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MolDraw2D.h
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1//
2// Copyright (C) 2014-2021 David Cosgrove and other RDKit contributors
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10// Original author: David Cosgrove (AstraZeneca)
11// 27th May 2014
12//
13// This class makes a 2D drawing of an RDKit molecule.
14// It draws heavily on $RDBASE/GraphMol/MolDrawing/MolDrawing.h.
15// One purpose of this is to make it easier to overlay annotations on top of
16// the molecule drawing, which is difficult to do from the output of
17// MolDrawing.h
18// The class design philosophy echoes a standard one:
19// a virtual base class defines the interface and does all
20// the heavy lifting and concrete derived classes implement
21// library-specific drawing code such as drawing lines, writing strings
22// etc.
23
24#include <RDGeneral/export.h>
25#ifndef RDKITMOLDRAW2D_H
26#define RDKITMOLDRAW2D_H
27
28#include <vector>
29
30#include <Geometry/point.h>
32#include <GraphMol/RDKitBase.h>
35
36// ****************************************************************************
37using RDGeom::Point2D;
38
39namespace RDKit {
40
41namespace MolDraw2D_detail {
42class DrawMol;
43class DrawText;
44} // namespace MolDraw2D_detail
45
46//! MolDraw2D is the base class for doing 2D renderings of molecules
48 public:
49 //! constructor for a particular size
50 /*!
51 \param width : width (in pixels) of the rendering
52 set this to -1 to have the canvas size set automatically
53 \param height : height (in pixels) of the rendering
54 set this to -1 to have the canvas size set automatically
55 \param panelWidth : (optional) width (in pixels) of a single panel
56 \param panelHeight : (optional) height (in pixels) of a single panel
57
58 The \c panelWidth and \c panelHeight arguments are used to provide the
59 sizes of the panels individual molecules are drawn in when
60 \c drawMolecules() is called.
61 */
62 MolDraw2D(int width, int height, int panelWidth, int panelHeight);
63 MolDraw2D(const MolDraw2D &rhs) = delete;
64 MolDraw2D(MolDraw2D &&rhs) = delete;
65 MolDraw2D &operator=(const MolDraw2D &rhs) = delete;
66 MolDraw2D &operator=(MolDraw2D &&rhs) = delete;
67 virtual ~MolDraw2D();
68
69 //! draw a single molecule
70 /*!
71 \param mol : the molecule to draw
72 \param legend : the legend (to be drawn under the molecule)
73 \param highlight_atoms : (optional) vector of atom ids to highlight
74 \param highlight_atoms : (optional) vector of bond ids to highlight
75 \param highlight_atom_map : (optional) map from atomId -> DrawColour
76 providing the highlight colors. If not provided the default highlight colour
77 from \c drawOptions() will be used.
78 \param highlight_bond_map : (optional) map from bondId -> DrawColour
79 providing the highlight colors. If not provided the default highlight colour
80 from \c drawOptions() will be used.
81 \param highlight_radii : (optional) map from atomId -> radius (in molecule
82 coordinates) for the radii of atomic highlights. If not provided the default
83 value from \c drawOptions() will be used.
84 \param confId : (optional) conformer ID to be used for atomic
85 coordinates
86
87 */
89 const ROMol &mol, const std::string &legend,
90 const std::vector<int> *highlight_atoms,
91 const std::vector<int> *highlight_bonds,
92 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
93 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
94 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
95
96 //! \overload
97 void drawMolecule(const ROMol &mol,
98 const std::vector<int> *highlight_atoms = nullptr,
99 const std::map<int, DrawColour> *highlight_map = nullptr,
100 const std::map<int, double> *highlight_radii = nullptr,
101 int confId = -1);
102
103 //! \overload
104 void drawMolecule(const ROMol &mol, const std::string &legend,
105 const std::vector<int> *highlight_atoms = nullptr,
106 const std::map<int, DrawColour> *highlight_map = nullptr,
107 const std::map<int, double> *highlight_radii = nullptr,
108 int confId = -1);
109
110 //! \overload
112 const ROMol &mol, const std::vector<int> *highlight_atoms,
113 const std::vector<int> *highlight_bonds,
114 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
115 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
116 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
117
118 //! draw molecule with multiple colours allowed per atom.
