* - fix indentation
- fix regex check (which currently always fails)
* wip
* - added clearMolBlockWedgingInfo()
- added invertMolBlockWedgingInfo()
- MinimalLib::generate_aligned_coords() now inverts stereochemistry if a rigid-body alignment transformation caused chiality inversion
- MinimalLib::generate_aligned_coords() now clears stereochemistry if coordinates changed
- added JSMol::clear_prop() to the already existing JSMol::get_prop() and JSMol::set_prop()
- renamed commonchem to rdkitjson in JS unit test
- added relevant unit tests
* fixed mistake in logic
* - added add_hs_in_place() and remove_hs_in_place() to the JS MinmalLib
- added relevant tests
* - removed check for existence of a property ahead of clearing it as it is not necessary; updated the clearProp docstring to reflect this
- updated the MolFileStereochem.h docstrings based on review comments and fixed a typo
- fixed two (legitimate) compiler warnings as get_molblock() and get_v3kmolblock() should return nullptr and not a pointer to an empty string; added tests for this as there was none
- in MinimalLib/common.h, moved the check of whether a molecule has undergone a flip around the Z axis to a function in the anonymous namespace
- in MinimalLib/common.h, added logic to preserve original wedging (and eventually invert it) also when alignOnly is set to false, in case the wedging is all within the constrained scaffold
- added thourough testing of the wedging logic on both CFFI and JS sides
* - added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms
- added relevant unit tests
* fix Windows build
* - enable building MinimalLib as a plain JS file for usage in legacy/headless browsers
- support alternative way to draw an ellipse on legacy canvas without ellipse support
- update tests.js to test both the standard and the legacy version of MinimalLib
- update demo.html to work with both versions of the library and automatically select one based on browser support of WebAssembly
- fix a regression in demo.html caused by a change in signature of generate_aligned_coords
* reverted most changes
* changes in response to review
* restored demo.html
added a comment to Dockerfile_legacy_browsers explaining how to test in a legacy browser
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.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>
* 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
* fixes#3852
- width should not be implicitly cast to unsigned int
- coordinates should not be rounded ahead of using them in context, as the context will do that with interpolation/antialiasing when generating the bitmap
* - removed another occurrence of std::round
- fixed test that was expecting an integer value which should instead be float
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* backup, does not work
* backup
* baby steps
* basics are now working
* more progress
* add substructure highlighting
* get the FT stuff working too
* get the FT stuff working too
* empirical corrections to dashed bonds
* enable coordgen support
* change min font size
* support dashed lines
* some cleanup
* support all MolDraw2D options when parsing from JSON
* parse MolDraw2D options from JSON
* show stereogroup labels when they are present
* switch to using the new CIP labels in minilib
* update demo to show controlling options
* move all the JS code into jswrapper.cpp
pass the canvas itself instead of the id to the JS functions
introduce offset
* remove extra emscripten load
* cleanup debugging stuff
* update freetype tests
* update non-freetype tests
* changes in response to review
