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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>
31 #include <Geometry/Transform2D.h>
32 #include <GraphMol/RDKitBase.h>
35 
36 // ****************************************************************************
37 using RDGeom::Point2D;
38 
39 namespace RDKit {
40 
41 namespace MolDraw2D_detail {
42 class DrawMol;
43 class 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() = 0;
199  //! draws a line from \c cds1 to \c cds2 using the current drawing style
200  //! in atom coords. If rawCoords is passed as true,
201  //! the coordinates are used as is, if not they are assumed to be in
202  //! the molecule coordinate frame and converted with getDrawCoords
203  //! into canvas coords.
204  virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
205  bool rawCoords = false) = 0;
206  //! draw a polygon. Note that if fillPolys() returns false, it
207  //! doesn't close the path. If you want it to in that case, you
208  //! do it explicitly yourself. If rawCoords is passed as true,
209  //! the coordinates are used as is, if not they are assumed to be in
210  //! the molecule coordinate frame and converted with getDrawCoords
211  //! into canvas coords.
212  virtual void drawPolygon(const std::vector<Point2D> &cds,
213  bool rawCoords = false) = 0;
214  //@}
215 
216  //! A Whole bunch of drawing primitives. They may be over-ridden
217  //! by different renderers, or they may be implemented in terms of
218  //! drawLine and drawPolygon above. If rawCoords is passed as true,
219  // the coordinates are used as is, if not they are assumed to be in
220  // the molecule coordinate frame and converted with getDrawCoords
221  // into canvas coords.
222  //! draw a line where the ends are different colours
223  virtual void drawLine(const Point2D &cds1, const Point2D &cds2,
224  const DrawColour &col1, const DrawColour &col2,
225  bool rawCoords = false);
226  //! draw a triangle
227  virtual void drawTriangle(const Point2D &cds1, const Point2D &cds2,
228  const Point2D &cds3, bool rawCoords = false);
229  //! draw an ellipse
230  virtual void drawEllipse(const Point2D &cds1, const Point2D &cds2,
231  bool rawCoords = false);
232  // draw the arc of a circle between ang1 and ang2. Note that 0 is
233  // at 3 o-clock and 90 at 12 o'clock as you'd expect from your maths.
234  // ang2 must be > ang1 - it won't draw backwards. This is not enforced.
235  // Angles in degrees.
236  virtual void drawArc(const Point2D &centre, double radius, double ang1,
237  double ang2, bool rawCoords = false);
238  // and a general ellipse form
239  virtual void drawArc(const Point2D &centre, double xradius, double yradius,
240  double ang1, double ang2, bool rawCoords = false);
241  //! draw a rectangle given two opposite corners
242  virtual void drawRect(const Point2D &cds1, const Point2D &cds2,
243  bool rawCoords = false);
244  //! draw a line indicating the presence of an attachment point (normally a
245  //! squiggle line perpendicular to a bond)
246  virtual void drawAttachmentLine(const Point2D &cds1, const Point2D &cds2,
247  const DrawColour &col, double len = 1.0,
248  unsigned int nSegments = 16,
249  bool rawCoords = false);
250  //! draw a wavy line like that used to indicate unknown stereochemistry
251  virtual void drawWavyLine(const Point2D &cds1, const Point2D &cds2,
252  const DrawColour &col1, const DrawColour &col2,
253  unsigned int nSegments = 16,
254  double vertOffset = 0.05, bool rawCoords = false);
255  //! Draw an arrow with either lines or a filled head (when asPolygon is true)
256  virtual void drawArrow(const Point2D &cds1, const Point2D &cds2,
257  bool asPolygon = false, double frac = 0.05,
258  double angle = M_PI / 6,
259  const DrawColour &col = DrawColour(0.0, 0.0, 0.0),
260  bool rawCoords = false);
261  // draw a plus sign with lines at the given position.
262  virtual void drawPlus(const Point2D &cds, int plusWidth,
263  const DrawColour &col, bool rawCoords = false);
264 
265  //! drawString centres the string on cds.
