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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 */
88 virtual void drawMolecule(
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 virtual void drawMolecule(
98 const ROMol &mol, 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, int confId = -1);
101
102 //! \overload
103 virtual void drawMolecule(
104 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, int confId = -1);
108
109 //! \overload
110 virtual void drawMolecule(
111 const ROMol &mol, const std::vector<int> *highlight_atoms,
112 const std::vector<int> *highlight_bonds,
113 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
114 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
115 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
116
117 //! draw molecule with multiple colours allowed per atom.
118 /*!
119 \param mol : the molecule to draw
120 \param legend : the legend (to be drawn under the molecule)
121 \param highlight_atom_map : map from atomId -> DrawColours
122 providing the highlight colours.
123 \param highlight_bond_map : map from bondId -> DrawColours
124 providing the highlight colours.
125 \param highlight_radii : map from atomId -> radius (in molecule
126 coordinates) for the radii of atomic highlights. If not provided for an
127 index, the default value from \c drawOptions() will be used.
128 \param highlight_linewidth_multipliers : map from atomId -> int, used to
129 vary the width the highlight lines. Only active if
130 drawOptions().fillHighlights is false.
131 \param confId : (optional) conformer ID to be used for atomic
132 coordinates
133 */
135 const ROMol &mol, const std::string &legend,
136 const std::map<int, std::vector<DrawColour>> &highlight_atom_map,
137 const std::map<int, std::vector<DrawColour>> &highlight_bond_map,
138 const std::map<int, double> &highlight_radii,
139 const std::map<int, int> &highlight_linewidth_multipliers,
140 int confId = -1);
141
142 //! draw multiple molecules in a grid
143 /*!
144 \param mols : the molecules to draw
145 \param legends : (optional) the legends (to be drawn under the
146 molecules)
147 \param highlight_atoms : (optional) vectors of atom ids to highlight
148 \param highlight_atoms : (optional) vectors of bond ids to highlight
149 \param highlight_atom_map : (optional) maps from atomId -> DrawColour
150 providing the highlight colors. If not provided the default highlight colour
151 from \c drawOptions() will be used.
152 \param highlight_bond_map : (optional) maps from bondId -> DrawColour
153 providing the highlight colors. If not provided the default highlight colour
154 from \c drawOptions() will be used.
155 \param highlight_radii : (optional) maps from atomId -> radius (in molecule
156 coordinates) for the radii of atomic highlights. If not provided the default
157 value from \c drawOptions() will be used.
158 \param confId : (optional) conformer IDs to be used for atomic
159 coordinates
160
161 The \c panelWidth and \c panelHeight values will be used to determine the
162 number of rows and columns to be drawn. Theres not a lot of error checking
163 here, so if you provide too many molecules for the number of panes things
164 are likely to get screwed up.
165 If the number of rows or columns ends up being <= 1, molecules will be
166 being drawn in a single row/column.
167 */
168 virtual void drawMolecules(
169 const std::vector<ROMol *> &mols,
170 const std::vector<std::string> *legends = nullptr,
171 const std::vector<std::vector<int>> *highlight_atoms = nullptr,
172 const std::vector<std::vector<int>> *highlight_bonds = nullptr,
173 const std::vector<std::map<int, DrawColour>> *highlight_atom_maps =
174 nullptr,
175 const std::vector<std::map<int, DrawColour>> *highlight_bond_maps =
176 nullptr,
177 const std::vector<std::map<int, double>> *highlight_radii = nullptr,
178 const std::vector<int> *confIds = nullptr);
179
180 //! draw a ChemicalReaction
181 /*!
182 \param rxn : the reaction to draw
183 \param highlightByReactant : (optional) if this is set, atoms and bonds will
184 be highlighted based on which reactant they come from. Atom map numbers
185 will not be shown.
186 \param highlightColorsReactants : (optional) provide a vector of colors for
187 the
188 reactant highlighting.
189 \param confIds : (optional) vector of confIds to use for rendering. These
190 are numbered by reactants, then agents, then products.
