* Fixed expected test results.
* Implements Github 3305.
Line widths don't scale by default. Line widths are now floats rather than ints.
* Suggestion that testGithub565 be removed.
* Corrected comment.
* Fixed test case.
* Added scaleBondWidth to Python wrappers.
* Fixed expected test values.
* Removed testGithub5.
* Added draw option to scale highlighted bond width.
* Put all the tests back in.
* Tweaked tests to allow for difference in scale between Freetype/No-Freetype images.
* Extra write for CI error.
* Extra write for CI error.
* removed extra write for CI error.
* update expected results
remove debugging output
* Fixed stroke-width to 1 decimal place in SVG files. Altered tests to cope.
* update expected results for python tests
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.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
* First working version with DrawText classes, original functionality only. No font scaling.
* Added font scaling.
* Added atom colours.
* First stab at freetype text drawing. A stash prior to major surgery.
* Freetype seems to be working. On to whack-a-mole.
* Added class flag to atom labels and annotations.
* Another intermim commit whilst re-factoring all string drawing code from MolDraw2D.
* Fixed scaling and implemented max font size.
* Fixed bugs in non-FT Cairo and SVG drawing.
* More re-factoring of drawStrings - now creates StringRwct for each char in all strings.
* More re-factoring of string drawing - all mentions removed from MolDraw2D, I think..
* Working native Cairo, simple tests.
* Working native Cairo, simple tests.
* Padding roumd rectangles.
* Working FT Cairo, FT SVG, native SVG, simple tests.
* Two line labels mostly sorted. Native SVG wrong.
* Two line SVG labels sorted.
* Two line SVG labels sorted.
* Tidied out debug writes.
* Tweaked merge.
* Annotations working, radicals now failing.
* Fixed radicals crash.
* All tests passed for freetype drawings. Grid drawings not right.
* Fixed bug in grid drawings.
* Better font size.
* Fixed legends in grids.
* Fixed rect intersection bug.
* Tidied up font sizes.
* moldraw2DTest1 all passing.
* All catch tests pass.
* Few rixes, and reactions look ok.
* Added minimum font size.
* Fixed radical drawing when max/min font size hit.
* Interim cmmmit, most test1.cpp working.
* Fixed uninitialised min_font_size_ in DrawText. Took out use of MolDraw2D::setFontSize() which probably needs to go back in at some point.
* More test1.cpp passing.
* test1.cpp all pass, freetype and non-freetype
* Fixed superscripts hitting min font size in test860. Made superscripts and subscripts same size.
* testc.pp all pass.
* Fixed bug in freetype text. All testt1.cpp pass.
* All tests passed.d
* Added option for different font.
* Added option for explicit terminal methyls.
* Added option to explicitly not use Freetype in drawers. Used same in catch_tests.cpp.
* Got sense of NO_FREETYPE wrong in catch_tests.cpp. D'oh!
* Fixed Python draw tests.
* Added new options to JSON interpreter.
* Fixed scale of text in contoured plots.
* Added optional molecule to grid drawer to help set scale.
* Fixed Python wrappers for drawing 2D grids .
* Added Greg's CMakeLists.txt
* Moved fonts out of code tree.
Improved handling of font files not found, including logging to rdWarningLog.
* Interim commit.
* Tidied up some namespace std issues.
* Reverted to previous version.
Took out 'using namespace std;'
* update expected java results
* Added multi-line legends. Also carves out a reserved bit for the legend, and sets the font size so the legend will fit.
* enable annotations on windows with freetype
* Removed stray font file.
* Removed stray font file.
* Re-instanted fontSize() and setFontSize(), though with change of units.
* Added RDK_BUILD_FREETYPE_SUPPORT to cmake.
* re-expose the fontsize controls to python.
document API change w.r.t. font size
* Update ReleaseNotes.md
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Several things here
1) move "atomNote" and "bondNote" to common_properties
2) move addStereoAnnotation to the MolDraw2DUtils namespace
3) add addAtomIndices and addBondIndices
4) initialize MolDrawOptions members directly instead of via the ctor
5) add tests for all that
6) the usual reformatting
* Move the annotations functions to MolDraw2DDetails,
no need for them to be in the public API
Remove MolDraw2DDetails.h from the installed headers.
* turn off redundant prepareMolsForDrawing in _moltoimg
* Commit of 2D draw annotation.
* update expected psql results
* First pass at improved radical drawing.
* Fix?
* Fixed different string draw behaviour.
* Removed vestiges of previous radical handling.
* Fixed bug with annnotation placement and added fallback postion.
* Removed unused var.
* update expected reaction svg
* Added option for always having circular highlights.
* Updated JSON to drawOptionns.
* Fixed bug in scale calculation. Centres drawn molecule with option not to.
* Tidied up scale calculation.
* Changed atomHighlightCircles to atomHighlightsAreCircles.
Used shared_ptr for StringRect as VS barfed on unique_ptr.
* Fixed bug with reaction cruft not following now-centred molecules.
* temporary stash
* Stepped back centring of molecule by drawMolecule and fixes to drawReaction prompted by it.
* allow annotations to be disabled at the class level.
disable them for MolDraw2DCairo on win32 (where they just don't work)
* some test cleanup
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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
* basic conrec integration
* basic conrec integration
* add molecule contouring
* update
* add an alpha channel to the color
* allow filling the grid
* cleanup
* remove some debugging output
* first pass at getting similarity maps to actually work
* updates
* add another test
explicitly set linewidth to 1
* some SVG cleanup
* add option for extra padding
* update expected test results
* efficiency
* at least something of a test
* forgot an import
* fix SWIG wrappers
* cleanups in response to review
* allow calling the functions without providing levels
* allow contouring numpy grids
* a bit of header cleanup
* Fixes#1106
* First pass, basics.
Still need tests and handling of parameters.
* initial pass at including JSON parsing of options (not complete)
* handle errors while parsing json instead of just crashing the server
* updated (and working) JSON configuration
* first drawing tests
* document the new function
* it helps to save before committing
* Fixes#982
also changes bond-wedging algorithm to favor lighter non-ring bonds
* prefer wedging bonds to lower-degree atoms
* Fixes#983
* small fixes
- Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom
- Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom.
* Fixes#985
This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
