// // Copyright (C) 2014-2021 David Cosgrove and other RDKit contributors // // @@ All Rights Reserved @@ // This file is part of the RDKit. // The contents are covered by the terms of the BSD license // which is included in the file license.txt, found at the root // of the RDKit source tree. // // Original author: David Cosgrove (CozChemIx Limited) // // A load of helper classes used by MolDraw2D. #ifndef RDKIT_MOLDRAW2DHELPERS_H #define RDKIT_MOLDRAW2DHELPERS_H #include using RDGeom::Point2D; namespace RDKit { namespace MolDraw2D_detail { // for aligning the drawing of text to the passed in coords. enum class OrientType : unsigned char { C = 0, N, E, S, W }; enum class TextAlignType : unsigned char { MIDDLE = 0, START, END }; } // namespace MolDraw2D_detail struct DrawColour { double r = 0.0, g = 0.0, b = 0.0, a = 1.0; DrawColour() = default; DrawColour(double r, double g, double b, double a = 1.0) : r(r), g(g), b(b), a(a) {} bool operator==(const DrawColour &other) const { return r == other.r && g == other.g && b == other.b && a == other.a; } bool operator!=(const DrawColour &other) const { return !(*this == other); } bool feq(const DrawColour &other, double tol = 0.001, bool ignoreAlpha = true) const { return fabs(r - other.r) <= tol && fabs(g - other.g) <= tol && fabs(b - other.b) <= tol && (ignoreAlpha || fabs(a - other.a) <= tol); } DrawColour operator+(const DrawColour &other) const { return {r + other.r, g + other.g, b + other.b, a + other.a}; } DrawColour operator-(const DrawColour &other) const { return {r - other.r, g - other.g, b - other.b, a - other.a}; } DrawColour operator/(double v) const { PRECONDITION(v != 0.0, "divide by zero"); return {r / v, g / v, b / v, a / v}; } DrawColour operator*(double v) const { return {r * v, g * v, b * v, a * v}; } }; typedef std::map ColourPalette; typedef std::vector DashPattern; // This is used to convert the line width into something that SVG and // Cairo use. It was picked by eye, and was formerly hidden in // MolDraw2D::getDrawLineWidth(). static const double lineWidthScaleFactor = 0.02; //! use the RDKit's default palette r // 201 is for hydrogens when atom symbols are not being drawn. inline void assignDefaultPalette(ColourPalette &palette) { palette.clear(); palette[-1] = DrawColour(0, 0, 0); palette[0] = DrawColour(0.1, 0.1, 0.1); palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0); palette[7] = DrawColour(0.0, 0.0, 1.0); palette[8] = DrawColour(1.0, 0.0, 0.0); palette[9] = DrawColour(0.2, 0.8, 0.8); palette[15] = DrawColour(1.0, 0.5, 0.0); palette[16] = DrawColour(0.8, 0.8, 0.0); palette[17] = DrawColour(0.0, 0.802, 0.0); palette[35] = DrawColour(0.5, 0.3, 0.1); palette[53] = DrawColour(0.63, 0.12, 0.94); palette[201] = DrawColour(0.68, 0.85, 0.90); }; //! use the color palette from the Avalon renderer // 201 is for hydrogens when atom symbols are not being drawn. inline void assignAvalonPalette(ColourPalette &palette) { palette.clear(); palette[-1] = DrawColour(0, 0, 0); palette[0] = DrawColour(0.1, 0.1, 0.1); palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0); palette[7] = DrawColour(0.0, 0.0, 1.0); palette[8] = DrawColour(1.0, 0.0, 0.0); palette[9] = DrawColour(0.0, 0.498, 0.0); palette[15] = DrawColour(0.498, 0.0, 0.498); palette[16] = DrawColour(0.498, 0.247, 0.0); palette[17] = DrawColour(0.0, 0.498, 0.0); palette[35] = DrawColour(0.0, 0.498, 0.0); palette[53] = DrawColour(0.247, 0.0, 0.498); palette[201] = DrawColour(0.68, 0.85, 0.90); }; //! use (part of) the CDK color palette /*! data source: https://github.com/cdk/cdk/blob/master/display/render/src/main/java/org/openscience/cdk/renderer/color/CDK2DAtomColors.java */ // 201 is for hydrogens when atom symbols are not being drawn. inline void assignCDKPalette(ColourPalette &palette) { palette.clear(); palette[-1] = DrawColour(0, 0, 0); palette[0] = DrawColour(0.1, 0.1, 0.1); palette[1] = palette[6] = DrawColour(0.0, 0.0, 0.0); palette[7] = DrawColour(0.188, 0.314, 0.972); palette[8] = DrawColour(1.0, 0.051, 0.051); palette[9] = DrawColour(0.565, 0.878, 0.314); palette[15] = DrawColour(1.0, 0.5, 0.0); palette[16] = DrawColour(0.776, 0.776, 0.173); palette[17] = DrawColour(0.122, 0.498, 0.122); palette[35] = DrawColour(0.651, 0.161, 