119 /*!
120 \param mol : the molecule to draw
121 \param legend : the legend (to be drawn under the molecule)
122 \param highlight_atom_map : map from atomId -> DrawColours
123 providing the highlight colours.
124 \param highlight_bond_map : map from bondId -> DrawColours
125 providing the highlight colours for the bonds. If the highlight style
126 is Lasso (as opposed to the default CircleAndLine) then the colours in the
127 highlight_bond_map will be ignored, although the entries in the map will
128 control which bonds are highlighted. The lasso will be coloured according
129 to the associated atom colours.
130 \param highlight_radii : map from atomId -> radius (in molecule
131 coordinates) for the radii of atomic highlights. If not provided for an
132 index, the default value from \c drawOptions() will be used.
133 \param highlight_linewidth_multipliers : map from atomId -> int, used to
134 vary the width the highlight lines. Only active if
135 drawOptions().fillHighlights is false.
136 \param confId : (optional) conformer ID to be used for atomic
137 coordinates
138 */
140 const ROMol &mol, const std::string &legend,
141 const std::map<int, std::vector<DrawColour>> &highlight_atom_map,
142 const std::map<int, std::vector<DrawColour>> &highlight_bond_map,
143 const std::map<int, double> &highlight_radii,
144 const std::map<int, int> &highlight_linewidth_multipliers,
145 int confId = -1);
146
147 //! draw multiple molecules in a grid
148 /*!
149 \param mols : the molecules to draw
150 \param legends : (optional) the legends (to be drawn under the
151 molecules)
152 \param highlight_atoms : (optional) vectors of atom ids to highlight
153 \param highlight_atoms : (optional) vectors of bond ids to highlight
154 \param highlight_atom_map : (optional) maps from atomId -> DrawColour
155 providing the highlight colors. If not provided the default highlight colour
156 from \c drawOptions() will be used.
157 \param highlight_bond_map : (optional) maps from bondId -> DrawColour
158 providing the highlight colors. If not provided the default highlight colour
159 from \c drawOptions() will be used.
160 \param highlight_radii : (optional) maps from atomId -> radius (in molecule
161 coordinates) for the radii of atomic highlights. If not provided the default
162 value from \c drawOptions() will be used.
163 \param confId : (optional) conformer IDs to be used for atomic
164 coordinates
165
166 The \c panelWidth and \c panelHeight values will be used to determine the
167 number of rows and columns to be drawn. Theres not a lot of error checking
168 here, so if you provide too many molecules for the number of panes things
169 are likely to get screwed up.
170 If the number of rows or columns ends up being <= 1, molecules will be
171 being drawn in a single row/column.
172 */
174 const std::vector<ROMol *> &mols,
175 const std::vector<std::string> *legends = nullptr,
176 const std::vector<std::vector<int>> *highlight_atoms = nullptr,
177 const std::vector<std::vector<int>> *highlight_bonds = nullptr,
178 const std::vector<std::map<int, DrawColour>> *highlight_atom_maps =
179 nullptr,
180 const std::vector<std::map<int, DrawColour>> *highlight_bond_maps =
181 nullptr,
182 const std::vector<std::map<int, double>> *highlight_radii = nullptr,
183 const std::vector<int> *confIds = nullptr);
184
185 //! draw a ChemicalReaction
186 /*!
187 \param rxn : the reaction to draw
188 \param highlightByReactant : (optional) if this is set, atoms and bonds will
189 be highlighted based on which reactant they come from. Atom map numbers
190 will not be shown.
191 \param highlightColorsReactants : (optional) provide a vector of colors for
192 the
193 reactant highlighting.
194 \param confIds : (optional) vector of confIds to use for rendering. These
195 are numbered by reactants, then agents, then products.
