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Author SHA1 Message Date
Ricardo Rodriguez
7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
 2025-10-08 16:08:01 +02:00
David Cosgrove
f9b47d907f Add ACS1996 drawing style (#5425) 
* 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>
 2022-07-21 18:11:33 +02:00
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
Greg Landrum
ef5ec47b1d Embed default truetype font (#3288) 
* Embed default font in source.
Unfortunately there's some reformatting in here too.

* make moldraw2d build correctly with _static and in emscripten

* get minmalllib working with freetype and emscripten
 2020-07-15 08:03:58 +02:00
David Cosgrove
bc9e4d6478 Support using FreeType for text rendering (#3237) 
* 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>
 2020-06-23 17:31:50 +02:00