266  virtual void drawString(const std::string &str, const Point2D &cds,
267  bool rawCoords = false);
268  // unless the specific drawer over-rides this overload, it will just call
269  // the first one. SVG for one needs the alignment flag.
270  virtual void drawString(const std::string &str, const Point2D &cds,
272  bool rawCoords = false);
273 
274  //! \name Transformations
275  //@{
276  // transform a set of coords in the molecule's coordinate system
277  // to drawing system coordinates and vice versa. Note that the coordinates
278  // have
279  // the origin in the top left corner, which is how Qt and Cairo have it, no
280  // doubt a holdover from X Windows. This means that a higher y value will be
281  // nearer the bottom of the screen. This doesn't really matter except when
282  // doing text superscripts and subscripts.
283 
284  //! transform a point from the molecule coordinate system into the drawing
285  //! coordinate system.
286  //! Prefers globalDrawTrans_ if it exists, otherwise
287  //! uses drawMols_[activeMolIdx_].
288  virtual Point2D getDrawCoords(const Point2D &mol_cds) const;
289  //! returns the drawing coordinates of a particular atom
290  virtual Point2D getDrawCoords(int at_num) const;
291  //! Prefers globalDrawTrans_ if it exists, otherwise
292  //! uses drawMols_[activeMolIdx_].
293  virtual Point2D getAtomCoords(const std::pair<int, int> &screen_cds) const;
294  //! transform a point from drawing coordinates to the molecule coordinate
295  //! system. Prefers globalDrawTrans_ if it exists, otherwise
296  //! uses drawMols_[activeMolIdx_].
298  const std::pair<double, double> &screen_cds) const;
299  //! returns the molecular coordinates of a particular atom. at_num refers
300  //! to the atom in activeMolIdx_.
301  virtual Point2D getAtomCoords(int at_num) const;
302  //@}
303  //! returns the coordinates of the atoms of the activeMolIdx_ molecule in
304  //! molecular coordinates.
305  const std::vector<Point2D> &atomCoords() const;
306  //! returns the atomic symbols of the activeMolIdx_ molecule
307  const std::vector<std::pair<std::string, MolDraw2D_detail::OrientType>>
308  &atomSyms() const;
309 
310  //! return the width of the drawing area.
311  virtual int width() const { return width_; }
312  //! return the height of the drawing area.
313  virtual int height() const { return height_; }
314  //! return the width of the drawing panels.
315  virtual int panelWidth() const { return panel_width_; }
316  //! return the height of the drawing panels.
317  virtual int panelHeight() const { return panel_height_; }
318  virtual int drawHeight() const { return panel_height_ - legend_height_; }
319  // returns the width to draw a line in draw coords.
320  virtual double getDrawLineWidth() const;
321 
322  //! returns the drawing scale (conversion from molecular coords -> drawing
323  /// coords)
324  double scale() const;
325  //! explicitly sets the scaling factors for the drawing
326  void setScale(double newScale);
327  void setScale(int width, int height, const Point2D &minv, const Point2D &maxv,
328  const ROMol *mol = nullptr);
329  //! sets the drawing offset (in drawing coords)
330  void setOffset(int x, int y) {
331  x_offset_ = x;
332  y_offset_ = y;
333  }
334  //! returns the drawing offset (in drawing coords)
335  Point2D offset() const { return Point2D(x_offset_, y_offset_); }
336 
337  //! returns the minimum point of the drawing (in molecular coords)
338  Point2D minPt() const;
339  //! returns the width and height of the grid (in molecular coords)
340  Point2D range() const;
341 
342  //! font size in drawing coordinate units. That's probably pixels.