196 */
198 const ChemicalReaction &rxn, bool highlightByReactant = false,
199 const std::vector<DrawColour> *highlightColorsReactants = nullptr,
200 const std::vector<int> *confIds = nullptr);
201
202 //! returns the size of the box for the molecule with current drawing settings
203 std::pair<int, int> getMolSize(
204 const ROMol &mol, const std::string &legend = "",
205 const std::vector<int> *highlight_atoms = nullptr,
206 const std::vector<int> *highlight_bonds = nullptr,
207 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
208 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
209 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
210
211 //! clears the contents of the drawing
212 virtual void clearDrawing() {
213 if (needs_init_) {
214 initDrawing();
215 needs_init_ = false;
216 }
217 };
218 //! draws a line from \c cds1 to \c cds2 using the current drawing style
219 //! in atom coords. If rawCoords is passed as true,
220 //! the coordinates are used as is, if not they are assumed to be in
221 //! the molecule coordinate frame and converted with getDrawCoords
222 //! into canvas coords.
223 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
224 bool rawCoords = false) = 0;
225 //! draw a polygon. Note that if fillPolys() returns false, it
226 //! doesn't close the path. If you want it to in that case, you
227 //! do it explicitly yourself. If rawCoords is passed as true,
228 //! the coordinates are used as is, if not they are assumed to be in
229 //! the molecule coordinate frame and converted with getDrawCoords
230 //! into canvas coords.
231 virtual void drawPolygon(const std::vector<Point2D> &cds,
232 bool rawCoords = false) = 0;
233 //! @}
234
235 //! A Whole bunch of drawing primitives. They may be over-ridden
236 //! by different renderers, or they may be implemented in terms of
237 //! drawLine and drawPolygon above. If rawCoords is passed as true,
238 // the coordinates are used as is, if not they are assumed to be in
239 // the molecule coordinate frame and converted with getDrawCoords
240 // into canvas coords.
241 //! draw a line where the ends are different colours
242 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
243 const DrawColour &col1, const DrawColour &col2,
244 bool rawCoords = false);
245 //! draw a triangle
246 virtual void drawTriangle(const Point2D &cds1, const Point2D &cds2,
247 const Point2D &cds3, bool rawCoords = false);
248 //! draw an ellipse
249 virtual void drawEllipse(const Point2D &cds1, const Point2D &cds2,
250 bool rawCoords = false);
251 // draw the arc of a circle between ang1 and ang2. Note that 0 is
252 // at 3 o-clock and 90 at 12 o'clock as you'd expect from your maths.
253 // ang2 must be > ang1 - it won't draw backwards. This is not enforced.
254 // Angles in degrees.
255 virtual void drawArc(const Point2D &centre, double radius, double ang1,
256 double ang2, bool rawCoords = false);
257 // and a general ellipse form
258 virtual void drawArc(const Point2D &centre, double xradius, double yradius,
259 double ang1, double ang2, bool rawCoords = false);
260 //! draw a rectangle given two opposite corners
261 virtual void drawRect(const Point2D &cds1, const Point2D &cds2,
262 bool rawCoords = false);
263 //! draw a line indicating the presence of an attachment point (normally a
264 //! squiggle line perpendicular to a bond)
265 virtual void drawAttachmentLine(const Point2D &cds1, const Point2D &cds2,
266 const DrawColour &col, double len = 1.0,
267 unsigned int nSegments = 16,
268 bool rawCoords = false);
269 //! draw a wavy line like that used to indicate unknown stereochemistry
270 virtual void drawWavyLine(const Point2D &cds1, const Point2D &cds2,
271 const DrawColour &col1, const DrawColour &col2,
272 unsigned int nSegments = 16,
273 double vertOffset = 0.05, bool rawCoords = false);
274 //! Draw an arrow with either lines or a filled head (when asPolygon is true)
275 virtual void drawArrow(const Point2D &cds1, const Point2D &cds2,
276 bool asPolygon = false, double frac = 0.05,
277 double angle = M_PI / 6,
278 const DrawColour &col = DrawColour(0.0, 0.0, 0.0),
279 bool rawCoords = false);
280 // draw a plus sign with lines at the given position.
281 virtual void drawPlus(const Point2D &cds, int plusWidth,
282 const DrawColour &col, bool rawCoords = false);
283
284 //! drawString centres the string on cds.
285 virtual void drawString(const std::string &str, const Point2D &cds,
286 bool rawCoords = false);
287 // unless the specific drawer over-rides this overload, it will just call
288 // the first one. SVG for one needs the alignment flag.
