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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.
126 \param highlight_radii : map from atomId -> radius (in molecule
127 coordinates) for the radii of atomic highlights. If not provided for an
128 index, the default value from \c drawOptions() will be used.
129 \param highlight_linewidth_multipliers : map from atomId -> int, used to
130 vary the width the highlight lines. Only active if
131 drawOptions().fillHighlights is false.
132 \param confId : (optional) conformer ID to be used for atomic
133 coordinates
134 */
136 const ROMol &mol, const std::string &legend,
137 const std::map<int, std::vector<DrawColour>> &highlight_atom_map,
138 const std::map<int, std::vector<DrawColour>> &highlight_bond_map,
139 const std::map<int, double> &highlight_radii,
140 const std::map<int, int> &highlight_linewidth_multipliers,
141 int confId = -1);
142
143 //! draw multiple molecules in a grid
144 /*!
145 \param mols : the molecules to draw
146 \param legends : (optional) the legends (to be drawn under the
147 molecules)
148 \param highlight_atoms : (optional) vectors of atom ids to highlight
149 \param highlight_atoms : (optional) vectors of bond ids to highlight
150 \param highlight_atom_map : (optional) maps from atomId -> DrawColour
151 providing the highlight colors. If not provided the default highlight colour
152 from \c drawOptions() will be used.
153 \param highlight_bond_map : (optional) maps from bondId -> DrawColour
154 providing the highlight colors. If not provided the default highlight colour
155 from \c drawOptions() will be used.
156 \param highlight_radii : (optional) maps from atomId -> radius (in molecule
157 coordinates) for the radii of atomic highlights. If not provided the default
158 value from \c drawOptions() will be used.
159 \param confId : (optional) conformer IDs to be used for atomic
160 coordinates
161
162 The \c panelWidth and \c panelHeight values will be used to determine the
163 number of rows and columns to be drawn. Theres not a lot of error checking
164 here, so if you provide too many molecules for the number of panes things
165 are likely to get screwed up.
166 If the number of rows or columns ends up being <= 1, molecules will be
167 being drawn in a single row/column.
168 */
170 const std::vector<ROMol *> &mols,
171 const std::vector<std::string> *legends = nullptr,
172 const std::vector<std::vector<int>> *highlight_atoms = nullptr,
173 const std::vector<std::vector<int>> *highlight_bonds = nullptr,
174 const std::vector<std::map<int, DrawColour>> *highlight_atom_maps =
175 nullptr,
176 const std::vector<std::map<int, DrawColour>> *highlight_bond_maps =
177 nullptr,
178 const std::vector<std::map<int, double>> *highlight_radii = nullptr,
179 const std::vector<int> *confIds = nullptr);
180
181 //! draw a ChemicalReaction
182 /*!
183 \param rxn : the reaction to draw
184 \param highlightByReactant : (optional) if this is set, atoms and bonds will
185 be highlighted based on which reactant they come from. Atom map numbers
186 will not be shown.
187 \param highlightColorsReactants : (optional) provide a vector of colors for
188 the
189 reactant highlighting.
190 \param confIds : (optional) vector of confIds to use for rendering. These
191 are numbered by reactants, then agents, then products.
192 */
194 const ChemicalReaction &rxn, bool highlightByReactant = false,
195 const std::vector<DrawColour> *highlightColorsReactants = nullptr,
196 const std::vector<int> *confIds = nullptr);
197
198 //! returns the size of the box for the molecule with current drawing settings
199 std::pair<int, int> getMolSize(
200 const ROMol &mol, const std::string &legend = "",
201 const std::vector<int> *highlight_atoms = nullptr,
202 const std::vector<int> *highlight_bonds = nullptr,
203 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
204 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
205 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
206
207 //! clears the contents of the drawing
208 virtual void clearDrawing() {
209 if (needs_init_) {
210 initDrawing();
211 needs_init_ = false;
212 }
213 };
214 //! draws a line from \c cds1 to \c cds2 using the current drawing style
215 //! in atom coords. If rawCoords is passed as true,
216 //! the coordinates are used as is, if not they are assumed to be in
217 //! the molecule coordinate frame and converted with getDrawCoords
218 //! into canvas coords.
