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MolDraw2DDetails.h
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//
// Copyright (C) 2015-2022 Greg Landrum 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.
//
#include <RDGeneral/export.h>
#ifndef RDKITMOLDRAW2DDETAILS_H
#define RDKITMOLDRAW2DDETAILS_H
#include <vector>
#include <Geometry/point.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <tuple>
#include <boost/format.hpp>
// ****************************************************************************
using RDGeom::Point2D;
namespace RDKit {
namespace MolDraw2D_detail {
struct StringRect;
// data taken from the helvetica font info in
// $RDBASE/rdkit/sping/PDF/pdfmetrics.py
const int char_widths[] = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 278, 278, 355, 556, 556, 889, 667, 222, 333, 333,
389, 584, 278, 333, 278, 278, 556, 556, 556, 556, 556, 556, 556, 556,
556, 556, 278, 278, 584, 584, 584, 556, 1015, 667, 667, 722, 722, 667,
611, 778, 722, 278, 500, 667, 556, 833, 722, 778, 667, 778, 722, 667,
611, 722, 667, 944, 667, 667, 611, 278, 278, 278, 469, 556, 222, 556,
556, 500, 556, 556, 278, 556, 556, 222, 222, 500, 222, 833, 556, 556,
556, 556, 333, 500, 278, 556, 500, 722, 500, 500, 500, 334, 260, 334,
584, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 333, 556, 556, 167, 556, 556, 556,
556, 191, 333, 556, 333, 333, 500, 500, 0, 556, 556, 556, 278, 0,
537, 350, 222, 333, 333, 556, 1000, 1000, 0, 611, 0, 333, 333, 333,
333, 333, 333, 333, 333, 0, 333, 333, 0, 333, 333, 333, 1000, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1000, 0, 370, 0, 0, 0, 0, 556, 778, 1000, 365, 0, 0,
0, 0, 0, 889, 0, 0, 0, 278, 0, 0, 222, 611, 944, 611,
0, 0, 834};
// angles in degrees.
RDKIT_MOLDRAW2D_EXPORT void arcPoints(const Point2D &cds1, const Point2D &cds2,
std::vector<Point2D> &res,
float startAng = 0, float extent = 360);
//! add annotations with atom indices.
RDKIT_MOLDRAW2D_EXPORT inline void addAtomIndices(const ROMol &mol) {
// we don't need this in the global set of tags since it will only be used
// here
if (mol.hasProp("_atomIndicesAdded")) {
return;
}
bool computed = true;
mol.setProp("_atomIndicesAdded", 1, computed);
for (auto atom : mol.atoms()) {
auto lab = std::to_string(atom->getIdx());
if (atom->hasProp(common_properties::atomNote)) {
lab += "," + atom->getProp<std::string>(common_properties::atomNote);
}
atom->setProp(common_properties::atomNote, lab);
}
};
//! add annotations with bond indices.
RDKIT_MOLDRAW2D_EXPORT inline void addBondIndices(const ROMol &mol) {
// we don't need this in the global set of tags since it will only be used
// here
if (mol.hasProp("_bondIndicesAdded")) {
return;
}
bool computed = true;
mol.setProp("_bondIndicesAdded", 1, computed);
for (auto bond : mol.bonds()) {
auto lab = std::to_string(bond->getIdx());
if (bond->hasProp(common_properties::bondNote)) {
lab += "," + bond->getProp<std::string>(common_properties::bondNote);
}
bond->setProp(common_properties::bondNote, lab);
}
};
RDKIT_MOLDRAW2D_EXPORT std::vector<Point2D> getBracketPoints(
const Point2D &p1, const Point2D &p2, const Point2D &refPt,
const std::vector<std::pair<Point2D, Point2D>> &bondSegments,
double bracketFrac = 0.1);
// there are a several empirically determined constants here.
RDKIT_MOLDRAW2D_EXPORT std::vector<Point2D> handdrawnLine(
Point2D cds1, Point2D cds2, double scale, bool shiftBegin = false,
bool shiftEnd = false, unsigned nSteps = 4, double deviation = 0.03,
double endShift = 0.5);
inline std::string formatDouble(double val) {
return boost::str(boost::format("%.1f") % val);
}
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersect(const StringRect &rect,
const Point2D &end1,
const Point2D &end2,
double padding);
// returns true if any corner of triangle is inside the rectangle.
