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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 <tuple>
17
18// ****************************************************************************
19
20namespace RDKit {
21class MolDraw2D;
22
23namespace MolDraw2DUtils {
24
25//! Does some cleanup operations on the molecule to prepare it to draw nicely
26/*
27The operations include: kekulization, addition of chiral Hs (so that we can draw
28wedges to them), wedging of bonds at chiral centers, and generation of a 2D
29conformation 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
39NOTE: the kekulization step can fail, throwing a MolSanitizeExecption. If this
40happens the molecule will be in an inconsistent, partially kekulized, state.
41This isn't normally a problem for molecules that have been sanitized, but can be
42problematic 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, bool addChiralHs = true, bool wedgeBonds = true,
74 bool forceCoords = false, bool wavyBonds = false);
75
77 const char *json);
79 const std::string &json);
81 const char *json);
83 MolDrawOptions &opts, const std::string &json);
84
86 bool setScale = true; // assumes the grid is drawn first
87 bool dashNegative = true; // use dashed lines for negative contours
88 bool fillGrid = false; // shade the grid
89 double gridResolution = 0.15; // spacing between elements of the grid
90 double contourWidth = 1.0; // linewidth for drawing contours
91 double extraGridPadding = 0.0; // extra padding (in molecule coordinates)
92 DrawColour contourColour = {0.5, 0.5, 0.5,
93 0.5}; // color for drawing contours
94 std::vector<DrawColour> colourMap = {
95 {0.557, 0.004, 0.322, 0.5},
96 {1, 1, 1, 0.5},
97 {0.153, 0.392, 0.098, 0.5}}; // similarity map color scheme
98};
99
100//! Generates and draws contours for data on a grid
101/*
102 \param drawer: the MolDraw2D object to use
103 \param grid: the data to be contoured
104 \param xcoords: x positions of the grid points
105 \param ycoords: y positions of the grid points
106 \param nContours: the number of contours to draw
107 \param levels: the contours to use
108 \param ps: additional parameters controlling the contouring.
109 \param mol: molecule to be used to adjust the scale of the drawing.
110 If the \c levels argument is empty, the contour levels will be determined
111 automatically from the max and min values on the grid and \c levels will
112 be updated to include the contour levels.
113
114 If \c ps.fillGrid is set, the data on the grid will also be drawn using
115 the color scheme in \c ps.colourMap
116
117 if the \c mol argument is given, it will be used to adjust the scale of
118 drawing. This is because a common use is to draw the molecule onto
119 the contour, and it makes sense if it fits.
120
121*/
123 MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
124 const std::vector<double> &ycoords, size_t nContours,
125 std::vector<double> &levels, const ContourParams &ps = ContourParams(),
126 const ROMol *mol = nullptr);
127//! \overload
129 MolDraw2D &drawer, const double *grid, const std::vector<double> &xcoords,
130 const std::vector<double> &ycoords, size_t nContours = 10,
131 const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr) {
132 std::vector<double> levels;
133 contourAndDrawGrid(drawer, grid, xcoords, ycoords, nContours, levels, ps,
134 mol);
135};
136
137//! Generates and draws contours for a set of gaussians
138/*
139 \param drawer: the MolDraw2D object to use
140 \param locs: locations of the gaussians
141 \param heights: the heights (or weights) of the gaussians
142 \param widths: the standard deviations of the gaussians
143 \param nContours: the number of contours to draw
144 \param levels: the contours to use
145 \param ps: additional parameters controlling the contouring.
146 \param mol: molecule to be used to adjust the scale of the drawing.
147
148 The values are calculated on a grid with spacing \c ps.gridResolution.
149 If \c ps.setScale is set, the grid size will be calculated based on the
150 locations of the gaussians and \c ps.extraGridPadding. Otherwise the current
151 size of the viewport will be used.
152
153 If the \c levels argument is empty, the contour levels will be determined
154 automatically from the max and min values on the grid and \c levels will
155 be updated to include the contour levels.
156
157 If \c ps.fillGrid is set, the data on the grid will also be drawn using
158 the color scheme in \c ps.colourMap
159
160 if the \c mol argument is given, it will be used to adjust the scale of
161 drawing. This is because a common use is to draw the molecule onto
162 the contour, and it makes sense if it fits.
163
164*/
166 MolDraw2D &drawer, const std::vector<Point2D> &locs,
167 const std::vector<double> &heights, const std::vector<double> &widths,
168 size_t nContours, std::vector<double> &levels,
169 const ContourParams &ps = ContourParams(), const ROMol *mol = nullptr);
170//! \overload
172 MolDraw2D &drawer, const std::vector<Point2D> &locs,
173 const std::vector<double> &heights, const std::vector<double> &widths,
174 size_t nContours = 10, const ContourParams &ps = ContourParams(),
175 const ROMol *mol = nullptr) {
176 std::vector<double> levels;
177 contourAndDrawGaussians(drawer, locs, heights, widths, nContours, levels, ps,
178 mol);
179};
180
181//! Draw a molecule to a MolDraw2D object according to ACS 1996 guidelines
182/*
183 The ACS1996 guidelines, as described at
184 https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing
185 A number of values in drawer.drawOptions() are changed.
186 This is designed to be used with a flexiCanvas, i.e. a MolDraw2D object
187 created with width and height -1, because it works to a fixed scale.
188 It will issue a warning if the dimensions are otherwise and the picture may
189 look sub-optimal.
190 */
192 MolDraw2D &drawer, const ROMol &mol, const std::string &legend,
193 const std::vector<int> *highlight_atoms,
194 const std::vector<int> *highlight_bonds,
195 const std::map<int, DrawColour> *highlight_atom_map = nullptr,
196 const std::map<int, DrawColour> *highlight_bond_map = nullptr,
197 const std::map<int, double> *highlight_radii = nullptr, int confId = -1);
198
199//! Set the draw options to produce something as close as possible to
200//! the ACS 1996 guidelines as described at
201//! https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing
202/*
203 \param MolDrawOptions opt - the options what will be changed
204 \param float meanBondLength - mean bond length of the molecule
205
206 Works best if the MolDraw2D object is created with width and height -1 (a
207 flexiCanvas).
208 The mean bond length may be calculated with MolDraw2DUtils::meanBondLength.
209 It is used to calculate the offset for the lines in multiple bonds.
210
211 Options changed are:
212 bondLineWidth = 0.6
213 scaleBondWidth = false
214 scalingFactor = 14.4 / meanBondLen
215 multipleBondOffset = 0.18
216 highlightBondWidthMultiplier = 32
217 setMonochromeMode - black and white
218 fixedFontSize = 10
219 additionalAtomLabelPadding = 0.066
220 fontFile - if it isn't set already, then if RDBASE is set and the file
221 exists, uses $RDBASE/Fonts/Data/FreeSans.ttf. Otherwise uses
222 BuiltinRobotoRegular.
223 */
225 double meanBondLen = 1.0);
226RDKIT_MOLDRAW2D_EXPORT double meanBondLength(const ROMol &mol, int confId = -1);
227} // namespace MolDraw2DUtils
228
229} // namespace RDKit
230#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 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, bool addChiralHs=true, bool wedgeBonds=true, bool forceCoords=false, bool wavyBonds=false)
prepare a molecule for drawing and draw it
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.
Std stuff.
Definition: Abbreviations.h:19
std::vector< DrawColour > colourMap