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MolDraw2DUtils.h
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1 //
2 // Copyright (C) 2016-2021 Greg Landrum 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 
11 #include <RDGeneral/export.h>
12 #ifndef MOLDRAW2DUTILS_H
13 #define MOLDRAW2DUTILS_H
14 #include <GraphMol/RWMol.h>
15 
16 #include <boost/tuple/tuple.hpp>
17 
18 // ****************************************************************************
19 
20 namespace RDKit {
21 class MolDraw2D;
22 
23 namespace MolDraw2DUtils {
24 
25 //! Does some cleanup operations on the molecule to prepare it to draw nicely
26 /*
27 The operations include: kekulization, addition of chiral Hs (so that we can draw
28 wedges to them), wedging of bonds at chiral centers, and generation of a 2D
29 conformation if the molecule does not already have a conformation
30 
31 \param mol: the molecule to be modified
32 \param kekulize: toggles kekulization (this can fail, see below)
33 \param addChiralHs: adds Hs to the graph on chiral atoms
34 \param wedgeBonds: calls WedgeMolBonds()
35 \param forceCoords: generates a 2D conformation even if one is present already
36 \param wavyBonds: calls addWavyBondsForStereoAny() and clears other markers that
37  double bond stereo is unknown
38 
39 NOTE: the kekulization step can fail, throwing a MolSanitizeExecption. If this
40 happens the molecule will be in an inconsistent, partially kekulized, state.
41 This isn't normally a problem for molecules that have been sanitized, but can be
42 problematic if the molecules have been modified post santitization.
43 */
45  RWMol &mol, bool kekulize = true, bool addChiralHs = true,
46  bool wedgeBonds = true, bool forceCoords = false, bool wavyBonds = false);
47 
48 //! prepare a molecule for drawing and draw it
49 /*
50  \param mol: the molecule to draw
51  \param legend: (optional) the legend (to be drawn under the molecule)
52  \param highlight_atoms: (optional) vector of atom ids to highlight
53  \param highlight_atoms: (optional) vector of bond ids to highlight
54  \param highlight_atom_map: (optional) map from atomId -> DrawColour
55  providing the highlight colors. If not provided the default
56  highlight colour from \c drawOptions() will be used.
57  \param highlight_bond_map: (optional) map from bondId -> DrawColour
58  providing the highlight colors. If not provided the default
59  highlight colour from \c drawOptions() will be used.
60  \param highlight_radii: (optional) map from atomId -> radius (in molecule
61  coordinates) for the radii of atomic highlights. If not provided
62  the default value from \c drawOptions() will be used.
63  \param confId: (optional) conformer ID to be used for atomic coordinates
64 
65 */
67  MolDraw2D &drawer, const ROMol &mol, const std::string &legend = "",
68  const std::vector<int> *highlight_atoms = nullptr,
69  const std::vector<int> *highlight_bonds = nullptr,
70  const std::map<int, DrawColour> *highlight_atom_map = nullptr,
71  const std::map<int, DrawColour> *highlight_bond_map = nullptr,
72  const std::map<int, double> *highlight_radii = nullptr, int confId = -1,
73  bool kekulize = true);
74 
76  const char *json);
78  const std::string &json);
80  const char *json);
82  MolDrawOptions &opts, const std::string &json);
83 
84 struct ContourParams {
85  bool setScale = true; // assumes the grid is drawn first
86  bool dashNegative = true; // use dashed lines for negative contours
87  bool fillGrid = false; // shade the grid
88  double gridResolution = 0.15; // spacing between elements of the grid
89  double contourWidth = 1.0; // linewidth for drawing contours
90  double extraGridPadding = 0.0; // extra padding (in molecule coordinates)
91  DrawColour contourColour = {0.5, 0.5, 0.5,
92  0.5}; // color for drawing contours
93  std::vector<DrawColour> colourMap = {
94  {0.557, 0.004, 0.322, 0.5},
95  {1, 1, 1, 0.5},
96  {0.153, 0.392, 0.098, 0.5}}; // similarity map color scheme
97 };
98 
99 //! Generates and draws contours for data on a grid
100 /*
101  \param drawer: the MolDraw2D object to use
102  \param grid: the data to be contoured
103  \param xcoords: x positions of the grid points
104  \param ycoords: y positions of the grid points
105  \param nContours: the number of contours to draw
106  \param levels: the contours to use
107  \param ps: additional parameters controlling the contouring.
108  \param mol: molecule to be used to adjust the scale of the drawing.
109  If the \c levels argument is empty, the contour levels will be determined
110  automatically from the max and min values on the grid and \c levels will
111  be updated to include the contour levels.
112 
113  If \c ps.fillGrid is set, the data on the grid will also be drawn using
114  the color scheme in \c ps.colourMap
115 
116  if the \c mol argument is given, it will be used to adjust the scale of
117  drawing. This is because a common use is to draw the molecule onto
118  the contour, and it makes sense if it fits.
119 
120 */
122  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
123  const std::vector<double> &ycoords, size_t nContours,
124  std::vector<double> &levels, const ContourParams &ps = ContourParams(),
125  const ROMol *mol = nullptr);
126 //! \overload
128  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
129  const std::vector<double> &ycoords, size_t nContours = 10,
130  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr) {
131  std::vector<double> levels;
132  contourAndDrawGrid(drawer, grid, xcoords, ycoords, nContours, levels, ps,
133  mol);
134 };
135 
136 //! Generates and draws contours for a set of gaussians
137 /*
138  \param drawer: the MolDraw2D object to use
139  \param locs: locations of the gaussians
140  \param heights: the heights (or weights) of the gaussians
141  \param widths: the standard deviations of the gaussians
142  \param nContours: the number of contours to draw
143  \param levels: the contours to use
144  \param ps: additional parameters controlling the contouring.