0.161); palette[53] = DrawColour(0.580, 0.0, 0.580); palette[5] = DrawColour(1.000, 0.710, 0.710); palette[201] = DrawColour(0.68, 0.85, 0.90); }; // 201 is for hydrogens when atom symbols are not being drawn. inline void assignDarkModePalette(ColourPalette &palette) { palette.clear(); palette[-1] = DrawColour(0.8, 0.8, 0.8); palette[0] = DrawColour(0.9, 0.9, 0.9); palette[1] = palette[6] = DrawColour(0.9, 0.9, 0.9); palette[7] = DrawColour(0.33, 0.41, 0.92); palette[8] = DrawColour(1.0, 0.2, 0.2); palette[9] = DrawColour(0.2, 0.8, 0.8); palette[15] = DrawColour(1.0, 0.5, 0.0); palette[16] = DrawColour(0.8, 0.8, 0.0); palette[17] = DrawColour(0.0, 0.802, 0.0); palette[35] = DrawColour(0.71, 0.4, 0.07); palette[53] = DrawColour(0.89, 0.004, 1); palette[201] = DrawColour(0.68, 0.85, 0.90); }; inline void assignBWPalette(ColourPalette &palette) { palette.clear(); palette[-1] = DrawColour(0, 0, 0); }; struct RDKIT_MOLDRAW2D_EXPORT MolDrawOptions { bool atomLabelDeuteriumTritium = false; // toggles replacing 2H with D and 3H with T bool dummiesAreAttachments = false; // draws "breaks" at dummy atoms bool circleAtoms = true; // draws circles under highlighted atoms bool splitBonds = false; // split bonds into per atom segments // most useful for dynamic manipulation of drawing // especially for svg DrawColour highlightColour{1, 0.5, 0.5, 1.0}; // default highlight color bool continuousHighlight = true; // highlight by drawing an outline // *underneath* the molecule bool fillHighlights = true; // fill the areas used to highlight atoms and // atom regions double highlightRadius = 0.3; // default if nothing given for a particular // atom. units are "Angstrom" int flagCloseContactsDist = 3; // if positive, this will be used as a cutoff // (in pixels) for highlighting close contacts bool includeAtomTags = false; // toggles inclusion of atom tags in the output. does // not make sense for all renderers. bool clearBackground = true; // toggles clearing the background before // drawing a molecule DrawColour backgroundColour{ 1, 1, 1, 1}; // color to be used while clearing the background int legendFontSize = 16; // font size (in pixels) to be used for the legend // (if present) double legendFraction = 0.1; // fraction of the draw panel to be used for the legend if present int maxFontSize = 40; // maximum size in pixels for font in drawn molecule. // -1 means no max. int minFontSize = 6; // likewise for -1. int fixedFontSize = -1; // font size to use, in pixels. Default -1 means not fixed. If set, // always used irrespective of scale, minFontSize and maxFontSize. double annotationFontScale = 0.5; // scales font relative to atom labels for // atom and bond annotation. std::string fontFile = ""; // name of font file for freetype rendering. If // given, over-rides default // (BuiltinTelexRegular). Can also be // BuiltinRobotoRegular. DrawColour legendColour{0, 0, 0}; // color to be used for the legend (if present) double multipleBondOffset = 0.15; // offset for the extra lines // in a multiple bond as a fraction of // mean bond length double padding = 0.05; // fraction of empty space to leave around the molecule double additionalAtomLabelPadding = 0.0; // additional padding to leave // around atom labels. Expressed as // a fraction of the font size. std::map atomLabels; // replacement labels for atoms bool noAtomLabels = false; // disables inclusion of atom labels in the rendering std::vector> atomRegions; // regions DrawColour symbolColour{ 0, 0, 0, 1}; // color to be used for the symbols and arrows in reactions DrawColour annotationColour{0, 0, 0, 1}; // color to be used for annotations double bondLineWidth = 2.0; // default line width when drawing bonds bool scaleBondWidth = false; // whether to apply scale() to the bond width bool scaleHighlightBondWidth = true; // likewise with bond highlights. int highlightBondWidthMultiplier = 8; // what to multiply standard bond width // by for highlighting. bool prepareMolsBeforeDrawing = true; // call prepareMolForDrawing() on each // molecule passed to drawMolecules() std::vector highlightColourPalette; // defining 10 default colors // for highlighting atoms and bonds // or reactants in a reactions ColourPalette atomColourPalette; // the palette used to assign // colors to