191 */
192 virtual void drawReaction(
193 const ChemicalReaction &rxn, bool highlightByReactant = false,
194 const std::vector<DrawColour> *highlightColorsReactants = nullptr,
195 const std::vector<int> *confIds = nullptr);
196
197 //! clears the contents of the drawing
198 virtual void clearDrawing() {
199 if (needs_init_) {
200 initDrawing();
201 needs_init_ = false;
202 }
203 };
204 //! draws a line from \c cds1 to \c cds2 using the current drawing style
205 //! in atom coords. If rawCoords is passed as true,
206 //! the coordinates are used as is, if not they are assumed to be in
207 //! the molecule coordinate frame and converted with getDrawCoords
208 //! into canvas coords.
209 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
210 bool rawCoords = false) = 0;
211 //! draw a polygon. Note that if fillPolys() returns false, it
212 //! doesn't close the path. If you want it to in that case, you
213 //! do it explicitly yourself. If rawCoords is passed as true,
214 //! the coordinates are used as is, if not they are assumed to be in
215 //! the molecule coordinate frame and converted with getDrawCoords
216 //! into canvas coords.
217 virtual void drawPolygon(const std::vector<Point2D> &cds,
218 bool rawCoords = false) = 0;
219 //! @}
220
221 //! A Whole bunch of drawing primitives. They may be over-ridden
222 //! by different renderers, or they may be implemented in terms of
223 //! drawLine and drawPolygon above. If rawCoords is passed as true,
224 // the coordinates are used as is, if not they are assumed to be in
225 // the molecule coordinate frame and converted with getDrawCoords
226 // into canvas coords.
227 //! draw a line where the ends are different colours
228 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
229 const DrawColour &col1, const DrawColour &col2,
230 bool rawCoords = false);
231 //! draw a triangle
232 virtual void drawTriangle(const Point2D &cds1, const Point2D &cds2,
233 const Point2D &cds3, bool rawCoords = false);
234 //! draw an ellipse
235 virtual void drawEllipse(const Point2D &cds1, const Point2D &cds2,
236 bool rawCoords = false);
237 // draw the arc of a circle between ang1 and ang2. Note that 0 is
238 // at 3 o-clock and 90 at 12 o'clock as you'd expect from your maths.
239 // ang2 must be > ang1 - it won't draw backwards. This is not enforced.
240 // Angles in degrees.
241 virtual void drawArc(const Point2D &centre, double radius, double ang1,
242 double ang2, bool rawCoords = false);
243 // and a general ellipse form
244 virtual void drawArc(const Point2D &centre, double xradius, double yradius,
245 double ang1, double ang2, bool rawCoords = false);
246 //! draw a rectangle given two opposite corners
247 virtual void drawRect(const Point2D &cds1, const Point2D &cds2,
248 bool rawCoords = false);
249 //! draw a line indicating the presence of an attachment point (normally a
250 //! squiggle line perpendicular to a bond)
251 virtual void drawAttachmentLine(const Point2D &cds1, const Point2D &cds2,
252 const DrawColour &col, double len = 1.0,
253 unsigned int nSegments = 16,
254 bool rawCoords = false);
255 //! draw a wavy line like that used to indicate unknown stereochemistry
256 virtual void drawWavyLine(const Point2D &cds1, const Point2D &cds2,
257 const DrawColour &col1, const DrawColour &col2,
258 unsigned int nSegments = 16,
259 double vertOffset = 0.05, bool rawCoords = false);
260 //! Draw an arrow with either lines or a filled head (when asPolygon is true)
261 virtual void drawArrow(const Point2D &cds1, const Point2D &cds2,
262 bool asPolygon = false, double frac = 0.05,
263 double angle = M_PI / 6,
264 const DrawColour &col = DrawColour(0.0, 0.0, 0.0),
265 bool rawCoords = false);
266 // draw a plus sign with lines at the given position.
267 virtual void drawPlus(const Point2D &cds, int plusWidth,
268 const DrawColour &col, bool rawCoords = false);
269
270 //! drawString centres the string on cds.
