RDKit
Open-source cheminformatics and machine learning.
MolDraw2DUtils.h
Go to the documentation of this file.
1 //
2 // Copyright (C) 2016-2019 Greg Landrum
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 //! 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 
37 NOTE: the kekulization step can fail, throwing a MolSanitizeExecption. If this
38 happens the molecule will be in an inconsistent, partially kekulized, state.
39 This isn't normally a problem for molecules that have been sanitized, but can be
40 problematic if the molecules have been modified post santitization.
41 */
43  bool kekulize = true,
44  bool addChiralHs = true,
45  bool wedgeBonds = true,
46  bool forceCoords = 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 
75  const char *json);
77  const std::string &json);
78 
79 struct ContourParams {
80  bool setScale = true; // assumes the grid is drawn first
81  bool dashNegative = true; // use dashed lines for negative contours
82  bool fillGrid = false; // shade the grid
83  double gridResolution = 0.15; // spacing between elements of the grid
84  double contourWidth = 1.0; // linewidth for drawing contours
85  double extraGridPadding = 0.0; // extra padding (in molecule coordinates)
86  DrawColour contourColour = {0.5, 0.5, 0.5,
87  0.5}; // color for drawing contours
88  std::vector<DrawColour> colourMap = {
89  {0.557, 0.004, 0.322, 0.5},
90  {1, 1, 1, 0.5},
91  {0.153, 0.392, 0.098, 0.5}}; // similarity map color scheme
92 };
93 
94 //! Generates and draws contours for data on a grid
95 /*
96  \param drawer: the MolDraw2D object to use
97  \param grid: the data to be contoured
98  \param xcoords: x positions of the grid points
99  \param ycoords: y positions of the grid points
100  \param nContours: the number of contours to draw
101  \param levels: the contours to use
102  \param ps: additional parameters controlling the contouring.
103  \param mol: molecule to be used to adjust the scale of the drawing.
104  If the \c levels argument is empty, the contour levels will be determined
105  automatically from the max and min values on the grid and \c levels will
106  be updated to include the contour levels.
107 
108  If \c ps.fillGrid is set, the data on the grid will also be drawn using
109  the color scheme in \c ps.colourMap
110 
111  if the \c mol argument is given, it will be used to adjust the scale of
112  drawing. This is because a common use is to draw the molecule onto
113  the contour, and it makes sense if it fits.
114 
115 */
117  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
118  const std::vector<double> &ycoords, size_t nContours,
119  std::vector<double> &levels, const ContourParams &ps = ContourParams(),
120  const ROMol *mol = nullptr);
121 //! \overload
123  MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
124  const std::vector<double> &ycoords, size_t nContours = 10,
125  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr) {
126  std::vector<double> levels;
127  contourAndDrawGrid(drawer, grid, xcoords, ycoords, nContours, levels, ps,
128  mol);
129 };
130 
131 //! Generates and draws contours for a set of gaussians
132 /*
133  \param drawer: the MolDraw2D object to use
134  \param locs: locations of the gaussians
135  \param heights: the heights (or weights) of the gaussians
136  \param widths: the standard deviations of the gaussians
137  \param nContours: the number of contours to draw
138  \param levels: the contours to use
139  \param ps: additional parameters controlling the contouring.
140  \param mol: molecule to be used to adjust the scale of the drawing.
141 
142  The values are calculated on a grid with spacing \c ps.gridResolution.
143  If \c ps.setScale is set, the grid size will be calculated based on the
144  locations of the gaussians and \c ps.extraGridPadding. Otherwise the current
145  size of the viewport will be used.
146 
147  If the \c levels argument is empty, the contour levels will be determined
148  automatically from the max and min values on the grid and \c levels will
149  be updated to include the contour levels.
150 
151  If \c ps.fillGrid is set, the data on the grid will also be drawn using
152  the color scheme in \c ps.colourMap
153 
154  if the \c mol argument is given, it will be used to adjust the scale of
155  drawing. This is because a common use is to draw the molecule onto
156  the contour, and it makes sense if it fits.
157 
158 */
160  MolDraw2D &drawer, const std::vector<Point2D> &locs,
161  const std::vector<double> &heights, const std::vector<double> &widths,
162  size_t nContours, std::vector<double> &levels,
163  const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr);
164 //! \overload
166  MolDraw2D &drawer, const std::vector<Point2D> &locs,
167  const std::vector<double> &heights, const std::vector<double> &widths,
168  size_t nContours = 10, const ContourParams &ps = ContourParams(),
169  const ROMol *mol = nullptr) {
170  std::vector<double> levels;
171  contourAndDrawGaussians(drawer, locs, heights, widths, nContours, levels, ps,
172  mol);
173 };
174 
175 } // namespace MolDraw2DUtils
176 } // namespace RDKit
177 #endif // MOLDRAW2DUTILS_H
Defines the editable molecule class RWMol.
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition: MolDraw2D.h:281
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:31
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:437
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)
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:17
std::vector< DrawColour > colourMap