289 virtual void drawString(const std::string &str, const Point2D &cds,
291 bool rawCoords = false);
292
293 //! \name Transformations
294 //! @{
295 // transform a set of coords in the molecule's coordinate system
296 // to drawing system coordinates and vice versa. Note that the coordinates
297 // have
298 // the origin in the top left corner, which is how Qt and Cairo have it, no
299 // doubt a holdover from X Windows. This means that a higher y value will be
300 // nearer the bottom of the screen. This doesn't really matter except when
301 // doing text superscripts and subscripts.
302
303 //! transform a point from the molecule coordinate system into the drawing
304 //! coordinate system.
305 //! Prefers globalDrawTrans_ if it exists, otherwise
306 //! uses drawMols_[activeMolIdx_].
307 virtual Point2D getDrawCoords(const Point2D &mol_cds) const;
308 //! returns the drawing coordinates of a particular atom
309 virtual Point2D getDrawCoords(int at_num) const;
310 //! Prefers globalDrawTrans_ if it exists, otherwise
311 //! uses drawMols_[activeMolIdx_].
312 virtual Point2D getAtomCoords(const std::pair<int, int> &screen_cds) const;
313 //! transform a point from drawing coordinates to the molecule coordinate
314 //! system. Prefers globalDrawTrans_ if it exists, otherwise
315 //! uses drawMols_[activeMolIdx_].
317 const std::pair<double, double> &screen_cds) const;
318 //! returns the molecular coordinates of a particular atom. at_num refers
319 //! to the atom in activeMolIdx_.
320 virtual Point2D getAtomCoords(int at_num) const;
321 //! @}
322 //! returns the coordinates of the atoms of the activeMolIdx_ molecule in
323 //! molecular coordinates.
324 const std::vector<Point2D> &atomCoords() const;
325 //! returns the atomic symbols of the activeMolIdx_ molecule
326 const std::vector<std::pair<std::string, MolDraw2D_detail::OrientType>> &
327 atomSyms() const;
328
329 //! return the width of the drawing area.
330 int width() const { return width_; }
331 //! return the height of the drawing area.
332 int height() const { return height_; }
333 //! return the width of the drawing panels.
334 int panelWidth() const { return panel_width_; }
335 //! return the height of the drawing panels.
336 int panelHeight() const { return panel_height_; }
337
338 //! when FlexiMode is set, molecules will always be drawn
339 //! with the default values for bond length, font size, etc.
340 void setFlexiMode(bool mode) {
341 flexiMode_ = mode;
342 if (mode) {
343 panel_width_ = -1;
344 panel_height_ = -1;
345 }
346 }
347 bool flexiMode() const { return flexiMode_; }
348
349 int drawHeight() const { return panel_height_ - legend_height_; }
350 // returns the width to draw a line in draw coords.
351 double getDrawLineWidth() const;
352
353 //! returns the drawing scale (conversion from molecular coords -> drawing
354 /// coords)
355 double scale() const;
356 //! explicitly sets the scaling factors for the drawing
357 void setScale(double newScale);
358 void setScale(int width, int height, const Point2D &minv, const Point2D &maxv,
359 const ROMol *mol = nullptr);
360 //! sets the drawing offset (in drawing coords)
361 void setOffset(int x, int y) {
362 x_offset_ = x;
363 y_offset_ = y;
364 }
365 //! returns the drawing offset (in drawing coords)
366 Point2D offset() const { return Point2D(x_offset_, y_offset_); }
367
368 //! returns the minimum point of the drawing (in molecular coords)
369 Point2D minPt() const;
370 //! returns the width and height of the grid (in molecular coords)
371 Point2D range() const;
372
373 //! font size in drawing coordinate units. That's probably pixels.
374 virtual double fontSize() const;
375 virtual void setFontSize(double new_size);
376
377 //! sets the current draw color
378 virtual void setColour(const DrawColour &col) { curr_colour_ = col; }
379 //! returns the current draw color
380 virtual DrawColour colour() const { return curr_colour_; }
381 //! sets the current dash pattern
382 virtual void setDash(const DashPattern &patt) { curr_dash_ = patt; }
383 //! returns the current dash pattern
384 virtual const DashPattern &dash() const { return curr_dash_; }
385
386 //! sets the current line width
387 virtual void setLineWidth(double width) {
388 drawOptions().bondLineWidth = width;
389 }
390 //! returns the current line width
391 virtual double lineWidth() const { return drawOptions().bondLineWidth; }
392
393 //! using the current scale, work out the size of the label in molecule
394 //! coordinates.
