Adds a new function MolDraw2D_detail::getSGroupDataLabels() that returns
the text and molecule-coordinate positions of DAT SGroup labels, using
the same placement logic as the drawing code. This allows external
renderers to display SGroup labels consistently with RDKit's placement.
Refactors DrawMol::extractSGroupData() to call getSGroupDataLabels()
internally, eliminating the duplicate FIELDDISP parsing and position
computation logic.
Closes#7829
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* 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
* 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.
* 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>
* 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>
* Started on ACS 1996 drawing mode.
Significant change (not by itself, sadly) is that MolDrawOptions::lineWidth has changed from int to double to allow for ACS requirement of 0.6px bond widths.
* Wavy lines and dashed wedges.
* Better dashed wedges.
* Rounder wavy bonds, same as SVG.
* Added FreeSans font for ACS1996 mode.
* Add help functions to write enum classes to ostream.
* Dashed wedge separation now 2.5px between line edges rather than line middles. Therefore wider gap between lines.
* Increase offset for wavy bond. Get classes for atoms and bonds in wavy bond correct.
* For SMILES input, option to force wavy and crossed bonds for unspecified stereochem.
* Tidy debugging.
* Extra space round atom labels.
* Extra space between chars in freetype string.
* Reformats.
* Change double bond offset.
* Improve ring double bonds.
* Simple non-ring double bonds all working.
* Tidy.
* All double bonds seem good.
* Remove redundant function.
Move calcTripleBondLines into DrawMol for consistency with calcDoubleBondLines.
Use doubleBondOffset for wavy lines.
* Correct spacing between FT chars.
* Tidying.
* Use MolBlock wedging if there is any. Needs to be made an option.
* If dashed wedge thick end has bonds of it, stop one dash short.
* Adjust solid wedge ends to line with attached bonds.
* Width of wedge ends now based on double bond separation.
* Change catch_tests.cpp
* Rounder waves in wavy lines.
* Dashed wedges same width even if one dash less..
* Embedded Roboto-Regular font in code.
* Fix docstrings.
* doubleBondTerminal swapped ends.
Deal with O2 - 2 terminal atoms of degree 1.
* Fix terminal double bonds.
* Slightly fatter truncated wedge bonds.
* Fix crash on complicated double bonds.
* Control more assert tests with DO_TEST_ASSERT.
* Fix 2 colour solid wedges.
Fix slanted wedge for morphine (test1_5).
* Change definittion of multipleBondOffset to fraction of mean bond length.
* Don't slant end of solid wedge to atom symbol.
* Fix wiggle separation.
* Fix 2-colour terminal double bonds.
* Fix colours on triple bonds.
* Don't attempt to draw non-existent points in triangle..
* Symmetric bond for P=O and like.
* Fix query bonds.
* Reformatting.
* Tidy up use of font.
* Add FreeSans font and license to $RDBASE/Data/Fonts.
* Draw unspecified stereo as unknown.
* Add check_file_hash.
* Tidying.
* Tidying.
* Start Python wrappers.
* Fix solid wedges for 3-connected atoms.
* Docstrings.
* Tidying.
* Alter width of bond highlights in ACS 1996 mode.
* Expose setACS1996Options and mean BondLength in Python.
* Expose drawMolACS1996Cairo in Python.
Docstrings.
* Extra padding between legend and picture in flexicanvas.
* Python tests.
* Tidy catch tests.
* Tidying.
* Fix catch tests.
* Fix no Freetype tests.
* Draw solid wedge more sensibly..
* Fix bond end at solid wedge.
* Tidy.
* Fix Python Cairo build issues.
* Fix wedge end shape for terminal double bonds.
* Hide the joins at the bond ends.
* Fix gcc pickiness.
* Extra test for no atom labels.
* Change where it looks for FreeSans.ttf for ACS1996 drawings.
* Same number of waves for wavy bonds in SVG and Cairo.