271 virtual void drawString(const std::string &str, const Point2D &cds,
272 bool rawCoords = false);
273 // unless the specific drawer over-rides this overload, it will just call
274 // the first one. SVG for one needs the alignment flag.
275 virtual void drawString(const std::string &str, const Point2D &cds,
277 bool rawCoords = false);
278
279 //! \name Transformations
280 //! @{
281 // transform a set of coords in the molecule's coordinate system
282 // to drawing system coordinates and vice versa. Note that the coordinates
283 // have
284 // the origin in the top left corner, which is how Qt and Cairo have it, no
285 // doubt a holdover from X Windows. This means that a higher y value will be
286 // nearer the bottom of the screen. This doesn't really matter except when
287 // doing text superscripts and subscripts.
288
289 //! transform a point from the molecule coordinate system into the drawing
290 //! coordinate system.
291 //! Prefers globalDrawTrans_ if it exists, otherwise
292 //! uses drawMols_[activeMolIdx_].
293 virtual Point2D getDrawCoords(const Point2D &mol_cds) const;
294 //! returns the drawing coordinates of a particular atom
295 virtual Point2D getDrawCoords(int at_num) const;
296 //! Prefers globalDrawTrans_ if it exists, otherwise
297 //! uses drawMols_[activeMolIdx_].
298 virtual Point2D getAtomCoords(const std::pair<int, int> &screen_cds) const;
299 //! transform a point from drawing coordinates to the molecule coordinate
300 //! system. Prefers globalDrawTrans_ if it exists, otherwise
301 //! uses drawMols_[activeMolIdx_].
303 const std::pair<double, double> &screen_cds) const;
304 //! returns the molecular coordinates of a particular atom. at_num refers
305 //! to the atom in activeMolIdx_.
306 virtual Point2D getAtomCoords(int at_num) const;
307 //! @}
308 //! returns the coordinates of the atoms of the activeMolIdx_ molecule in
309 //! molecular coordinates.
310 const std::vector<Point2D> &atomCoords() const;
311 //! returns the atomic symbols of the activeMolIdx_ molecule
312 const std::vector<std::pair<std::string, MolDraw2D_detail::OrientType>>
313 &atomSyms() const;
314
315 //! return the width of the drawing area.
316 virtual int width() const { return width_; }
317 //! return the height of the drawing area.
318 virtual int height() const { return height_; }
319 //! return the width of the drawing panels.
320 virtual int panelWidth() const { return panel_width_; }
321 //! return the height of the drawing panels.
322 virtual int panelHeight() const { return panel_height_; }
323 virtual int drawHeight() const { return panel_height_ - legend_height_; }
324 // returns the width to draw a line in draw coords.
325 virtual double getDrawLineWidth() const;
326
327 //! returns the drawing scale (conversion from molecular coords -> drawing
328 /// coords)
329 double scale() const;
330 //! explicitly sets the scaling factors for the drawing
331 void setScale(double newScale);
332 void setScale(int width, int height, const Point2D &minv, const Point2D &maxv,
333 const ROMol *mol = nullptr);
334 //! sets the drawing offset (in drawing coords)
335 void setOffset(int x, int y) {
336 x_offset_ = x;
337 y_offset_ = y;
338 }
339 //! returns the drawing offset (in drawing coords)
340 Point2D offset() const { return Point2D(x_offset_, y_offset_); }
341
342 //! returns the minimum point of the drawing (in molecular coords)
343 Point2D minPt() const;
344 //! returns the width and height of the grid (in molecular coords)
345 Point2D range() const;
346
347 //! font size in drawing coordinate units. That's probably pixels.