343  virtual double fontSize() const;
344  virtual void setFontSize(double new_size);
345 
346  //! sets the current draw color
347  virtual void setColour(const DrawColour &col) { curr_colour_ = col; }
348  //! returns the current draw color
349  virtual DrawColour colour() const { return curr_colour_; }
350  //! sets the current dash pattern
351  virtual void setDash(const DashPattern &patt) { curr_dash_ = patt; }
352  //! returns the current dash pattern
353  virtual const DashPattern &dash() const { return curr_dash_; }
354 
355  //! sets the current line width
356  virtual void setLineWidth(int width) { drawOptions().bondLineWidth = width; }
357  //! returns the current line width
358  virtual int lineWidth() const { return drawOptions().bondLineWidth; }
359 
360  //! using the current scale, work out the size of the label in molecule
361  //! coordinates.
362  /*!
363  Bear in mind when implementing this, that, for example, NH2 will appear as
364  NH<sub>2</sub> to convey that the 2 is a subscript, and this needs to
365  accounted for in the width and height.
366  */
367  virtual void getStringSize(const std::string &label, double &label_width,
368  double &label_height) const;
369  // get the overall size of the label, allowing for it being split
370  // into pieces according to orientation.
371  void getLabelSize(const std::string &label,
372  MolDraw2D_detail::OrientType orient, double &label_width,
373  double &label_height) const;
374  // return extremes for string in molecule coords.
375  void getStringExtremes(const std::string &label,
377  const Point2D &cds, double &x_min, double &y_min,
378  double &x_max, double &y_max) const;
379 
380  //! adds additional information about the atoms to the output. Does not make
381  //! sense for all renderers.
382  virtual void tagAtoms(const ROMol &mol) { RDUNUSED_PARAM(mol); }
383  //! set whether or not polygons are being filled
384  virtual bool fillPolys() const { return fill_polys_; }
385  //! returns either or not polygons should be filled
386  virtual void setFillPolys(bool val) { fill_polys_ = val; }
387 
388  //! returns our current drawing options
389  MolDrawOptions &drawOptions() { return options_; }
390  //! \overload
391  const MolDrawOptions &drawOptions() const { return options_; }
392 
393  virtual bool supportsAnnotations() const { return true; }
394 
395  void setActiveMolIdx(int newIdx);
396  bool hasActiveAtmIdx() const { return activeAtmIdx1_ >= 0; }
397  int getActiveAtmIdx1() const { return activeAtmIdx1_; }
398  int getActiveAtmIdx2() const { return activeAtmIdx2_; }
399  void setActiveAtmIdx(int at_idx1 = -1, int at_idx2 = -1);
400  bool hasActiveBndIdx() const { return activeBndIdx_ >= 0; }
401  int getActiveBndIdx() const { return activeBndIdx_; }
402  void setActiveBndIdx(int bnd_idx = -1) {
403  activeBndIdx_ = (bnd_idx < 0 ? -1 : bnd_idx);
404  }
405  void setActiveClass(std::string actClass = std::string("")) {
406  d_activeClass = actClass;
407  }
408  std::string getActiveClass() const { return d_activeClass; }
409 
410  protected:
411  std::unique_ptr<MolDraw2D_detail::DrawText> text_drawer_;
412  std::string d_activeClass;
413  bool needs_init_ = true;
414  std::vector<std::pair<std::string, std::string>> d_metadata;
415  unsigned int d_numMetadataEntries = 0;
416 
417  private:
418  //! \name Methods that must be provided by child classes
419  //@{
420  virtual void initDrawing() = 0;
421  virtual void initTextDrawer(bool noFreetype) = 0;
422 
423  // if the width or height of the DrawMol was -1, the new dimensions need to be
424  // transferred to MolDraw2D.
425  void fixVariableDimensions(const MolDraw2D_detail::DrawMol &drawMol);
426 
427  // split the reaction up into the reagents, products and agents, each as
428  // a separate entity with its own scale.
429  void getReactionDrawMols(
430  const ChemicalReaction &rxn, bool highlightByReactant,
431  const std::vector<DrawColour> *highlightColorsReactants,
432  const std::vector<int> *confIds,
433  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
434  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
435  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
436  int &plusWidth);
437  // take the given components from the reaction (bits will be either
438  // reagents, products or agents) and create the corresponding DrawMols.