* Same number of waves for wavy bonds in SVG and Cairo.
* rename unspecifiedStereoIsUnknown to markUnspecifiedStereoAsUnknown and move to MolFileStereochem.h
* refactor use of iterators
* py docs update
* undo a bunch of bad formatting changes
* remove FreeSans
* get windows builds working
* Fix problem with Windows build.
* Changes in response to review.
* Align description of unspecifiedStereoIsUnknown in C++ to match Python.
* Still working on file open modes.
* Took out extraneous functions for drawing in ACS1996 mode, including the one that was breaking the windows build.
* Add RDKIT_MOLDRAW2D_EXPORT.
* Fix expected test results.
* Clarified warning.
* RDKIT_MOLDRAW2D_EXPORT missing.
* Windows!
* Update Code/GraphMol/MolDraw2D/rxn_test1.cpp
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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>
* backup
* further progress
* backup
* refactor handling of atom/bond annotations
move to a single annotation list to make it easier to add new annotation
types
* backup, doesn't actually work
* not unhappy with how the bracket rendering now works
still need to do bracket annotations
* backup
* commit first pass at brackets annotations
* add a bit more flexibility to how we handle annotations
Stll needs to be elaborated a bit, but the tests currently pass
* cleanup
* support comic mode with brackets
moves the handdrawnLine code to MolDraw2D_detail, which is a better place for it
* updates in response to review
* First pass of fixing layout of OH/NH type drawing.
* Fixed scale for N/S NH type groups.
* Fixed bond end points with new display of heteroatoms.
* Fixed case where it drew aromatic dashed bonds in wrong ring for morphine.
* Minor edit.
* Fixed non-drawing of chiral bonds.
* Removed use of boost for_each.
* Modern atom traversal.
* Put in fixed scale for drawings.
Made drawMolecule() take note of prepareMolsBeforeDrawing.
Updated more iterators to modern idiom.
* Added fixed bond length for drawing.
* Fixed drawing of CH4, NH3 etc.
* Stash of working but ugly, prior to re-work.
* Better, simpler splitting of atom symbols.
* Took clang-tidy's advice about use of override.
* Tidied up drawing of text strings.
* Tweaked what is classed as vertical bond in drawing.
* fixedBondLength now down-scales if it would overflow the draw window.
* Some tidying.
* Tests for new parameters in JSON.
Fixed some existing tests where, for example, scale on picture is now different.
* Added option to rotate 2D draw coords before drawing.
* First pass at highlighting atoms in multiple colours. Circles only at the moment.
* Line width scales if big enough.
* Tweaked SVG text drawing.
* Added highlighting with more than 1 colour on an atom. C++ only.
* Fixed some issues with widths of highlights in a frustrating game of whackamole.
Updated some tests accordingly.
* Added Python wrapper for new drawing code.
* Removed debugging writes.
* Added C++ test for multi-coloured highlights.
* Added python test for multi-coloured highlights.
* Attempt to show radicals.
* Tidied up radicals in drawing, including a bullet instead of full stop in SVG.
* Fixed catch_tests.cpp for MolDraw2D.
* Fixed crash in Python wrappers on OSX.
* Fixed test5_2.svg bug (trailing </tspan>).
Made wavy line width scale as other lines do.
* Improved placing of charges.
* We're already in the future.
* Fixed a number of bugs that made drawMolecules not set the scales properly.
* Fixed Cairo wavy line width.
* Fixed non-closure of collision boxes.
* Added maximum font size for text, with tests.
* Addressed all Greg's first PR change requests.
* Fixed crash in extractAtomsymbols.
* stop using coordgen and adjust tests to reflect that
there's a bit of reformatting in here too
* Fixed layout of reactions.
* Fiddled with moldraw2DTest1 tests again.
* Fiddled with catch test.
* Fixed istope postion in W atom labels.
* Minor tweak to cairo,
* update expected results
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