395 /*!
396 Bear in mind when implementing this, that, for example, NH2 will appear as
397 NH<sub>2</sub> to convey that the 2 is a subscript, and this needs to
398 accounted for in the width and height.
399 */
400 virtual void getStringSize(const std::string &label, double &label_width,
401 double &label_height) const;
402 // get the overall size of the label, allowing for it being split
403 // into pieces according to orientation.
404 void getLabelSize(const std::string &label,
405 MolDraw2D_detail::OrientType orient, double &label_width,
406 double &label_height) const;
407 // return extremes for string in molecule coords.
408 void getStringExtremes(const std::string &label,
410 const Point2D &cds, double &x_min, double &y_min,
411 double &x_max, double &y_max) const;
412
413 //! adds additional information about the atoms to the output. Does not make
414 //! sense for all renderers.
415 virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); }
416 //! set whether or not polygons are being filled
417 virtual bool fillPolys() const { return fill_polys_; }
418 //! returns either or not polygons should be filled
419 virtual void setFillPolys(bool val) { fill_polys_ = val; }
420
421 //! returns our current drawing options
422 MolDrawOptions &drawOptions() { return options_; }
423 //! \overload
424 const MolDrawOptions &drawOptions() const { return options_; }
425
426 virtual bool supportsAnnotations() const { return true; }
427
428 void setActiveMolIdx(int newIdx);
429 bool hasActiveAtmIdx() const { return activeAtmIdx1_ >= 0; }
430 int getActiveAtmIdx1() const { return activeAtmIdx1_; }
431 int getActiveAtmIdx2() const { return activeAtmIdx2_; }
432 void setActiveAtmIdx(int at_idx1 = -1, int at_idx2 = -1);
433 bool hasActiveBndIdx() const { return activeBndIdx_ >= 0; }
434 int getActiveBndIdx() const { return activeBndIdx_; }
435 void setActiveBndIdx(int bnd_idx = -1) {
436 activeBndIdx_ = (bnd_idx < 0 ? -1 : bnd_idx);
437 }
438 void setActiveClass(std::string actClass = std::string("")) {
439 d_activeClass = actClass;
440 }
441 std::string getActiveClass() const { return d_activeClass; }
442
443 protected:
444 std::unique_ptr<MolDraw2D_detail::DrawText> text_drawer_;
445 std::string d_activeClass;
446 bool needs_init_ = true;
447 std::vector<std::pair<std::string, std::string>> d_metadata;
448 unsigned int d_numMetadataEntries = 0;
449
450 private:
451 //! \name Methods that must be provided by child classes
452 //! @{
453 virtual void initDrawing() = 0;
454 virtual void initTextDrawer(bool noFreetype) = 0;
455
456 // if the width or height of the DrawMol was -1, the new dimensions need to be
457 // transferred to MolDraw2D.
458 void fixVariableDimensions(const MolDraw2D_detail::DrawMol &drawMol);
459
460 // split the reaction up into the reagents, products and agents, each as
461 // a separate entity with its own scale.
462 void getReactionDrawMols(
463 const ChemicalReaction &rxn, bool highlightByReactant,
464 const std::vector<DrawColour> *highlightColorsReactants,
465 const std::vector<int> *confIds,
466 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
467 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
468 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
469 int &plusWidth);
470 // take the given components from the reaction (bits will be either
471 // reagents, products or agents) and create the corresponding DrawMols.
472 void makeReactionComponents(
473 std::vector<RDKit::ROMOL_SPTR> const &bits,
474 const std::vector<int> *confIds, int heightToUse,
475 std::map<int, DrawColour> &atomColours,
476 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
477 double &minScale, double &minFontScale);
478 // this puts a pointer to the DrawMol into _drawMols as well, hence the use
479 // of shared_ptr for reagents, products and agents above.
480 void makeReactionDrawMol(
481 RWMol &mol, int confId, int molHeight,
482 const std::vector<int> &highlightAtoms,
483 const std::vector<int> &highlightBonds,
484 const std::map<int, DrawColour> &highlightAtomMap,
485 const std::map<int, DrawColour> &highlightBondMap,
486 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &mols);
487 // Strictly speaking, this isn't actually a const function, although the
488 // compiler can't spot it, because the scales of reagents etc may be changed,
489 // and they are also in drawMols_.