348 virtual double fontSize() const;
349 virtual void setFontSize(double new_size);
350
351 //! sets the current draw color
352 virtual void setColour(const DrawColour &col) { curr_colour_ = col; }
353 //! returns the current draw color
354 virtual DrawColour colour() const { return curr_colour_; }
355 //! sets the current dash pattern
356 virtual void setDash(const DashPattern &patt) { curr_dash_ = patt; }
357 //! returns the current dash pattern
358 virtual const DashPattern &dash() const { return curr_dash_; }
359
360 //! sets the current line width
361 virtual void setLineWidth(double width) { drawOptions().bondLineWidth = width; }
362 //! returns the current line width
363 virtual double lineWidth() const { return drawOptions().bondLineWidth; }
364
365 //! using the current scale, work out the size of the label in molecule
366 //! coordinates.
367 /*!
368 Bear in mind when implementing this, that, for example, NH2 will appear as
369 NH<sub>2</sub> to convey that the 2 is a subscript, and this needs to
370 accounted for in the width and height.
371 */
372 virtual void getStringSize(const std::string &label, double &label_width,
373 double &label_height) const;
374 // get the overall size of the label, allowing for it being split
375 // into pieces according to orientation.
376 void getLabelSize(const std::string &label,
377 MolDraw2D_detail::OrientType orient, double &label_width,
378 double &label_height) const;
379 // return extremes for string in molecule coords.
380 void getStringExtremes(const std::string &label,
382 const Point2D &cds, double &x_min, double &y_min,
383 double &x_max, double &y_max) const;
384
385 //! adds additional information about the atoms to the output. Does not make
386 //! sense for all renderers.
387 virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); }
388 //! set whether or not polygons are being filled
389 virtual bool fillPolys() const { return fill_polys_; }
390 //! returns either or not polygons should be filled
391 virtual void setFillPolys(bool val) { fill_polys_ = val; }
392
393 //! returns our current drawing options
394 MolDrawOptions &drawOptions() { return options_; }
395 //! \overload
396 const MolDrawOptions &drawOptions() const { return options_; }
397
398 virtual bool supportsAnnotations() const { return true; }
399
400 void setActiveMolIdx(int newIdx);
401 bool hasActiveAtmIdx() const { return activeAtmIdx1_ >= 0; }
402 int getActiveAtmIdx1() const { return activeAtmIdx1_; }
403 int getActiveAtmIdx2() const { return activeAtmIdx2_; }
404 void setActiveAtmIdx(int at_idx1 = -1, int at_idx2 = -1);
405 bool hasActiveBndIdx() const { return activeBndIdx_ >= 0; }
406 int getActiveBndIdx() const { return activeBndIdx_; }
407 void setActiveBndIdx(int bnd_idx = -1) {
408 activeBndIdx_ = (bnd_idx < 0 ? -1 : bnd_idx);
409 }
410 void setActiveClass(std::string actClass = std::string("")) {
411 d_activeClass = actClass;
412 }
413 std::string getActiveClass() const { return d_activeClass; }
414
415 protected:
416 std::unique_ptr<MolDraw2D_detail::DrawText> text_drawer_;
417 std::string d_activeClass;
418 bool needs_init_ = true;
419 std::vector<std::pair<std::string, std::string>> d_metadata;
420 unsigned int d_numMetadataEntries = 0;
421
422 private:
423 //! \name Methods that must be provided by child classes
424 //! @{
425 virtual void initDrawing() = 0;
426 virtual void initTextDrawer(bool noFreetype) = 0;
427
428 // if the width or height of the DrawMol was -1, the new dimensions need to be
429 // transferred to MolDraw2D.
430 void fixVariableDimensions(const MolDraw2D_detail::DrawMol &drawMol);
431
432 // split the reaction up into the reagents, products and agents, each as
433 // a separate entity with its own scale.
434 void getReactionDrawMols(
435 const ChemicalReaction &rxn, bool highlightByReactant,
436 const std::vector<DrawColour> *highlightColorsReactants,
437 const std::vector<int> *confIds,
438 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
439 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
440 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
441 int &plusWidth);
442 // take the given components from the reaction (bits will be either
443 // reagents, products or agents) and create the corresponding DrawMols.
