RDKit
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MolDraw2DHelpers.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 (CozChemIx Limited)
11//
12// A load of helper classes used by MolDraw2D.
13
14#ifndef RDKIT_MOLDRAW2DHELPERS_H
15#define RDKIT_MOLDRAW2DHELPERS_H
16
17#include <Geometry/point.h>
18
19using RDGeom::Point2D;
20
21namespace RDKit {
22
23namespace MolDraw2D_detail {
24// for aligning the drawing of text to the passed in coords.
25enum class OrientType : unsigned char { C = 0, N, E, S, W };
26enum class TextAlignType : unsigned char { MIDDLE = 0, START, END };
27}
28
29struct DrawColour {
30 double r = 0.0, g = 0.0, b = 0.0, a = 1.0;
31 DrawColour() = default;
32 DrawColour(double r, double g, double b, double a = 1.0)
33 : r(r), g(g), b(b), a(a) {}
34 bool operator==(const DrawColour &other) const {
35 return r == other.r && g == other.g && b == other.b && a == other.a;
36 }
37 bool feq(const DrawColour &other, double tol = 0.001,
38 bool ignoreAlpha = true) const {
39 return fabs(r - other.r) <= tol && fabs(g - other.g) <= tol &&
40 fabs(b - other.b) <= tol &&
41 (ignoreAlpha || fabs(a - other.a) <= tol);
42 }
43 DrawColour operator+(const DrawColour &other) const {
44 return {r + other.r, g + other.g, b + other.b, a + other.a};
45 }
46 DrawColour operator-(const DrawColour &other) const {
47 return {r - other.r, g - other.g, b - other.b, a - other.a};
48 }
49 DrawColour operator/(double v) const {
50 PRECONDITION(v != 0.0, "divide by zero");
51 return {r / v, g / v, b / v, a / v};
52 }
53 DrawColour operator*(double v) const { return {r * v, g * v, b * v, a * v}; }
54};
55
56typedef std::map<int, DrawColour> ColourPalette;
57typedef std::vector<double> DashPattern;
58
59//! use the RDKit's default palette r
60inline void assignDefaultPalette(ColourPalette &palette) {
61 palette.clear();
62 palette[-1] = DrawColour(0, 0, 0);
63 palette[0] = DrawColour(0.1, 0.1, 0.1);
64 palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0);
65 palette[7] = DrawColour(0.0, 0.0, 1.0);
66 palette[8] = DrawColour(1.0, 0.0, 0.0);
67 palette[9] = DrawColour(0.2, 0.8, 0.8);
68 palette[15] = DrawColour(1.0, 0.5, 0.0);
69 palette[16] = DrawColour(0.8, 0.8, 0.0);
70 palette[17] = DrawColour(0.0, 0.802, 0.0);
71 palette[35] = DrawColour(0.5, 0.3, 0.1);
72 palette[53] = DrawColour(0.63, 0.12, 0.94);
73};
74
75//! use the color palette from the Avalon renderer
76inline void assignAvalonPalette(ColourPalette &palette) {
77 palette.clear();
78 palette[-1] = DrawColour(0, 0, 0);
79 palette[0] = DrawColour(0.1, 0.1, 0.1);
80 palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0);
81 palette[7] = DrawColour(0.0, 0.0, 1.0);
82 palette[8] = DrawColour(1.0, 0.0, 0.0);
83 palette[9] = DrawColour(0.0, 0.498, 0.0);
84 palette[15] = DrawColour(0.498, 0.0, 0.498);
85 palette[16] = DrawColour(0.498, 0.247, 0.0);
86 palette[17] = DrawColour(0.0, 0.498, 0.0);
87 palette[35] = DrawColour(0.0, 0.498, 0.0);
88 palette[53] = DrawColour(0.247, 0.0, 0.498);
89};
90
91//! use (part of) the CDK color palette
92/*!