490 void calcReactionOffsets(
491 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
492 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
493 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
494 int &plusWidth, std::vector<Point2D> &offsets, Point2D &arrowBeg,
495 Point2D &arrowEnd);
496 // returns the final offset. plusWidth of 0 means no pluses to be drawn.
497 int drawReactionPart(
498 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reactBit,
499 int plusWidth, int initOffset, const std::vector<Point2D> &offsets);
500 // returns a map of colours indexed by the atomMapNum. Each reagent gives
501 // a different colour.
502 void findReactionHighlights(
503 const ChemicalReaction &rxn, bool highlightByReactant,
504 const std::vector<DrawColour> *highlightColorsReactants,
505 std::map<int, DrawColour> &atomColours) const;
506
507 int width_, height_, panel_width_, panel_height_, legend_height_;
508 // if the user calls setScale() to explicitly force a scale on the
509 // DrawMols, this is set to true.
510 bool forceScale_ = false;
511 bool flexiMode_ = false;
512 double scale_, fontScale_;
513 int x_offset_, y_offset_; // translation in screen coordinates
514 bool fill_polys_;
515 int activeMolIdx_;
516 int activeAtmIdx1_;
517 int activeAtmIdx2_;
518 int activeBndIdx_;
519 // these are shared_ptr rather than unique_ptr because the reactions
520 // keep their own copy.
521 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> drawMols_;
522 // this is for when we want to set up a MolDraw2D to a given scale and be
523 // able to draw molecules and arbitrary lines, arcs etc. onto it all to the
524 // same drawing transformation. If present, it will always be applied to
525 // any new drawMols_ before they are drawn. A separate class might have
526 // been better, but this is convenient.
527 std::unique_ptr<MolDraw2D_detail::DrawMol> globalDrawTrans_;
528
529 DrawColour curr_colour_;
530 DashPattern curr_dash_;
531 MolDrawOptions options_;
532
533 // Do the drawing, the new way
534 void startDrawing();
535 void drawTheMolecule(MolDraw2D_detail::DrawMol &drawMol);
536 void setupTextDrawer();
537
538 virtual void updateMetadata(const ROMol &mol, int confId) {
539 RDUNUSED_PARAM(mol);
540 RDUNUSED_PARAM(confId);
541 }
542 virtual void updateMetadata(const ChemicalReaction &rxn) {
543 RDUNUSED_PARAM(rxn);
544 }
545};
546
548 assignDarkModePalette(opts.atomColourPalette);
549 opts.backgroundColour = DrawColour{0.0, 0.0, 0.0, 1.0};
550 opts.annotationColour = DrawColour{0.9, 0.9, 0.9, 1.0};
551 opts.legendColour = DrawColour{0.9, 0.9, 0.9, 1.0};
552 opts.symbolColour = DrawColour{0.9, 0.9, 0.9, 1.0};
553 opts.variableAttachmentColour = DrawColour{0.3, 0.3, 0.3, 1.0};
554}
555inline void setDarkMode(MolDraw2D &d2d) { setDarkMode(d2d.drawOptions()); }
557 const DrawColour &bgColour) {
558 opts.atomColourPalette.clear();
559 opts.atomColourPalette[-1] = fgColour;
560 opts.backgroundColour = bgColour;
561 opts.annotationColour = fgColour;
562 opts.legendColour = fgColour;
563 opts.symbolColour = fgColour;
564 opts.variableAttachmentColour = fgColour;
565}
567 const DrawColour &bgColour) {
568 setMonochromeMode(drawer.drawOptions(), fgColour, bgColour);
569}
570
571} // namespace RDKit
572
573#endif // RDKITMOLDRAW2D_H
#define RDUNUSED_PARAM(x)
Definition Invariant.h:196
#define M_PI
Definition MMFF/Params.h:26
pulls in the core RDKit functionality
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition MolDraw2D.h:47
virtual void tagAtoms(const ROMol &mol)
Definition MolDraw2D.h:415
void drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, DrawColour > *highlight_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
This is an overloaded member function, provided for convenience. It differs from the above function o...
void setActiveBndIdx(int bnd_idx=-1)
Definition MolDraw2D.h:435
MolDraw2D & operator=(MolDraw2D &&rhs)=delete
void drawMoleculeWithHighlights(const ROMol &mol, const std::string &legend, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1)
draw molecule with multiple colours allowed per atom.
void setScale(int width, int height, const Point2D &minv, const Point2D &maxv, const ROMol *mol=nullptr)
int panelHeight() const
return the height of the drawing panels.