444 void makeReactionComponents(
445 std::vector<RDKit::ROMOL_SPTR> const &bits,
446 const std::vector<int> *confIds, int heightToUse,
447 std::map<int, DrawColour> &atomColours,
448 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
449 double &minScale, double &minFontScale);
450 // this puts a pointer to the DrawMol into _drawMols as well, hence the use
451 // of shared_ptr for reagents, products and agents above.
452 void makeReactionDrawMol(
453 RWMol &mol, int confId, int molHeight,
454 const std::vector<int> &highlightAtoms,
455 const std::vector<int> &highlightBonds,
456 const std::map<int, DrawColour> &highlightAtomMap,
457 const std::map<int, DrawColour> &highlightBondMap,
458 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &mols);
459 // Strictly speaking, this isn't actually a const function, although the
460 // compiler can't spot it, because the scales of reagents etc may be changed,
461 // and they are also in drawMols_.
462 void calcReactionOffsets(
463 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
464 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
465 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
466 int &plusWidth, std::vector<Point2D> &offsets, Point2D &arrowBeg,
467 Point2D &arrowEnd);
468 // returns the final offset. plusWidth of 0 means no pluses to be drawn.
469 int drawReactionPart(
470 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reactBit,
471 int plusWidth, int initOffset, const std::vector<Point2D> &offsets);
472 // returns a map of colours indexed by the atomMapNum. Each reagent gives
473 // a different colour.
474 void findReactionHighlights(
475 const ChemicalReaction &rxn, bool highlightByReactant,
476 const std::vector<DrawColour> *highlightColorsReactants,
477 std::map<int, DrawColour> &atomColours) const;
478
479 int width_, height_, panel_width_, panel_height_, legend_height_;
480 // if the user calls setScale() to explicitly force a scale on the
481 // DrawMols, this is set to true.
482 bool forceScale_ = false;
483 double scale_, fontScale_;
484 int x_offset_, y_offset_; // translation in screen coordinates
485 bool fill_polys_;
486 int activeMolIdx_;
487 int activeAtmIdx1_;
488 int activeAtmIdx2_;
489 int activeBndIdx_;
490 // these are shared_ptr rather than unique_ptr because the reactions
491 // keep their own copy.
492 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> drawMols_;
493 // this is for when we want to set up a MolDraw2D to a given scale and be
494 // able to draw molecules and arbitrary lines, arcs etc. onto it all to the
495 // same drawing transformation. If present, it will always be applied to
496 // any new drawMols_ before they are drawn. A separate class might have
497 // been better, but this is convenient.
498 std::unique_ptr<MolDraw2D_detail::DrawMol> globalDrawTrans_;
499
500 DrawColour curr_colour_;
501 DashPattern curr_dash_;
502 MolDrawOptions options_;
503
504 // Do the drawing, the new way
505 void startDrawing();
506 void drawTheMolecule(MolDraw2D_detail::DrawMol &drawMol);
507 void setupTextDrawer();
508
509 virtual void updateMetadata(const ROMol &mol, int confId) {
510 RDUNUSED_PARAM(mol);
511 RDUNUSED_PARAM(confId);
512 }
513 virtual void updateMetadata(const ChemicalReaction &rxn) {
514 RDUNUSED_PARAM(rxn);
515 }
516};
517
518inline void setDarkMode(MolDrawOptions &opts) {
520 opts.backgroundColour = DrawColour{0, 0, 0, 1};
521 opts.annotationColour = DrawColour{0.9, 0.9, 0.9, 1};
522 opts.legendColour = DrawColour{0.9, 0.9, 0.9, 1};
523 opts.symbolColour = DrawColour{0.9, 0.9, 0.9, 1};
524 opts.variableAttachmentColour = DrawColour{0.3, 0.3, 0.3, 1};
525}
526inline void setDarkMode(MolDraw2D &d2d) { setDarkMode(d2d.drawOptions()); }
527inline void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour,
528 const DrawColour &bgColour) {
529 opts.atomColourPalette.clear();
530 opts.atomColourPalette[-1] = fgColour;
531 opts.backgroundColour = bgColour;
532 opts.annotationColour = fgColour;
533 opts.legendColour = fgColour;
534 opts.symbolColour = fgColour;
535 opts.variableAttachmentColour = fgColour;
536}
537inline void setMonochromeMode(MolDraw2D &drawer, const DrawColour &fgColour,
538 const DrawColour &bgColour) {
539 setMonochromeMode(drawer.drawOptions(), fgColour, bgColour);
540}
541
542} // namespace RDKit
543
544#endif // RDKITMOLDRAW2D_H
#define RDUNUSED_PARAM(x)
Definition: Invariant.h:196
#define M_PI
Definition: MMFF/Params.h:27
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 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.
