* Option to use standard atom colours under highlights.
* Update hash codes for catch_tests.cpp.
* Update hash codes for test1.cpp and rxn_test1.cpp.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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!
* Option to remove brackets from atom lists.
* Python wrapper.
* Change option name after review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
* 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>
* drawMolACS1996 should not throw with no coords.
* Only calculate coords once.
* Scrub the last bit, it loses the coords again when changing back to ROMol *.
* Hash code check.
* Doh!
* Only generate coords once.
* Always generate 2D coords if needed.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* enable optional visualization of complex query atoms in a more compact form
* disable alpha channel support on legacy browsers
* - changes in response to review
- added metal queries
- fixed a docstring
* fix Windows build
* gave up and tested indirectly as I really do not want to export internal functions
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - extend prepareAndDrawMolecule() with missing optional parameters already supported by prepareMolForDrawing()
- enable useMolBlockWedging, wedgeBonds, addChiralHs, forceCoords, wavyBonds in CFFI/MinimalLib
- add relevant CFFI and JS unit tests
* Replace AllProps with a smaller subset
* make sure we pickle properties Python-side
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* 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>
* Add draw option to force use of wedge information in MolBlock if present.
* Add check_file_hash.
* Move reapplyMolBlockWedging to MolFileStereochem and test case.
Expose to Python as ReapplyMolBlockWedging.
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* - adds normalizeDepiction() and Python wrappers
- adds straightenDepiction() and Python wrappers
- adds an early check for R-labels to be in the accepted range to avoid throwing an exception later on
- adds a kekulize flag to process_details() to enable depicting molecules which fail to kekulize from JavaScript
- adds JavaScript functions to get fingerprints as Uint8Array
- adds JavaScript function to generate pickled molecule as Uint8Array
- adds JavaScript function to restore molecule from Uint8Array pickled
- adds has_coords() JavaScript function
- adds set_new_coords() to set JSMol coordinates in-place
- adds get_mol_copy() to obtain a JSMol copy
* fix build failures
* changes in response to review
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>
* prefer to not wedge bonds to double bonds
* addWavyBondsForStereoAny() works
* add option to clear bond stereo
* support wavy bonds in prepareMolForDrawing()
get rid of MolDraw2D/catch_main.cpp
* add a drawing example
* name the bug correctly
* add that new functionality to the python wrapper
* remove some debugging cruft
* 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>
* 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>
* 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
* 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
* works
* auto download of comic-neue font
* support it in the python layer
* getting ready for a PR
* tone down the wobbly line effect a bit
* add end-point shifts
tone the wiggles down a bit
* 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
