* Fixes#7140
deprecates the old version and creates a new one in Chirality.h
adds it to the python wrappers
* changes in response to review
* backup
* support custom labels with templates
* Before making a wedged bond meet a single bond, check if they're co-linear and skip if so.
* Write the file before the test so we can still look at it if the test fails.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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>
* Diatomic tests working.
* Working with simple multi-atom tests.
* Most tests not working.
* Minor tidy.
* Almost working. Failure in lasso_highlights_6.svg.
* Intersecting circles looks ok for same radius.
* All seems to be working.
* Better tests.
* Tidy up.
* More tidying.
* Fix warnings.
* Fix warnings.
* Change REQUIRE to CHECK.
* Changes after review.
* 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.
* Make reaction drawings deal with padding properly.
* Move large lambdas into anonymous namespace.
Correct totWidth after scaling plusWidth.
* Update some hashcodes.
* Take out debugging setting. Bugger.
* Padding on height as well.
* Hash codes.
* Delay padding use in flexiCanvas.
* More centring.
* Light grey background in side_by_side table.
* Tweak agents layout for testReactionCoords.
* Fully ignore missing reagents and products.
* Hash codes.
* Const references.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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
* First working lasso.
* Adjust lasso radii in non-overlapping sets of atoms.
* Move MultiColourHighlightStyle enum out of MolDrawOptions class.
Add Python wrappers.
* Update copyright notices.
* Fix bug where order of lines off arc wasn't clockwise, so circle wasn't trimmed properly.
* Use highlight_bond_map in lassos.
* Fix bug in colour selection for multi-coloured lasso bonds.
* Response to review.
* Attempt to add new option to JSON input.
* Fix bug with larger radii.
* Fix yet another bug with the arc tidying.
* Remove separate colouring of bond highlights in Lasso.
* Fix intersection between line and arc not on end of line.
* Another pernickety fix.
* Tidy.
* I should know better than to use the web editor
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix bug where large padding gave a legend font size of 0.
The padding is now implemented by making a smaller, offset drawing area within the width_ and height_, dimensions drawWidth_, drawHeight_. The previous drawHeight_ has been replaced by molHeight_.
* Update test results.
* Update hash codes.
* Update test results.
* Update test results for no freetype.
* Update hash codes for no freetype.
* Update hash codes for freetype.
* Update hash codes for no freetype.
* Update hash codes for freetype.
* Update expected test results.
* Update hash codes.
* Fix contour plots not being lined up with atoms.
* Fix shrinkToFit.
* Update expected test result.
* Fix typo in test name.
* Update expected test result.
* Update expected test result.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* change default behavior so that dative bonds are not included in ring finding
* make sure that generating 2D coords does not lose the rings
* cleanup some leftover problems
* Test for Github6160
* Basic fix. Problem caused by 4 coordinate sulfur.
* Get the test right.
* Fix truncation of double bonds to atom symbols.
* Fix double bond lines if both ends have atomic symbol.
* Tidy.
Add hash codes.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* drawMolACS1996 should not throw with no coords.
* Only calculate coords once.
* Scrub the last bit, it loses the coords again when changing back to ROMol *.
* Hash code check.
* Doh!
* Only generate coords once.
* Always generate 2D coords if needed.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* enable optional visualization of complex query atoms in a more compact form
* disable alpha channel support on legacy browsers
* - changes in response to review
- added metal queries
- fixed a docstring
* fix Windows build
* gave up and tested indirectly as I really do not want to export internal functions
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* Adapt allene drawing code to cope with other linear groups.
* Remove stray debugging write.
* Over-eager tidying remove key aspect of the fix. Doh.
* Changes after review.
* Better solution that doesn't change the public API.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Make arrowhead of dative bond a consistent number of pixels in size, based on doubleBondOffset.
* Improve test.
* Clang noticed incorrect order of panelWidth, panelHeight for some tests.
* Fix some hash codes.
* Give correct github issue number.
* Update hash codes.
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fix ellipse extremes calculation.
* Fix tests.
* fix a typo I made during the merge
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Draw type of SGroups (STY) in picture.
* Move drawBottomLabel from lambda to anonymous namespace.
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* MolDraw2D::drawMolecules() should not crash on null molecules
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