219 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
220 bool rawCoords = false) = 0;
221 //! draw a polygon. Note that if fillPolys() returns false, it
222 //! doesn't close the path. If you want it to in that case, you
223 //! do it explicitly yourself. 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 virtual void drawPolygon(const std::vector<Point2D> &cds,
228 bool rawCoords = false) = 0;
229 //! @}
230
231 //! A Whole bunch of drawing primitives. They may be over-ridden
232 //! by different renderers, or they may be implemented in terms of
233 //! drawLine and drawPolygon above. If rawCoords is passed as true,
234 // the coordinates are used as is, if not they are assumed to be in
235 // the molecule coordinate frame and converted with getDrawCoords
236 // into canvas coords.
237 //! draw a line where the ends are different colours
238 virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
239 const DrawColour &col1, const DrawColour &col2,
240 bool rawCoords = false);
241 //! draw a triangle
242 virtual void drawTriangle(const Point2D &cds1, const Point2D &cds2,
243 const Point2D &cds3, bool rawCoords = false);
244 //! draw an ellipse
245 virtual void drawEllipse(const Point2D &cds1, const Point2D &cds2,
246 bool rawCoords = false);
247 // draw the arc of a circle between ang1 and ang2. Note that 0 is
248 // at 3 o-clock and 90 at 12 o'clock as you'd expect from your maths.
249 // ang2 must be > ang1 - it won't draw backwards. This is not enforced.
250 // Angles in degrees.
251 virtual void drawArc(const Point2D &centre, double radius, double ang1,
252 double ang2, bool rawCoords = false);
253 // and a general ellipse form
254 virtual void drawArc(const Point2D &centre, double xradius, double yradius,
255 double ang1, double ang2, bool rawCoords = false);
256 //! draw a rectangle given two opposite corners
257 virtual void drawRect(const Point2D &cds1, const Point2D &cds2,
258 bool rawCoords = false);
259 //! draw a line indicating the presence of an attachment point (normally a
260 //! squiggle line perpendicular to a bond)
261 virtual void drawAttachmentLine(const Point2D &cds1, const Point2D &cds2,
262 const DrawColour &col, double len = 1.0,
263 unsigned int nSegments = 16,
264 bool rawCoords = false);
265 //! draw a wavy line like that used to indicate unknown stereochemistry
266 virtual void drawWavyLine(const Point2D &cds1, const Point2D &cds2,
267 const DrawColour &col1, const DrawColour &col2,
268 unsigned int nSegments = 16,
269 double vertOffset = 0.05, bool rawCoords = false);
270 //! Draw an arrow with either lines or a filled head (when asPolygon is true)
271 virtual void drawArrow(const Point2D &cds1, const Point2D &cds2,
272 bool asPolygon = false, double frac = 0.05,
273 double angle = M_PI / 6,
274 const DrawColour &col = DrawColour(0.0, 0.0, 0.0),
275 bool rawCoords = false);
276 // draw a plus sign with lines at the given position.
277 virtual void drawPlus(const Point2D &cds, int plusWidth,
278 const DrawColour &col, bool rawCoords = false);
279
280 //! drawString centres the string on cds.
281 virtual void drawString(const std::string &str, const Point2D &cds,
282 bool rawCoords = false);
283 // unless the specific drawer over-rides this overload, it will just call
284 // the first one. SVG for one needs the alignment flag.
285 virtual void drawString(const std::string &str, const Point2D &cds,
287 bool rawCoords = false);
288
289 //! \name Transformations
290 //! @{
291 // transform a set of coords in the molecule's coordinate system
292 // to drawing system coordinates and vice versa. Note that the coordinates
293 // have
294 // the origin in the top left corner, which is how Qt and Cairo have it, no
295 // doubt a holdover from X Windows. This means that a higher y value will be
296 // nearer the bottom of the screen. This doesn't really matter except when
297 // doing text superscripts and subscripts.
298
299 //! transform a point from the molecule coordinate system into the drawing
300 //! coordinate system.
301 //! Prefers globalDrawTrans_ if it exists, otherwise
302 //! uses drawMols_[activeMolIdx_].
303 virtual Point2D getDrawCoords(const Point2D &mol_cds) const;
304 //! returns the drawing coordinates of a particular atom
305 virtual Point2D getDrawCoords(int at_num) const;
306 //! Prefers globalDrawTrans_ if it exists, otherwise
307 //! uses drawMols_[activeMolIdx_].
308 virtual Point2D getAtomCoords(const std::pair<int, int> &screen_cds) const;
309 //! transform a point from drawing coordinates to the molecule coordinate
310 //! system. Prefers globalDrawTrans_ if it exists, otherwise
311 //! uses drawMols_[activeMolIdx_].