93 data source:
94 https://github.com/cdk/cdk/blob/master/display/render/src/main/java/org/openscience/cdk/renderer/color/CDK2DAtomColors.java
95*/
96inline void assignCDKPalette(ColourPalette &palette) {
97 palette.clear();
98 palette[-1] = DrawColour(0, 0, 0);
99 palette[0] = DrawColour(0.1, 0.1, 0.1);
100 palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0);
101 palette[7] = DrawColour(0.188, 0.314, 0.972);
102 palette[8] = DrawColour(1.0, 0.051, 0.051);
103 palette[9] = DrawColour(0.565, 0.878, 0.314);
104 palette[15] = DrawColour(1.0, 0.5, 0.0);
105 palette[16] = DrawColour(0.776, 0.776, 0.173);
106 palette[17] = DrawColour(0.122, 0.498, 0.122);
107 palette[35] = DrawColour(0.651, 0.161, 0.161);
108 palette[53] = DrawColour(0.580, 0.0, 0.580);
109 palette[5] = DrawColour(1.000, 0.710, 0.710);
110};
111
113 palette.clear();
114 palette[-1] = DrawColour(0.8, 0.8, 0.8);
115 palette[0] = DrawColour(0.9, 0.9, 0.9);
116 palette[1] = palette[6] = DrawColour(0.9, 0.9, 0.9);
117 palette[7] = DrawColour(0.33, 0.41, 0.92);
118 palette[8] = DrawColour(1.0, 0.2, 0.2);
119 palette[9] = DrawColour(0.2, 0.8, 0.8);
120 palette[15] = DrawColour(1.0, 0.5, 0.0);
121 palette[16] = DrawColour(0.8, 0.8, 0.0);
122 palette[17] = DrawColour(0.0, 0.802, 0.0);
123 palette[35] = DrawColour(0.71, 0.4, 0.07);
124 palette[53] = DrawColour(0.89, 0.004, 1);
125};
126
127inline void assignBWPalette(ColourPalette &palette) {
128 palette.clear();
129 palette[-1] = DrawColour(0, 0, 0);
130};
131
133 bool atomLabelDeuteriumTritium =
134 false; // toggles replacing 2H with D and 3H with T
135 bool dummiesAreAttachments = false; // draws "breaks" at dummy atoms
136 bool circleAtoms = true; // draws circles under highlighted atoms
137 bool splitBonds = false; // split bonds into per atom segments
138 // most useful for dynamic manipulation of drawing
139 // especially for svg
140 DrawColour highlightColour{1, 0.5, 0.5, 1.0}; // default highlight color
141 bool continuousHighlight = true; // highlight by drawing an outline
142 // *underneath* the molecule
143 bool fillHighlights = true; // fill the areas used to highlight atoms and
144 // atom regions
145 double highlightRadius = 0.3; // default if nothing given for a particular
146 // atom. units are "Angstrom"
147 int flagCloseContactsDist = 3; // if positive, this will be used as a cutoff
148 // (in pixels) for highlighting close contacts
149 bool includeAtomTags =
150 false; // toggles inclusion of atom tags in the output. does
151 // not make sense for all renderers.
152 bool clearBackground = true; // toggles clearing the background before
153 // drawing a molecule
154 DrawColour backgroundColour{
155 1, 1, 1, 1}; // color to be used while clearing the background
156 int legendFontSize = 16; // font size (in pixels) to be used for the legend
157 // (if present)
158 double legendFraction =
159 0.1; // fraction of the draw panel to be used for the legend if present
160 int maxFontSize = 40; // maximum size in pixels for font in drawn molecule.
161 // -1 means no max.
162 int minFontSize = 6; // likewise for -1.
163 int fixedFontSize =
164 -1; // font size to use, in pixels. Default -1 means not fixed. If set,
165 // always used irrespective of scale, minFontSize and maxFontSize.
166 double annotationFontScale = 0.5; // scales font relative to atom labels for
167 // atom and bond annotation.
168 std::string fontFile = ""; // name of font for freetype rendering. If given,
169 // over-rides default
170 DrawColour legendColour{0, 0,
171 0}; // color to be used for the legend (if present)
172 double multipleBondOffset = 0.15; // offset (in Angstrom) for the extra lines
173 // in a multiple bond
174 double padding =
175 0.05; // fraction of empty space to leave around the molecule
176 double additionalAtomLabelPadding = 0.0; // additional padding to leave
177 // around atom labels. Expressed as
178 // a fraction of the font size.
179 std::map<int, std::string> atomLabels; // replacement labels for atoms
180 bool noAtomLabels =
181 false; // disables inclusion of atom labels in the rendering
182 std::vector<std::vector<int>> atomRegions; // regions
183 DrawColour symbolColour{
184 0, 0, 0, 1}; // color to be used for the symbols and arrows in reactions
185 DrawColour annotationColour{0, 0, 0, 1}; // color to be used for annotations
186 int bondLineWidth = 2; // default line width when drawing bonds
187 bool scaleBondWidth = false; // whether to apply scale() to the bond width
188 bool scaleHighlightBondWidth = true; // likewise with bond highlights.
189 int highlightBondWidthMultiplier = 8; // what to multiply standard bond width
190 // by for highlighting.
191 bool prepareMolsBeforeDrawing = true; // call prepareMolForDrawing() on each
192 // molecule passed to drawMolecules()
193 std::vector<DrawColour> highlightColourPalette; // defining 10 default colors
194 // for highlighting atoms and bonds
195 // or reactants in a reactions
196 ColourPalette atomColourPalette; // the palette used to assign
197 // colors to atoms based on
198 // atomic number.
199 double fixedScale =
200 -1.0; // fixes scale to this fraction of draw window width, so
201 // an average bond is this fraction of the width. If
202 // scale comes out smaller than this, reduces scale, but
203 // won't make it larger. The default of -1.0 means no fix.
204 double fixedBondLength =
205 -1.0; // fixes the bond length (and hence the scale) to
206 // always be this number of pixels. Assuming a bond
207 // length in coordinates is 1, as is normal. If
208 // scale comes out smaller than this, reduces scale,
209 // but won't make it larger. The default -1.0 means no
210 // fix. If both fixedScale and fixedBondLength are >
211 // 0.0, fixedScale wins.
212 double rotate = 0.0; // angle in degrees to rotate coords by about centre
213 // before drawing.
214 bool addAtomIndices = false; // adds atom indices to drawings.