Definition MolDraw2D.h:336
virtual ~MolDraw2D()
virtual void drawLine(const Point2D &cds1, const Point2D &cds2, const DrawColour &col1, const DrawColour &col2, bool rawCoords=false)
draw a line where the ends are different colours
virtual void setFontSize(double new_size)
virtual Point2D getAtomCoords(int at_num) const
virtual void getStringSize(const std::string &label, double &label_width, double &label_height) const
virtual void drawArrow(const Point2D &cds1, const Point2D &cds2, bool asPolygon=false, double frac=0.05, double angle=M_PI/6, const DrawColour &col=DrawColour(0.0, 0.0, 0.0), bool rawCoords=false)
Draw an arrow with either lines or a filled head (when asPolygon is true)
void drawReaction(const ChemicalReaction &rxn, bool highlightByReactant=false, const std::vector< DrawColour > *highlightColorsReactants=nullptr, const std::vector< int > *confIds=nullptr)
draw a ChemicalReaction
void setFlexiMode(bool mode)
Definition MolDraw2D.h:340
bool hasActiveBndIdx() const
Definition MolDraw2D.h:433
void drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
draw a single molecule
int getActiveAtmIdx2() const
Definition MolDraw2D.h:431
virtual void drawLine(const Point2D &cds1, const Point2D &cds2, bool rawCoords=false)=0
MolDraw2D(int width, int height, int panelWidth, int panelHeight)
constructor for a particular size
void getLabelSize(const std::string &label, MolDraw2D_detail::OrientType orient, double &label_width, double &label_height) const
double getDrawLineWidth() const
std::unique_ptr< MolDraw2D_detail::DrawText > text_drawer_
Definition MolDraw2D.h:444
virtual double lineWidth() const
returns the current line width
Definition MolDraw2D.h:391
int height() const
return the height of the drawing area.
Definition MolDraw2D.h:332
void getStringExtremes(const std::string &label, MolDraw2D_detail::OrientType orient, const Point2D &cds, double &x_min, double &y_min, double &x_max, double &y_max) const
virtual bool fillPolys() const
set whether or not polygons are being filled
Definition MolDraw2D.h:417
virtual void drawWavyLine(const Point2D &cds1, const Point2D &cds2, const DrawColour &col1, const DrawColour &col2, unsigned int nSegments=16, double vertOffset=0.05, bool rawCoords=false)
draw a wavy line like that used to indicate unknown stereochemistry
virtual void drawPlus(const Point2D &cds, int plusWidth, const DrawColour &col, bool rawCoords=false)
virtual bool supportsAnnotations() const
Definition MolDraw2D.h:426
int drawHeight() const
Definition MolDraw2D.h:349
virtual void setDash(const DashPattern &patt)
sets the current dash pattern
Definition MolDraw2D.h:382
virtual void drawString(const std::string &str, const Point2D &cds, bool rawCoords=false)
drawString centres the string on cds.