313 const std::pair<double, double> &screen_cds) const;
314 //! returns the molecular coordinates of a particular atom. at_num refers
315 //! to the atom in activeMolIdx_.
316 virtual Point2D getAtomCoords(int at_num) const;
317 //! @}
318 //! returns the coordinates of the atoms of the activeMolIdx_ molecule in
319 //! molecular coordinates.
320 const std::vector<Point2D> &atomCoords() const;
321 //! returns the atomic symbols of the activeMolIdx_ molecule
322 const std::vector<std::pair<std::string, MolDraw2D_detail::OrientType>>
323 &atomSyms() const;
324
325 //! return the width of the drawing area.
326 int width() const { return width_; }
327 //! return the height of the drawing area.
328 int height() const { return height_; }
329 //! return the width of the drawing panels.
330 int panelWidth() const { return panel_width_; }
331 //! return the height of the drawing panels.
332 int panelHeight() const { return panel_height_; }
333
334 //! when FlexiMode is set, molecules will always be drawn
335 //! with the default values for bond length, font size, etc.
336 void setFlexiMode(bool mode) {
337 flexiMode_ = mode;
338 if (mode) {
339 panel_width_ = -1;
340 panel_height_ = -1;
341 }
342 }
343 bool flexiMode() const { return flexiMode_; }
344
345 int drawHeight() const { return panel_height_ - legend_height_; }
346 // returns the width to draw a line in draw coords.
347 double getDrawLineWidth() const;
348
349 //! returns the drawing scale (conversion from molecular coords -> drawing
350 /// coords)
351 double scale() const;
352 //! explicitly sets the scaling factors for the drawing
353 void setScale(double newScale);
354 void setScale(int width, int height, const Point2D &minv, const Point2D &maxv,
355 const ROMol *mol = nullptr);
356 //! sets the drawing offset (in drawing coords)
357 void setOffset(int x, int y) {
358 x_offset_ = x;
359 y_offset_ = y;
360 }
361 //! returns the drawing offset (in drawing coords)
362 Point2D offset() const { return Point2D(x_offset_, y_offset_); }
363
364 //! returns the minimum point of the drawing (in molecular coords)
365 Point2D minPt() const;
366 //! returns the width and height of the grid (in molecular coords)
367 Point2D range() const;
368
369 //! font size in drawing coordinate units. That's probably pixels.
370 virtual double fontSize() const;
371 virtual void setFontSize(double new_size);
372
373 //! sets the current draw color
374 virtual void setColour(const DrawColour &col) { curr_colour_ = col; }
375 //! returns the current draw color
376 virtual DrawColour colour() const { return curr_colour_; }
377 //! sets the current dash pattern
378 virtual void setDash(const DashPattern &patt) { curr_dash_ = patt; }
379 //! returns the current dash pattern
380 virtual const DashPattern &dash() const { return curr_dash_; }
381
382 //! sets the current line width
383 virtual void setLineWidth(double width) {
384 drawOptions().bondLineWidth = width;
385 }
386 //! returns the current line width
387 virtual double lineWidth() const { return drawOptions().bondLineWidth; }
388
389 //! using the current scale, work out the size of the label in molecule
390 //! coordinates.
391 /*!
392 Bear in mind when implementing this, that, for example, NH2 will appear as
393 NH<sub>2</sub> to convey that the 2 is a subscript, and this needs to
394 accounted for in the width and height.
395 */
396 virtual void getStringSize(const std::string &label, double &label_width,
397 double &label_height) const;
398 // get the overall size of the label, allowing for it being split
399 // into pieces according to orientation.
400 void getLabelSize(const std::string &label,
401 MolDraw2D_detail::OrientType orient, double &label_width,
402 double &label_height) const;
403 // return extremes for string in molecule coords.
404 void getStringExtremes(const std::string &label,
406 const Point2D &cds, double &x_min, double &y_min,
407 double &x_max, double &y_max) const;
408
409 //! adds additional information about the atoms to the output. Does not make
410 //! sense for all renderers.
