David Cosgrove f93016a77f Refactor mol draw2 d (#4948) ...

* 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>

2022-02-18 16:30:21 +01:00

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