atoms based on // atomic number. double fixedScale = -1.0; // fixes scale to this fraction of draw window width, so // an average bond is this fraction of the width. If // scale comes out smaller than this, reduces scale, but // won't make it larger. The default of -1.0 means no fix. double fixedBondLength = -1.0; // fixes the bond length (and hence the scale) to // always be this number of pixels. Assuming a bond // length in coordinates is 1, as is normal. If // scale comes out smaller than this, reduces scale, // but won't make it larger. The default -1.0 means no // fix. If both fixedScale and fixedBondLength are > // 0.0, fixedScale wins. double rotate = 0.0; // angle in degrees to rotate coords by about centre // before drawing. bool addAtomIndices = false; // adds atom indices to drawings. bool addBondIndices = false; // adds bond indices to drawings. bool isotopeLabels = true; // adds isotope to non-dummy atoms. bool dummyIsotopeLabels = true; // adds isotope labels to dummy atoms. bool addStereoAnnotation = false; // adds E/Z and R/S to drawings. bool atomHighlightsAreCircles = false; // forces atom highlights always to be // circles. Default (false) is to put // ellipses round longer labels. bool centreMoleculesBeforeDrawing = false; // moves the centre of the drawn // molecule to (0,0) bool explicitMethyl = false; // draw terminal methyl and related as CH3 bool includeRadicals = true; // include radicals in the drawing (it can be useful to turn this // off for reactions and queries) bool includeMetadata = true; // when possible include metadata about molecules and reactions in // the output to allow them to be reconstructed bool comicMode = false; // simulate hand-drawn lines for bonds. When combined // with a font like Comic-Sans or Comic-Neue, this // gives xkcd-like drawings. int variableBondWidthMultiplier = 16; // what to multiply standard bond width // by for variable attachment points. double variableAtomRadius = 0.4; // radius value to use for atoms involved in // variable attachment points. DrawColour variableAttachmentColour = { 0.8, 0.8, 0.8, 1.0}; // colour to use for variable attachment points bool includeChiralFlagLabel = false; // add a molecule annotation with "ABS" if the chiral flag is set bool simplifiedStereoGroupLabel = false; // if all specified stereocenters are in a single StereoGroup, // show a molecule-level annotation instead of the individual // labels bool unspecifiedStereoIsUnknown = false; // if true, double bonds with // unspecified stereo are drawn // crossed, potential stereocenters // with unspecified stereo are drawn // with a wavy bond. bool singleColourWedgeBonds = false; // if true wedged and dashed bonds are drawn // using symbolColour rather than inheriting // their colour from the atoms bool useMolBlockWedging = false; // If the molecule came from a MolBlock, // prefer the wedging information that // provides. If false, use RDKit rules. double scalingFactor = 20.0; // scaling factor used for pixels->angstrom // when auto scaling is being used double baseFontSize = -1.0; // when > 0 this is used to set the baseFontSize used for text // drawing. As a reference point: the default value for // DrawText::baseFontSize is 0.6 bool drawMolsSameScale = true; // when drawing multiple molecules with // DrawMolecules, forces them to use the same // scale. Default is true. MolDrawOptions() { highlightColourPalette.emplace_back( DrawColour(1., 1., .67)); // popcorn yellow highlightColourPalette.emplace_back(DrawColour(1., .8, .6)); // sand highlightColourPalette.emplace_back( DrawColour(1., .71, .76)); // light pink highlightColourPalette.emplace_back( DrawColour(.8, 1., .8)); // offwhitegreen highlightColourPalette.emplace_back(DrawColour(.87, .63, .87)); // plum highlightColourPalette.emplace_back( DrawColour(.76, .94, .96)); // pastel blue highlightColourPalette.emplace_back( DrawColour(.67, .67, 1.)); // periwinkle highlightColourPalette.emplace_back(DrawColour(.64, .76, .34)); // avocado highlightColourPalette.emplace_back( DrawColour(.56, .93, .56)); // light green highlightColourPalette.emplace_back(DrawColour(.20, .63, .79)); // peacock assignDefaultPalette(atomColourPalette); } }; } // namespace RDKit #endif // RDKIT_MOLDRAW2DHELPERS_H