411 virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); }
412 //! set whether or not polygons are being filled
413 virtual bool fillPolys() const { return fill_polys_; }
414 //! returns either or not polygons should be filled
415 virtual void setFillPolys(bool val) { fill_polys_ = val; }
416
417 //! returns our current drawing options
418 MolDrawOptions &drawOptions() { return options_; }
419 //! \overload
420 const MolDrawOptions &drawOptions() const { return options_; }
421
422 virtual bool supportsAnnotations() const { return true; }
423
424 void setActiveMolIdx(int newIdx);
425 bool hasActiveAtmIdx() const { return activeAtmIdx1_ >= 0; }
426 int getActiveAtmIdx1() const { return activeAtmIdx1_; }
427 int getActiveAtmIdx2() const { return activeAtmIdx2_; }
428 void setActiveAtmIdx(int at_idx1 = -1, int at_idx2 = -1);
429 bool hasActiveBndIdx() const { return activeBndIdx_ >= 0; }
430 int getActiveBndIdx() const { return activeBndIdx_; }
431 void setActiveBndIdx(int bnd_idx = -1) {
432 activeBndIdx_ = (bnd_idx < 0 ? -1 : bnd_idx);
433 }
434 void setActiveClass(std::string actClass = std::string("")) {
435 d_activeClass = actClass;
436 }
437 std::string getActiveClass() const { return d_activeClass; }
438
439 protected:
440 std::unique_ptr<MolDraw2D_detail::DrawText> text_drawer_;
441 std::string d_activeClass;
442 bool needs_init_ = true;
443 std::vector<std::pair<std::string, std::string>> d_metadata;
444 unsigned int d_numMetadataEntries = 0;
445
446 private:
447 //! \name Methods that must be provided by child classes
448 //! @{
449 virtual void initDrawing() = 0;
450 virtual void initTextDrawer(bool noFreetype) = 0;
451
452 // if the width or height of the DrawMol was -1, the new dimensions need to be
453 // transferred to MolDraw2D.
454 void fixVariableDimensions(const MolDraw2D_detail::DrawMol &drawMol);
455
456 // split the reaction up into the reagents, products and agents, each as
457 // a separate entity with its own scale.
458 void getReactionDrawMols(
459 const ChemicalReaction &rxn, bool highlightByReactant,
460 const std::vector<DrawColour> *highlightColorsReactants,
461 const std::vector<int> *confIds,
462 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
463 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
464 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
465 int &plusWidth);
466 // take the given components from the reaction (bits will be either
467 // reagents, products or agents) and create the corresponding DrawMols.
468 void makeReactionComponents(
469 std::vector<RDKit::ROMOL_SPTR> const &bits,
470 const std::vector<int> *confIds, int heightToUse,
471 std::map<int, DrawColour> &atomColours,
472 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
473 double &minScale, double &minFontScale);
474 // this puts a pointer to the DrawMol into _drawMols as well, hence the use
475 // of shared_ptr for reagents, products and agents above.
476 void makeReactionDrawMol(
477 RWMol &mol, int confId, int molHeight,
478 const std::vector<int> &highlightAtoms,
479 const std::vector<int> &highlightBonds,
480 const std::map<int, DrawColour> &highlightAtomMap,
481 const std::map<int, DrawColour> &highlightBondMap,
482 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &mols);
483 // Strictly speaking, this isn't actually a const function, although the
484 // compiler can't spot it, because the scales of reagents etc may be changed,
485 // and they are also in drawMols_.
486 void calcReactionOffsets(
487 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
488 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
489 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
490 int &plusWidth, std::vector<Point2D> &offsets, Point2D &arrowBeg,
491 Point2D &arrowEnd);
492 // returns the final offset. plusWidth of 0 means no pluses to be drawn.
493 int drawReactionPart(
494 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reactBit,
495 int plusWidth, int initOffset, const std::vector<Point2D> &offsets);
496 // returns a map of colours indexed by the atomMapNum. Each reagent gives
497 // a different colour.
498 void findReactionHighlights(
499 const ChemicalReaction &rxn, bool highlightByReactant,
500 const std::vector<DrawColour> *highlightColorsReactants,
501 std::map<int, DrawColour> &atomColours) const;
502
503 int width_, height_, panel_width_, panel_height_, legend_height_;
504 // if the user calls setScale() to explicitly force a scale on the
505 // DrawMols, this is set to true.
506 bool forceScale_ = false;
507 bool flexiMode_ = false;
508 double scale_, fontScale_;
509 int x_offset_, y_offset_; // translation in screen coordinates
510 bool fill_polys_;
511 int activeMolIdx_;
512 int activeAtmIdx1_;
513 int activeAtmIdx2_;
514 int activeBndIdx_;
515 // these are shared_ptr rather than unique_ptr because the reactions
516 // keep their own copy.
