* Option to put padding round elements of reaction.
* Rename the option to componentPadding.
* Missed one.
* Correct filename.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fix bond smoothing - apply atom index offset to products.
Update Hash codes.
Tweak side_by_side_images.py.
* Added hash code for new file. Doh!
---------
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>
* 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>
* 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
* 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>
* MolDraw2D::drawMolecules() should not crash on null molecules
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* First draft.
Polyline round bond joins is smaller.
Continuous highlight bonds mitre.
* Remove historical and now misleading comment.
* Mitre the continuous bond highlights.
* Better bond highlighting with not continuous highlighting.
* Updated hash codes. Extra test.
* Updated hash codes.
* Script to update hash codes automatically.
* Fix test.
* Fix test.
* Remove debugging file write.
* Removed redundant code.
* More auto.
* Removed newly redundant function.
* More explanation and an extra example/test.
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* disable the info and debug logs by default
* adjust tests to the newly disabled logs
* add LogStateSetter
* namespace reorg
* add some tests
* remove vestigial code
* switch to using std::vector
* MolDraw2D refactoring
- rename setupMoleculeDraw->initMoleculeDraw
- track whether or not initDrawing() has been called
- centralize calls to initDrawing() and clearDrawing() into initMoleculeDraw()
- update svg hashes in tests
* update some expected test results
* support changing font scale and default scale
add reaction test
* does not work... this is hard
* all tests pass
* do something about legends
* docs
* more tests
* more docs
* cleanup
* going around in circles...
hopefully converging
* cleanup
* Single bond skeleton works.
* Simple bond drawing seems to be working.
* Initial addition of atom symbols.
* Stash of not-quite-working atom symbols prior to major surgery.
* Atom symbols seem to be working. Major surgery not required, just inverted Y coords at the outset.
* Add classes to atom labels.
* Renamed AtomLabel AtomSymbol.
* Add highlights.
* Fix bug from PR4839.
* Molecule note.
* Added atom notes.
* Added bond notes.
* Extract radicals.
* Annotation via new DrawAnnotation class.
* Add brackets.
* Add linknodes.
* Add close contacts.
* Add attachment points. Fix wavy lines.
* Draw molecules in grid.
* Tidy.
* Fix radicals when font has hit maxFontSize.
Make getDrawCoords work.
* Draw primitives take atom or draw coords.
* Fix legends.
* More fixing for tests. DrawMol::setScale now takes font scale as well.
* tidy debug writes
* Variable fraction of panel for legend.
* Better legend positioning.
* Fix sub- and super-script spacing.
Added spaces to Freetype strings.
* Basic reaction drawing.
* Reaction highlighting.
* Minor tweak to reacctions.
* Tweaked reaction DrawMol widths.
* Fix atomTags.
* Fix catch tests except contours.
* Contouring working in catch_tests.cpp.
* Fix catch tests.
* AtomSymbol and DrawAnnotation into MolDraw2D_detail.
* DrawMol and DrawShape into MolDraw2D_detail.
* DrawText inot MolDraw2D_detail.
* Machete out.
* DrawText goes private.
* Move some stuff about, such as StringRect to its own header.
* Python wrapper compiles (but crashes when Draw imported).
* More tidying. Python DrawArrow failing.
* Linux changes.
* Fixed error in DrawShapeArrow spotted by valgrind.
Fixed some warnings from gcc.
* Maybe fixed DrawArrow.
* Added basic argparse interface.
* Added newlines.
* Changes in response to review.
Non-const args in move constructors and operator=.
Added missing classes to MolDraw2D_detail.
Deleted move operator= where it had been forgotten.
Fixed copyright dates.
* Deleted all default c'tors in derived classes.
* Changes in response to review:
Wedge widths now a proportion of mean bond length in draw coords..
Add padding below legend when positioning it.
* Fix tests.
* Fix the private/protected mess of the new classes.
* Moved doesLineIntersect etc.
* Reinstate original alignString for non-FT drawings.
* More faffing about with reaction layouts.
* Fix font sizes in testGitHub3391.
* Fix atom notes fitting inside fat wedges.
* Fix molecule annotation font size.
* More fixes of rectangle/triangle collision detection.
* Test for highlight linewidth multiplier.
* Use push_back not emplace_back.
* Attempt at better Freetype char spacing.
* Option to turn off TEST_ASSERT. Currently off.
* Fixed embarrassing maths to do with wedge fatness.
* More tidying post-review.
* Document highlight_linewidth_multipliers.
* Expose baseFontSize to Python.
* Changes in response to review.
* Allow DrawMolecules molecules to be drawn to different scales.
* Fix bond sneaking between C:8 in, for example, reactions.
* Fix bad re-factoring.
* Fix globbing.
* Changes in response to review.
* Add invariant check.
* Add draw option to fix font size.
* suggested changes
* Update catch test results.
* Fix expected freetype results.
* Fix non-freetype drawers.
* Fin non-freetype test results.
* get the Qt drawer working too
* Fix disappearing reaction highlights.
* Changes as result of review.
* Fixed non-FreeType hash codes for reaction SVGs. Extra comment in catch_tests.
* reactant highlighting was clearning properties
* Fix for failing contour python test.
* fix a non-freetype problem
* swig wrappers working
* Bump timeouts in test.
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* resolves oss-fuzz #24399
* clean up some undefined behavior
* fix some UB in mergeQueryHs
* be more defensive
* defensive programming
* fix a _cxsmilesBondIdx bug
* more defensive programming
* Fixes#4838
DrawString() with alignment argument does not work from Python
* Fixes#4837
MolDraw2D::DrawArc() not exposed to Python
* Fixes#4836
drawArc() starting at wrong angle
* add docs and tests for the alignment argument
* MolDraw2D refactoring
- rename setupMoleculeDraw->initMoleculeDraw
- track whether or not initDrawing() has been called
- centralize calls to initDrawing() and clearDrawing() into initMoleculeDraw()
- update svg hashes in tests
* update some expected test results
* support changing font scale and default scale
add reaction test
* does not work... this is hard
* all tests pass
* do something about legends
* docs
* more tests
* more docs
* cleanup
* going around in circles...
hopefully converging
* cleanup
* response to review
along with a bit of cleanup
* Fixed calculation of position of SGroup data.
* Updated hash codes.
* Fixed poor placement of SGroupData when drawing in grid.
* Tidier way of setting font size ignoring min and max font sizes.
* More sensible calling of string clash checks.
* Update updated test values.
* Updated comments.
* Changes in response to review.
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fixes#2976
Stops re-generating reaction coordinates when that's not required
* add better test
* try to deal with bad font sizes from mol files
* one more expected result update
* try to be smarter about font changes
* suppress a compiler warning
* remove debug output
* update some expected test results
* add a new mol draw option
to draw wedge bonds with a single color rather than two
* change option name, add option to json parser
Co-authored-by: Jason Biggs <jasonb@wolfram.com>
* cleanup a bunch of g++ warnings
* make it work with clang
* remove some additional warnings based on CI builds
* fix that version number
* stop being verbose when building
* adds isotopeLabels and dummyIsotopeLabels MolDrawOptions
* changes in response to review
* more changes in respons to review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* break out the LinkNode processing code
* initial version of linknode rendering
* add another test and fix a minor issue
* boost::format
* fix a bad merge
* first basic pass at molecule notes
FIX problem with updating bounding box based on non-centered annotations
* add chiral flags and simplified stereo annotations
* tests
* molecule annotations are the same font size as atom labels
