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d9d1fe2838
* fixes #6773
* removed unused captures
* update release notes and cmakelists for beta (#6788)
* Removed some code duplication between Depictor.cpp and common.h (#6368)
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730)
* Set _SmilesStart when parsing SMARTS.
* SmartsWriter should also invert first atoms, like SMILES.
* Update test cases now these SMILES match themselves as SMARTS.
* rerun bison
* cleanup a possible repeated define
* When an atom moves from the first to second position winding should flip in SMARTS (i.e. same as SMILES).
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Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Some small cleanups from the UGM Hackathon (#6744)
* move definition of a couple global constants from a .h to a .cpp
* careful removal of some redundant atom PRECONDITIONS
* careful remove of some redundant ROMol PRECONDITIONS
a bit of additional cleanup
* optimization masquerading as modernization
* some more tidying
* a bit more atom cleanup
* change in response to review
* Fixes #6756 (#6780)
* update release notes and cmakelists for beta (#6788)
* move problematic functions to Chirality namespace
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* move problematic functions to Chirality namespace
* added missing dependency
* let's check what is going wrong
* CoordGen tests should not run if CoordGen support is not available in the build
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Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
Co-authored-by: John Mayfield <john@nextmovesoftware.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Revert "Removed some code duplication between Depictor.cpp and common.h (#6368)" (#6797)
This reverts commit ddfe708b37.
* All 3d des (#6741)
* add function to calc all 3D descriptors
* fix indentation in CalcMolDescriptors3D
* add error handling for 2D molecules
* suggested changes
* change exception type
* add unit tests
* add random seed to conf gen in unit tests
* fix function call in unit tests
* fix expected PMI1 value in tests
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Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing (#6792)
* _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing and not run PrepareMolForDrawing if requested not to
* _moltoimg() and _moltoSVG() should honor drawOptions.prepareMolsForDrawing and not call PrepareMolForDrawing if asked not to
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Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Bad lasso (#6751)
* Better separation of lines.
* Only put atoms in colour list once.
* Test.
* Hash codes.
* Response to review.
* First attempt at fixing stray line.
* Tidier.
* Squared distances.
* tag release (#6801)
* fixes #6773
* removed unused captures
* - fixed comment
- fixed bug found in checkIfRingsAreClosed()
* - removed redundant NRing queries
- added ring size queries to avoid incorrect matches with MCS results originated with MatchFusedRingsStrict
* fixed doctests
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Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: John Mayfield <john@nextmovesoftware.com>
Co-authored-by: Rachael Pirie <56546141+RPirie96@users.noreply.github.com>
Co-authored-by: David Cosgrove <davidacosgroveaz@gmail.com>
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