517 std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> drawMols_;
518 // this is for when we want to set up a MolDraw2D to a given scale and be
519 // able to draw molecules and arbitrary lines, arcs etc. onto it all to the
520 // same drawing transformation. If present, it will always be applied to
521 // any new drawMols_ before they are drawn. A separate class might have
522 // been better, but this is convenient.
523 std::unique_ptr<MolDraw2D_detail::DrawMol> globalDrawTrans_;
524
525 DrawColour curr_colour_;
526 DashPattern curr_dash_;
527 MolDrawOptions options_;
528
529 // Do the drawing, the new way
530 void startDrawing();
531 void drawTheMolecule(MolDraw2D_detail::DrawMol &drawMol);
532 void setupTextDrawer();
533
534 virtual void updateMetadata(const ROMol &mol, int confId) {
535 RDUNUSED_PARAM(mol);
536 RDUNUSED_PARAM(confId);
537 }
538 virtual void updateMetadata(const ChemicalReaction &rxn) {
539 RDUNUSED_PARAM(rxn);
540 }
541};
542
544 assignDarkModePalette(opts.atomColourPalette);
545 opts.backgroundColour = DrawColour{0.0, 0.0, 0.0, 1.0};
546 opts.annotationColour = DrawColour{0.9, 0.9, 0.9, 1.0};
547 opts.legendColour = DrawColour{0.9, 0.9, 0.9, 1.0};
548 opts.symbolColour = DrawColour{0.9, 0.9, 0.9, 1.0};
549 opts.variableAttachmentColour = DrawColour{0.3, 0.3, 0.3, 1.0};
550}
551inline void setDarkMode(MolDraw2D &d2d) { setDarkMode(d2d.drawOptions()); }
553 const DrawColour &bgColour) {
554 opts.atomColourPalette.clear();
555 opts.atomColourPalette[-1] = fgColour;
556 opts.backgroundColour = bgColour;
557 opts.annotationColour = fgColour;
558 opts.legendColour = fgColour;
559 opts.symbolColour = fgColour;
560 opts.variableAttachmentColour = fgColour;
561}
563 const DrawColour &bgColour) {
564 setMonochromeMode(drawer.drawOptions(), fgColour, bgColour);
565}
566
567} // namespace RDKit
568
569#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 tagAtoms(const ROMol &mol)
Definition MolDraw2D.h:411
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:431
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:332
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:336
bool hasActiveBndIdx() const
Definition MolDraw2D.h:429
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:427
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:440
virtual double lineWidth() const
returns the current line width
Definition MolDraw2D.h:387
int height() const
return the height of the drawing area.
Definition MolDraw2D.h:328
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:413
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:422
int drawHeight() const
Definition MolDraw2D.h:345
virtual void setDash(const DashPattern &patt)
sets the current dash pattern
Definition MolDraw2D.h:378
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:376
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:374
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:426
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:420
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:441
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:357
virtual void setLineWidth(double width)
sets the current line width
Definition MolDraw2D.h:383
void setActiveClass(std::string actClass=std::string(""))
Definition MolDraw2D.h:434
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:415
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:330
virtual void clearDrawing()
clears the contents of the drawing
Definition MolDraw2D.h:208
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:362
virtual const DashPattern & dash() const
returns the current dash pattern
Definition MolDraw2D.h:380
bool hasActiveAtmIdx() const
Definition MolDraw2D.h:425
MolDraw2D & operator=(const MolDraw2D &rhs)=delete
int width() const
return the width of the drawing area.
Definition MolDraw2D.h:326
std::vector< std::pair< std::string, std::string > > d_metadata
Definition MolDraw2D.h:443
int getActiveBndIdx() const
Definition MolDraw2D.h:430
virtual double fontSize() const
font size in drawing coordinate units. That's probably pixels.
std::string getActiveClass() const
Definition MolDraw2D.h:437
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:418
bool flexiMode() const
Definition MolDraw2D.h:343
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.
std::vector< double > DashPattern
bool rdvalue_is(const RDValue_cast_t)
void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour)
Definition MolDraw2D.h:552
void assignDarkModePalette(ColourPalette &palette)
void setDarkMode(MolDrawOptions &opts)
Definition MolDraw2D.h:543