215 bool addBondIndices = false; // adds bond indices to drawings.
216 bool isotopeLabels = true; // adds isotope to non-dummy atoms.
217 bool dummyIsotopeLabels = true; // adds isotope labels to dummy atoms.
218
219 bool addStereoAnnotation = false; // adds E/Z and R/S to drawings.
220 bool atomHighlightsAreCircles = false; // forces atom highlights always to be
221 // circles. Default (false) is to put
222 // ellipses round longer labels.
223 bool centreMoleculesBeforeDrawing = false; // moves the centre of the drawn
224 // molecule to (0,0)
225 bool explicitMethyl = false; // draw terminal methyl and related as CH3
226 bool includeRadicals =
227 true; // include radicals in the drawing (it can be useful to turn this
228 // off for reactions and queries)
229 bool includeMetadata =
230 true; // when possible include metadata about molecules and reactions in
231 // the output to allow them to be reconstructed
232 bool comicMode = false; // simulate hand-drawn lines for bonds. When combined
233 // with a font like Comic-Sans or Comic-Neue, this
234 // gives xkcd-like drawings.
235 int variableBondWidthMultiplier = 16; // what to multiply standard bond width
236 // by for variable attachment points.
237 double variableAtomRadius = 0.4; // radius value to use for atoms involved in
238 // variable attachment points.
239 DrawColour variableAttachmentColour = {
240 0.8, 0.8, 0.8, 1.0}; // colour to use for variable attachment points
241 bool includeChiralFlagLabel =
242 false; // add a molecule annotation with "ABS" if the chiral flag is set
243 bool simplifiedStereoGroupLabel =
244 false; // if all specified stereocenters are in a single StereoGroup,
245 // show a molecule-level annotation instead of the individual
246 // labels
247 bool singleColourWedgeBonds =
248 false; // if true wedged and dashed bonds are drawn
249 // using symbolColour rather than inheriting
250 // their colour from the atoms
251 double scalingFactor = 20.0; // scaling factor used for pixels->angstrom
252 // when auto scaling is being used
253 double baseFontSize =
254 -1.0; // when > 0 this is used to set the baseFontSize used for text
255 // drawing. As a reference point: the default value for
256 // DrawText::baseFontSize is 0.6
257 bool drawMolsSameScale = true; // when drawing multiple molecules with
258 // DrawMolecules, forces them to use the same
259 // scale. Default is true.
260
262 highlightColourPalette.emplace_back(
263 DrawColour(1., 1., .67)); // popcorn yellow
264 highlightColourPalette.emplace_back(DrawColour(1., .8, .6)); // sand
265 highlightColourPalette.emplace_back(
266 DrawColour(1., .71, .76)); // light pink
267 highlightColourPalette.emplace_back(
268 DrawColour(.8, 1., .8)); // offwhitegreen
269 highlightColourPalette.emplace_back(DrawColour(.87, .63, .87)); // plum
270 highlightColourPalette.emplace_back(
271 DrawColour(.76, .94, .96)); // pastel blue
272 highlightColourPalette.emplace_back(
273 DrawColour(.67, .67, 1.)); // periwinkle
274 highlightColourPalette.emplace_back(DrawColour(.64, .76, .34)); // avocado
275 highlightColourPalette.emplace_back(
276 DrawColour(.56, .93, .56)); // light green
277 highlightColourPalette.emplace_back(DrawColour(.20, .63, .79)); // peacock
278 assignDefaultPalette(atomColourPalette);
279 }
280};
281
282} // namespace RDKit
283
284#endif // RDKIT_MOLDRAW2DHELPERS_H
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:273
RDKIT_MOLDRAW2D_EXPORT void addBondIndices(const ROMol &mol)
add annotations with bond indices.
RDKIT_MOLDRAW2D_EXPORT void addAtomIndices(const ROMol &mol)
add annotations with atom indices.
RDKIT_MOLDRAW2D_EXPORT void addStereoAnnotation(const ROMol &mol, bool includeRelativeCIP=false)
add R/S, relative stereo, and E/Z annotations to atoms and bonds
Std stuff.
Definition: Abbreviations.h:18
std::vector< double > DashPattern
void assignDefaultPalette(ColourPalette &palette)
use the RDKit's default palette r
void assignAvalonPalette(ColourPalette &palette)
use the color palette from the Avalon renderer
void assignDarkModePalette(ColourPalette &palette)
std::map< int, DrawColour > ColourPalette
void assignBWPalette(ColourPalette &palette)
void assignCDKPalette(ColourPalette &palette)
use (part of) the CDK color palette
bool feq(const DrawColour &other, double tol=0.001, bool ignoreAlpha=true) const
DrawColour()=default
DrawColour operator+(const DrawColour &other) const
DrawColour operator/(double v) const
DrawColour operator*(double v) const
DrawColour(double r, double g, double b, double a=1.0)
DrawColour operator-(const DrawColour &other) const
bool operator==(const DrawColour &other) const
std::vector< std::vector< int > > atomRegions
std::map< int, std::string > atomLabels
ColourPalette atomColourPalette
std::vector< DrawColour > highlightColourPalette