patrick Penner <patrick@ppenner.com>
* initial addition of MT support to MolStandardize
* do the other inplace functions
* add mt ops to python wrappers
including tests
* release the GIL
* remove exploratory code added during dev
* make normalizer thread safe
* refactor some repeated code
* Fixes for canonicalization, and stereochemistry
* chnages from code review
* test that was omitted for canon correction
* PR review changes
* changes as per PR review
* missed file checkint to make PR tests compile
* PR conflict resolution
* change to fix PR buld errors (hopefully)
* line delete to force re-running of tests
* changes as per PR review
* resolve merge conflicts with master
* some suggestions
* revert chirality modifications when sanitization isn't being done
* addl changes: no stereo percept when no sanitize
* missing test expected files added
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
* switch from boost::any to std::any
* changes in response to review
* handle the slightly different error messages from different compilers
* document changed error message
* try to use g++10 for the linux builds
* remove those CXX defns
* another spelling
* stupid typo
* bump all linux builds to g++-10
* some day this will be done
* small steps
* increase mac ci builds runtime
* backup
* fixes#6312
all tests pass
needs tests for atoms
* more optimization; tests pass
* get rid of the global variables so that the cartridge works with this
sooooooo weird
* expose RDLog to SWIG wrappers
* - added a SetTee() overload that takes a filename as parameter to simplify redirecting from wrappers that do not have interface with C++ streams (e.g., Java and C#)
- replaced some duplicate code with ClearTee() calls
- replaced RDLogger std::shared_ptr with boost::shared_ptr to make it more easily available from SWIG wrappers
- exposed the RDLogger methods to SWIG wrappers
- added Java test for RDLogger
* this should fix the segfault
* avoid issues on case-insensitive platforms
* here's a solution keeping std:;shared_ptr
* change in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* First stab at disconnecting organometallics the Syngenta way.
* Add support for Li and Na compounds, with tests.
* Correct docstrings.
* Add -1 valence to sodium.
* Add changes from PR 5997.
* Move declaration of disconnectOrganometallics.
* Re-factor tests for disconnectOrganometallics to read V3000 files rather than hard-code in file.
* Add optional options to constructor.
* Python wrapping for disconnectOrganometallics.
* Python tests.
* Correct docString.
* Test using in place overload of disconnect free function.
* options_ should not be a reference.
* Re-work the wrappers.
* Added test MOL files.
* Correct charge on iron atoms.
* Fix tests for charged iron.
* Added some more test complexes.
* Port Marco's oxidation number Python to C++ Descriptor.
* Rename functions.
* Another test.
* Python wrappers.
* Comment in test.
* Throws exception if atom-based function called with non-kekulized parent.
* Fix typo.
* Allow potassium as well.
* Whole molecule calculations for oxidation number only.
Rename prop to OxidationNumber.
* Add OxidationNumber to common_properties.
* Extra comment.
* When deleting atom, update any ENDPTS props on bonds.
Copied in from stale PR ExtraDoc.
* Added hapticBondsToDative with python wrapper.
* Extra test.
* Re-factor endpts parsing.
* Typo.
* Add function for haptic end points inc. Python wrapper.
* Add dative bonds in separate step.
* C++ version of dativeBondstoHaptic.
* Update test mols.
* Python wrapper.
* Fix indents in Python test script.
* Corrected expected test result.
* Only do non-metal to metal conversion of single bond to dative if the explicit valence of the non-metal allows it.
* Fix test broken in a non-material way by previous change.
* Export for DLL.
* Remove redundant function declaration.
* Dave hates Windows.
* Move hapticBondEndpoints to Molops::details.
* And take it out of the Python wrappers.
* Run yapf on reformatted test script.
* Get the DLL builds going.
* addDativeBond -> addHapticBond.
* Batch edits.
* Position arithmetic.
* setQuery.
* Dummy positions for all confs.
* Fix tests for dummy positions for all confs.
* Move tests to catch_organometallics.cpp.
* Modern docString.
* Change member variable names.
* sProp length, bonus batchEdit.
* Add options object to disconnectOrganometallics.
* Tidied license.
Atom precondition.
* GetIntProp.
* Test opts aren't defaults.
* Python wrapper for disconnectOrganometallics with options.
* Minor edit.
* Slightly random attempt to fix Java build.
* Response to review.
* Another stab at the doc strings.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Properly check for boost::any in rdvalue_is
* Response to self review
* Fix missing import in test
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