439  void makeReactionComponents(
440  std::vector<RDKit::ROMOL_SPTR> const &bits,
441  const std::vector<int> *confIds, int heightToUse,
442  std::map<int, DrawColour> &atomColours,
443  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
444  double &minScale, double &minFontScale);
445  // this puts a pointer to the DrawMol into _drawMols as well, hence the use
446  // of shared_ptr for reagents, products and agents above.
447  void makeReactionDrawMol(
448  RWMol &mol, int confId, int molHeight,
449  const std::vector<int> &highlightAtoms,
450  const std::vector<int> &highlightBonds,
451  const std::map<int, DrawColour> &highlightAtomMap,
452  const std::map<int, DrawColour> &highlightBondMap,
453  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &mols);
454  // Strictly speaking, this isn't actually a const function, although the
455  // compiler can't spot it, because the scales of reagents etc may be changed,
456  // and they are also in drawMols_.
457  void calcReactionOffsets(
458  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
459  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
460  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
461  int &plusWidth, std::vector<Point2D> &offsets, Point2D &arrowBeg,
462  Point2D &arrowEnd);
463  // returns the final offset. plusWidth of 0 means no pluses to be drawn.
464  int drawReactionPart(
465  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reactBit,
466  int plusWidth, int initOffset, const std::vector<Point2D> &offsets);
467  // returns a map of colours indexed by the atomMapNum. Each reagent gives
468  // a different colour.
469  void findReactionHighlights(
470  const ChemicalReaction &rxn, bool highlightByReactant,
471  const std::vector<DrawColour> *highlightColorsReactants,
472  std::map<int, DrawColour> &atomColours) const;
473 
474  int width_, height_, panel_width_, panel_height_, legend_height_;
475  // if the user calls setScale() to explicitly force a scale on the
476  // DrawMols, this is set to true.
477  bool forceScale_ = false;
478  double scale_, fontScale_;
479  int x_offset_, y_offset_; // translation in screen coordinates
480  bool fill_polys_;
481  int activeMolIdx_;
482  int activeAtmIdx1_;
483  int activeAtmIdx2_;
484  int activeBndIdx_;
485  // these are shared_ptr rather than unique_ptr because the reactions
486  // keep their own copy.
487  std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> drawMols_;
488  // this is for when we want to set up a MolDraw2D to a given scale and be
489  // able to draw molecules and arbitrary lines, arcs etc. onto it all to the
490  // same drawing transformation. If present, it will always be applied to
491  // any new drawMols_ before they are drawn. A separate class might have
492  // been better, but this is convenient.
493  std::unique_ptr<MolDraw2D_detail::DrawMol> globalDrawTrans_;
494 
495  DrawColour curr_colour_;
496  DashPattern curr_dash_;
497  MolDrawOptions options_;
498 
499  // Do the drawing, the new way
500  void startDrawing();
501  void drawTheMolecule(MolDraw2D_detail::DrawMol &drawMol);
502  void setupTextDrawer();
503 
504  virtual void updateMetadata(const ROMol &mol, int confId) {
505  RDUNUSED_PARAM(mol);
506  RDUNUSED_PARAM(confId);
507  }
508  virtual void updateMetadata(const ChemicalReaction &rxn) {
509  RDUNUSED_PARAM(rxn);
510  }
511 };
512 
513 inline void setDarkMode(MolDrawOptions &opts) {
515  opts.backgroundColour = DrawColour{0, 0, 0, 1};
516  opts.annotationColour = DrawColour{0.9, 0.9, 0.9, 1};
517  opts.legendColour = DrawColour{0.9, 0.9, 0.9, 1};
518  opts.symbolColour = DrawColour{0.9, 0.9, 0.9, 1};
519  opts.variableAttachmentColour = DrawColour{0.3, 0.3, 0.3, 1};
520 }
521 inline void setDarkMode(MolDraw2D &d2d) { setDarkMode(d2d.drawOptions()); }
522 inline void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour,
523  const DrawColour &bgColour) {
524  opts.atomColourPalette.clear();
525  opts.atomColourPalette[-1] = fgColour;
526  opts.backgroundColour = bgColour;
527  opts.annotationColour = fgColour;
528  opts.legendColour = fgColour;
529  opts.symbolColour = fgColour;
530  opts.variableAttachmentColour = fgColour;
531 }
532 inline void setMonochromeMode(MolDraw2D &opts, const DrawColour &fgColour,
533  const DrawColour &bgColour) {
534  setMonochromeMode(opts.drawOptions(), fgColour, bgColour);
535 }
536 
537 } // namespace RDKit
538 
539 #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:382
void setActiveBndIdx(int bnd_idx=-1)
Definition: MolDraw2D.h:402
MolDraw2D & operator=(MolDraw2D &&rhs)=delete
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.