MolDraw2D(MolDraw2D &&rhs)=delete
virtual DrawColour colour() const
returns the current draw color
Definition MolDraw2D.h:380
virtual void drawArc(const Point2D &centre, double radius, double ang1, double ang2, bool rawCoords=false)
virtual void setColour(const DrawColour &col)
sets the current draw color
Definition MolDraw2D.h:378
void drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr)
draw multiple molecules in a grid
const std::vector< Point2D > & atomCoords() const
int getActiveAtmIdx1() const
Definition MolDraw2D.h:430
std::pair< int, int > getMolSize(const ROMol &mol, const std::string &legend="", const std::vector< int > *highlight_atoms=nullptr, const std::vector< int > *highlight_bonds=nullptr, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
returns the size of the box for the molecule with current drawing settings
Point2D range() const
returns the width and height of the grid (in molecular coords)
MolDraw2D(const MolDraw2D &rhs)=delete
virtual Point2D getDrawCoords(const Point2D &mol_cds) const
virtual void drawTriangle(const Point2D &cds1, const Point2D &cds2, const Point2D &cds3, bool rawCoords=false)
draw a triangle
const MolDrawOptions & drawOptions() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition MolDraw2D.h:424
virtual void drawString(const std::string &str, const Point2D &cds, MolDraw2D_detail::TextAlignType align, bool rawCoords=false)
virtual Point2D getDrawCoords(int at_num) const
returns the drawing coordinates of a particular atom
virtual Point2D getAtomCoords(const std::pair< int, int > &screen_cds) const
std::string d_activeClass
Definition MolDraw2D.h:445
virtual void drawAttachmentLine(const Point2D &cds1, const Point2D &cds2, const DrawColour &col, double len=1.0, unsigned int nSegments=16, bool rawCoords=false)
void setOffset(int x, int y)
sets the drawing offset (in drawing coords)
Definition MolDraw2D.h:361
virtual void setLineWidth(double width)
sets the current line width
Definition MolDraw2D.h:387
void setActiveClass(std::string actClass=std::string(""))
Definition MolDraw2D.h:438
virtual Point2D getAtomCoords(const std::pair< double, double > &screen_cds) const
virtual void setFillPolys(bool val)
returns either or not polygons should be filled
Definition MolDraw2D.h:419
virtual void drawRect(const Point2D &cds1, const Point2D &cds2, bool rawCoords=false)
draw a rectangle given two opposite corners
virtual void drawPolygon(const std::vector< Point2D > &cds, bool rawCoords=false)=0
virtual void drawEllipse(const Point2D &cds1, const Point2D &cds2, bool rawCoords=false)
draw an ellipse
void drawMolecule(const ROMol &mol, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, DrawColour > *highlight_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
This is an overloaded member function, provided for convenience. It differs from the above function o...
void setActiveMolIdx(int newIdx)
int panelWidth() const
return the width of the drawing panels.
Definition MolDraw2D.h:334
virtual void clearDrawing()
clears the contents of the drawing
Definition MolDraw2D.h:212
Point2D minPt() const
returns the minimum point of the drawing (in molecular coords)
const std::vector< std::pair< std::string, MolDraw2D_detail::OrientType > > & atomSyms() const
returns the atomic symbols of the activeMolIdx_ molecule
void setActiveAtmIdx(int at_idx1=-1, int at_idx2=-1)
Point2D offset() const
returns the drawing offset (in drawing coords)
Definition MolDraw2D.h:366
virtual const DashPattern & dash() const
returns the current dash pattern
Definition MolDraw2D.h:384
bool hasActiveAtmIdx() const
Definition MolDraw2D.h:429
MolDraw2D & operator=(const MolDraw2D &rhs)=delete
int width() const
return the width of the drawing area.
Definition MolDraw2D.h:330
std::vector< std::pair< std::string, std::string > > d_metadata
Definition MolDraw2D.h:447
int getActiveBndIdx() const
Definition MolDraw2D.h:434
virtual double fontSize() const
font size in drawing coordinate units. That's probably pixels.
std::string getActiveClass() const
Definition MolDraw2D.h:441
double scale() const
void drawMolecule(const ROMol &mol, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
This is an overloaded member function, provided for convenience. It differs from the above function o...
void setScale(double newScale)
explicitly sets the scaling factors for the drawing
virtual void drawArc(const Point2D &centre, double xradius, double yradius, double ang1, double ang2, bool rawCoords=false)
MolDrawOptions & drawOptions()
returns our current drawing options
Definition MolDraw2D.h:422
bool flexiMode() const
Definition MolDraw2D.h:347
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
#define RDKIT_MOLDRAW2D_EXPORT
Definition export.h:297
Std stuff.
std::vector< double > DashPattern
bool rdvalue_is(const RDValue_cast_t)
void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour)
Definition MolDraw2D.h:556
void assignDarkModePalette(ColourPalette &palette)
void setDarkMode(MolDrawOptions &opts)
Definition MolDraw2D.h:547