145  \param mol: molecule to be used to adjust the scale of the drawing.
146 
147  The values are calculated on a grid with spacing \c ps.gridResolution.
148  If \c ps.setScale is set, the grid size will be calculated based on the
149  locations of the gaussians and \c ps.extraGridPadding. Otherwise the current
150  size of the viewport will be used.
151 
152  If the \c levels argument is empty, the contour levels will be determined
153  automatically from the max and min values on the grid and \c levels will
154  be updated to include the contour levels.
155 
156  If \c ps.fillGrid is set, the data on the grid will also be drawn using
157  the color scheme in \c ps.colourMap
158 
159  if the \c mol argument is given, it will be used to adjust the scale of
160  drawing. This is because a common use is to draw the molecule onto
161  the contour, and it makes sense if it fits.
162 
163 */
165  MolDraw2D &drawer, const std::vector<Point2D> &locs,
166  const std::vector<double> &heights, const std::vector<double> &widths,
167  size_t nContours, std::vector<double> &levels,
168  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr);
169 //! \overload
171  MolDraw2D &drawer, const std::vector<Point2D> &locs,
172  const std::vector<double> &heights, const std::vector<double> &widths,
173  size_t nContours = 10, const ContourParams &ps = ContourParams(),
174  const ROMol *mol = nullptr) {
175  std::vector<double> levels;
176  contourAndDrawGaussians(drawer, locs, heights, widths, nContours, levels, ps,
177  mol);
178 };
179 
180 //! Draw a molecule to a MolDraw2D object according to ACS 1996 guidelines
181 /*
182  The ACS1996 guidelines, as described at
183  https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing
184  A number of values in drawer.drawOptions() are changed.
185  This is designed to be used with a flexiCanvas, i.e. a MolDraw2D object
186  created with width and height -1, because it works to a fixed scale.
187  It will issue a warning if the dimensions are otherwise and the picture may
188  look sub-optimal.
189  */
191  MolDraw2D &drawer, const ROMol &mol, const std::string &legend,
192  const std::vector<int> *highlight_atoms,
193  const std::vector<int> *highlight_bonds,
194  const std::map<int, DrawColour> *highlight_atom_map = nullptr,
195  const std::map<int, DrawColour> *highlight_bond_map = nullptr,
196  const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
197 
198 //! Set the draw options to produce something as close as possible to
199 //! the ACS 1996 guidelines as described at
200 //! https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing
201 /*
202  \param MolDrawOptions opt - the options what will be changed
203  \param float meanBondLength - mean bond length of the molecule
204 
205  Works best if the MolDraw2D object is created with width and height -1 (a
206  flexiCanvas).
207  The mean bond length may be calculated with MolDraw2DUtils::meanBondLength.
208  It is used to calculate the offset for the lines in multiple bonds.
209 
210  Options changed are:
211  bondLineWidth = 0.6
212  scaleBondWidth = false
213  scalingFactor = 14.4 / meanBondLen
214  multipleBondOffset = 0.18
215  highlightBondWidthMultiplier = 32
216  setMonochromeMode - black and white
217  fixedFontSize = 10
218  additionalAtomLabelPadding = 0.066
219  fontFile - if it isn't set already, then if RDBASE is set and the file
220  exists, uses $RDBASE/Fonts/Data/FreeSans.ttf. Otherwise uses
221  BuiltinRobotoRegular.
222  */
224  double meanBondLen = 1.0);
225 RDKIT_MOLDRAW2D_EXPORT double meanBondLength(const ROMol &mol, int confId = -1);
226 } // namespace MolDraw2DUtils
227 
228 } // namespace RDKit
229 #endif // MOLDRAW2DUTILS_H
Defines the editable molecule class RWMol.
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition: MolDraw2D.h:47
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:281
RDKIT_MOLDRAW2D_EXPORT void updateMolDrawOptionsFromJSON(MolDrawOptions &opts, const char *json)
RDKIT_MOLDRAW2D_EXPORT void contourAndDrawGrid(MolDraw2D &drawer, const double *grid, const std::vector< double > &xcoords, const std::vector< double > &ycoords, size_t nContours, std::vector< double > &levels, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
Generates and draws contours for data on a grid.
RDKIT_MOLDRAW2D_EXPORT void prepareMolForDrawing(RWMol &mol, bool kekulize=true, bool addChiralHs=true, bool wedgeBonds=true, bool forceCoords=false, bool wavyBonds=false)
Does some cleanup operations on the molecule to prepare it to draw nicely.
RDKIT_MOLDRAW2D_EXPORT void setACS1996Options(MolDrawOptions &opts, double meanBondLen=1.0)
RDKIT_MOLDRAW2D_EXPORT void updateDrawerParamsFromJSON(MolDraw2D &drawer, const char *json)
RDKIT_MOLDRAW2D_EXPORT double meanBondLength(const ROMol &mol, int confId=-1)
RDKIT_MOLDRAW2D_EXPORT void drawMolACS1996(MolDraw2D &drawer, 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 molecule to a MolDraw2D object according to ACS 1996 guidelines.
RDKIT_MOLDRAW2D_EXPORT void contourAndDrawGaussians(MolDraw2D &drawer, const std::vector< Point2D > &locs, const std::vector< double > &heights, const std::vector< double > &widths, size_t nContours, std::vector< double > &levels, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
Generates and draws contours for a set of gaussians.
RDKIT_MOLDRAW2D_EXPORT void prepareAndDrawMolecule(MolDraw2D &drawer, 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, bool kekulize=true)
prepare a molecule for drawing and draw it
Std stuff.
Definition: Abbreviations.h:19
std::vector< DrawColour > colourMap