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:315
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:400
virtual int drawHeight() const
Definition: MolDraw2D.h:318
MolDraw2D & operator=(const MolDraw2D &rhs)=delete
int getActiveAtmIdx2() const
Definition: MolDraw2D.h:398
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
const std::vector< std::pair< std::string, MolDraw2D_detail::OrientType > > & atomSyms() const
returns the atomic symbols of the activeMolIdx_ molecule
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:411
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:384
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 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 bool supportsAnnotations() const
Definition: MolDraw2D.h:393
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 void clearDrawing()=0
clears the contents of the drawing
virtual int height() const
return the height of the drawing area.
Definition: MolDraw2D.h:313
virtual void setDash(const DashPattern &patt)
sets the current dash pattern
Definition: MolDraw2D.h:351
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:349
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:347
int getActiveAtmIdx1() const
Definition: MolDraw2D.h:397
Point2D range() const
returns the width and height of the grid (in molecular coords)
MolDraw2D(const MolDraw2D &rhs)=delete
MolDrawOptions & drawOptions()
returns our current drawing options
Definition: MolDraw2D.h:389
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
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:412
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:330
void setActiveClass(std::string actClass=std::string(""))
Definition: MolDraw2D.h:405
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:311
virtual void setFillPolys(bool val)
returns either or not polygons should be filled
Definition: MolDraw2D.h:386
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:317
Point2D minPt() const
returns the minimum point of the drawing (in molecular coords)
virtual void setLineWidth(int width)
sets the current line width
Definition: MolDraw2D.h:356
void setActiveAtmIdx(int at_idx1=-1, int at_idx2=-1)
Point2D offset() const
returns the drawing offset (in drawing coords)
Definition: MolDraw2D.h:335
bool hasActiveAtmIdx() const
Definition: MolDraw2D.h:396
std::vector< std::pair< std::string, std::string > > d_metadata
Definition: MolDraw2D.h:414
int getActiveBndIdx() const
Definition: MolDraw2D.h:401
virtual const DashPattern & dash() const
returns the current dash pattern
Definition: MolDraw2D.h:353
virtual double fontSize() const
font size in drawing coordinate units. That's probably pixels.
std::string getActiveClass() const
Definition: MolDraw2D.h:408
double scale() const
void setScale(double newScale)
explicitly sets the scaling factors for the drawing
const std::vector< Point2D > & atomCoords() const
virtual void drawArc(const Point2D &centre, double xradius, double yradius, double ang1, double ang2, bool rawCoords=false)
virtual int lineWidth() const
returns the current line width
Definition: MolDraw2D.h:358
const MolDrawOptions & drawOptions() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: MolDraw2D.h:391
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:273
Std stuff.
Definition: Abbreviations.h:18
std::vector< double > DashPattern
void setMonochromeMode(MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour)
Definition: MolDraw2D.h:522
void assignDarkModePalette(ColourPalette &palette)
void setDarkMode(MolDrawOptions &opts)
Definition: MolDraw2D.h:513
DrawColour variableAttachmentColour
ColourPalette atomColourPalette