RDKit
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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 class MolDraw2DColour;
23 
24 namespace MolDraw2DUtils {
25 
26 //! Does some cleanup operations on the molecule to prepare it to draw nicely
27 /*
28 The operations include: kekulization, addition of chiral Hs (so that we can draw
29 wedges to them), wedging of bonds at chiral centers, and generation of a 2D
30 conformation if the molecule does not already have a conformation
31 
32 \param mol: the molecule to be modified
33 \param kekulize: toggles kekulization (this can fail, see below)
34 \param addChiralHs: adds Hs to the graph on chiral atoms
35 \param wedgeBonds: calls WedgeMolBonds()
36 \param forceCoords: generates a 2D conformation even if one is present already
37 \param wavyBonds: calls addWavyBondsForStereoAny() and clears other markers that
38  double bond stereo is unknown
39 
40 NOTE: the kekulization step can fail, throwing a MolSanitizeExecption. If this
41 happens the molecule will be in an inconsistent, partially kekulized, state.
42 This isn't normally a problem for molecules that have been sanitized, but can be
43 problematic if the molecules have been modified post santitization.
44 */
46  RWMol &mol, bool kekulize = true, bool addChiralHs = true,
47  bool wedgeBonds = true, bool forceCoords = false, bool wavyBonds = false);
48 
49 //! prepare a molecule for drawing and draw it
50 /*
51  \param mol: the molecule to draw
52  \param legend: (optional) the legend (to be drawn under the molecule)
53  \param highlight_atoms: (optional) vector of atom ids to highlight
54  \param highlight_atoms: (optional) vector of bond ids to highlight
55  \param highlight_atom_map: (optional) map from atomId -> DrawColour
56  providing the highlight colors. If not provided the default
57  highlight colour from \c drawOptions() will be used.
58  \param highlight_bond_map: (optional) map from bondId -> DrawColour
59  providing the highlight colors. If not provided the default
60  highlight colour from \c drawOptions() will be used.
61  \param highlight_radii: (optional) map from atomId -> radius (in molecule
62  coordinates) for the radii of atomic highlights. If not provided
63  the default value from \c drawOptions() will be used.
64  \param confId: (optional) conformer ID to be used for atomic coordinates
65 
66 */
68  MolDraw2D &drawer, const ROMol &mol, const std::string &legend = "",
69  const std::vector<int> *highlight_atoms = nullptr,
70  const std::vector<int> *highlight_bonds = nullptr,
71  const std::map<int, DrawColour> *highlight_atom_map = nullptr,
72  const std::map<int, DrawColour> *highlight_bond_map = nullptr,
73  const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
74 
76  const char *json);
78  const std::string &json);
79 
80 struct ContourParams {
81  bool setScale = true; // assumes the grid is drawn first
82  bool dashNegative = true; // use dashed lines for negative contours
83  bool fillGrid = false; // shade the grid
84  double gridResolution = 0.15; // spacing between elements of the grid
85  double contourWidth = 1.0; // linewidth for drawing contours
86  double extraGridPadding = 0.0; // extra padding (in molecule coordinates)
87  DrawColour contourColour = {0.5, 0.5, 0.5,
88  0.5}; // color for drawing contours
89  std::vector<DrawColour> colourMap = {
90  {0.557, 0.004, 0.322, 0.5},
91  {1, 1, 1, 0.5},
92  {0.153, 0.392, 0.098, 0.5}}; // similarity map color scheme
93 };
94 
95 //! Generates and draws contours for data on a grid
96 /*
97  \param drawer: the MolDraw2D object to use
98  \param grid: the data to be contoured
99  \param xcoords: x positions of the grid points
100  \param ycoords: y positions of the grid points
101  \param nContours: the number of contours to draw
102  \param levels: the contours to use
103  \param ps: additional parameters controlling the contouring.
104  \param mol: molecule to be used to adjust the scale of the drawing.
105  If the \c levels argument is empty, the contour levels will be determined
106  automatically from the max and min values on the grid and \c levels will
107  be updated to include the contour levels.
108 
109  If \c ps.fillGrid is set, the data on the grid will also be drawn using
110  the color scheme in \c ps.colourMap
111 
112  if the \c mol argument is given, it will be used to adjust the scale of
113  drawing. This is because a common use is to draw the molecule onto
114  the contour, and it makes sense if it fits.
115 
116 */
118  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
119  const std::vector<double> &ycoords, size_t nContours,
120  std::vector<double> &levels, const ContourParams &ps = ContourParams(),
121  const ROMol *mol = nullptr);
122 //! \overload
124  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
125  const std::vector<double> &ycoords, size_t nContours = 10,
126  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr) {
127  std::vector<double> levels;
128  contourAndDrawGrid(drawer, grid, xcoords, ycoords, nContours, levels, ps,
129  mol);
130 };
131 
132 //! Generates and draws contours for a set of gaussians
133 /*
134  \param drawer: the MolDraw2D object to use
135  \param locs: locations of the gaussians
136  \param heights: the heights (or weights) of the gaussians
137  \param widths: the standard deviations of the gaussians
138  \param nContours: the number of contours to draw
139  \param levels: the contours to use
140  \param ps: additional parameters controlling the contouring.
141  \param mol: molecule to be used to adjust the scale of the drawing.
142 
143  The values are calculated on a grid with spacing \c ps.gridResolution.
144  If \c ps.setScale is set, the grid size will be calculated based on the
145  locations of the gaussians and \c ps.extraGridPadding. Otherwise the current
146  size of the viewport will be used.
147 
148  If the \c levels argument is empty, the contour levels will be determined
149  automatically from the max and min values on the grid and \c levels will
150  be updated to include the contour levels.
151 
152  If \c ps.fillGrid is set, the data on the grid will also be drawn using
153  the color scheme in \c ps.colourMap
154 
155  if the \c mol argument is given, it will be used to adjust the scale of
156  drawing. This is because a common use is to draw the molecule onto
157  the contour, and it makes sense if it fits.
158 
159 */
161  MolDraw2D &drawer, const std::vector<Point2D> &locs,
162  const std::vector<double> &heights, const std::vector<double> &widths,
163  size_t nContours, std::vector<double> &levels,
164  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr);
165 //! \overload
167  MolDraw2D &drawer, const std::vector<Point2D> &locs,
168  const std::vector<double> &heights, const std::vector<double> &widths,
169  size_t nContours = 10, const ContourParams &ps = ContourParams(),
170  const ROMol *mol = nullptr) {
171  std::vector<double> levels;
172  contourAndDrawGaussians(drawer, locs, heights, widths, nContours, levels, ps,
173  mol);
174 };
175 
176 } // namespace MolDraw2DUtils
177 } // namespace RDKit
178 #endif // MOLDRAW2DUTILS_H
Defines the editable molecule class RWMol.
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition: MolDraw2D.h:337
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:265
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 updateDrawerParamsFromJSON(MolDraw2D &drawer, const char *json)
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)
prepare a molecule for drawing and draw it
Std stuff.
Definition: Abbreviations.h:18
std::vector< DrawColour > colourMap