virtual void tagAtoms(const ROMol &mol)
Definition: MolDraw2D.h:387
void setActiveBndIdx(int bnd_idx=-1)
Definition: MolDraw2D.h:407
MolDraw2D & operator=(MolDraw2D &&rhs)=delete
void setScale(int width, int height, const Point2D &minv, const Point2D &maxv, const ROMol *mol=nullptr)
virtual int panelWidth() const
return the width of the drawing panels.
Definition: MolDraw2D.h:320
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 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
virtual double getDrawLineWidth() const
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)
virtual 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...
bool hasActiveBndIdx() const
Definition: MolDraw2D.h:405
virtual 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
virtual int drawHeight() const
Definition: MolDraw2D.h:323
int getActiveAtmIdx2() const
Definition: MolDraw2D.h:403
virtual void drawReaction(const ChemicalReaction &rxn, bool highlightByReactant=false, const std::vector< DrawColour > *highlightColorsReactants=nullptr, const std::vector< int > *confIds=nullptr)
draw a ChemicalReaction
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
virtual 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...
std::unique_ptr< MolDraw2D_detail::DrawText > text_drawer_
Definition: MolDraw2D.h:416
virtual double lineWidth() const
returns the current line width
Definition: MolDraw2D.h:363
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:389
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:398
virtual 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...
virtual int height() const
return the height of the drawing area.
Definition: MolDraw2D.h:318
virtual void setDash(const DashPattern &patt)
sets the current dash pattern
Definition: MolDraw2D.h:356
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:354
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:352
const std::vector< Point2D > & atomCoords() const
int getActiveAtmIdx1() const
Definition: MolDraw2D.h:402
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:396
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:417
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:335
virtual void setLineWidth(double width)
sets the current line width
Definition: MolDraw2D.h:361
void setActiveClass(std::string actClass=std::string(""))
Definition: MolDraw2D.h:410
virtual Point2D getAtomCoords(const std::pair< double, double > &screen_cds) const
virtual int width() const
return the width of the drawing area.
Definition: MolDraw2D.h:316
virtual void setFillPolys(bool val)
returns either or not polygons should be filled
Definition: MolDraw2D.h:391
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 setActiveMolIdx(int newIdx)
virtual int panelHeight() const
return the height of the drawing panels.
Definition: MolDraw2D.h:322
virtual void clearDrawing()
clears the contents of the drawing
Definition: MolDraw2D.h:198
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:340
virtual const DashPattern & dash() const
returns the current dash pattern
Definition: MolDraw2D.h:358
bool hasActiveAtmIdx() const
Definition: MolDraw2D.h:401
MolDraw2D & operator=(const MolDraw2D &rhs)=delete
std::vector< std::pair< std::string, std::string > > d_metadata
Definition: MolDraw2D.h:419
int getActiveBndIdx() const
Definition: MolDraw2D.h:406
virtual double fontSize() const
font size in drawing coordinate units. That's probably pixels.
std::string getActiveClass() const
Definition: MolDraw2D.h:413
double scale() const
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:394
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:281
Std stuff.
Definition: Abbreviations.h:19
std::vector< double > DashPattern
void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour)
Definition: MolDraw2D.h:527
void assignDarkModePalette(ColourPalette &palette)
void setDarkMode(MolDrawOptions &opts)
Definition: MolDraw2D.h:518
DrawColour variableAttachmentColour
ColourPalette atomColourPalette