RDKIT_MOLDRAW2D_EXPORT bool doesTriangleIntersect(const StringRect &rect,
const Point2D &pt1,
const Point2D &pt2,
const Point2D &pt3,
double padding);
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersectEllipse(
const Point2D &centre, double xradius, double yradius, double padding,
const Point2D &end1, const Point2D &end2);
// angles expected in degrees, between 0 and 360.
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersectArc(
const Point2D &centre, double xradius, double yradius, double start_ang,
double stop_ang, double padding, const Point2D &end1, const Point2D &end2);
RDKIT_MOLDRAW2D_EXPORT bool doLinesIntersect(const Point2D &l1s,
const Point2D &l1f,
const Point2D &l2s,
const Point2D &l2f, Point2D *ip);
// This uses the barycentric coordinate system method from
// http://totologic.blogspot.com/2014/01/accurate-point-in-triangle-test.html
// where it notes and provides a solution for instabilities when the point
// in exactly on one of the edges of the triangle. That refinement is not
// implemented because it seems a bit of overkill for most uses. It is an
// issue when, for example, two triangles share an edge and the point is on that
// edge, when it might give the disappointing result that the point is in
// neither triangle.
RDKIT_MOLDRAW2D_EXPORT bool isPointInTriangle(const Point2D &pt,
const Point2D &t1,
const Point2D &t2,
const Point2D &t3);
// returns a vector of p1,c1,c2,p2 tuples for bezier curves
RDKIT_MOLDRAW2D_EXPORT
std::vector<std::tuple<Point2D, Point2D, Point2D, Point2D>> getWavyLineSegments(
const Point2D &p1, const Point2D &p2, unsigned int nSegments,
double vertOffset);
// calculate the points making up the arrowhead of a DrawShapeArrow, allowing
// for the fact that in polygon mode the point can extend over the end
// of the point, because of the mitring.
RDKIT_MOLDRAW2D_EXPORT void calcArrowHead(Point2D &arrowEnd, Point2D &arrow1,
Point2D &arrow2,
const Point2D &arrowBegin,
double frac, double lineWidth,
double angle);
// adjust p2 so that the line from p1 to p2 stops where it intersects
// the ellipse.
RDKIT_MOLDRAW2D_EXPORT void adjustLineEndForEllipse(const Point2D &centre,
double xradius,
double yradius, Point2D p1,
Point2D &p2);
} // namespace MolDraw2D_detail
} // namespace RDKit
#endif
MolDraw2D.h
RDKitBase.h
pulls in the core RDKit functionality
RDGeom::Point2D
Definition point.h:284
RDKit::RDProps::hasProp
bool hasProp(const std::string &key) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition RDProps.h:126
RDKit::RDProps::setProp
void setProp(const std::string &key, T val, bool computed=false) const
sets a property value
Definition RDProps.h:77
RDKit::ROMol
Definition ROMol.h:199
RDKit::ROMol::atoms
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Definition ROMol.h:277
RDKit::ROMol::bonds
CXXBondIterator< MolGraph, Bond * > bonds()
Definition ROMol.h:316
export.h
RDKIT_MOLDRAW2D_EXPORT
#define RDKIT_MOLDRAW2D_EXPORT
Definition export.h:313
RDKit::MolDraw2D_detail
Definition AtomSymbol.h:30
RDKit::MolDraw2D_detail::adjustLineEndForEllipse
RDKIT_MOLDRAW2D_EXPORT void adjustLineEndForEllipse(const Point2D &centre, double xradius, double yradius, Point2D p1, Point2D &p2)
RDKit::MolDraw2D_detail::arcPoints
RDKIT_MOLDRAW2D_EXPORT void arcPoints(const Point2D &cds1, const Point2D &cds2, std::vector< Point2D > &res, float startAng=0, float extent=360)
RDKit::MolDraw2D_detail::doesLineIntersect
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersect(const StringRect &rect, const Point2D &end1, const Point2D &end2, double padding)
RDKit::MolDraw2D_detail::doLinesIntersect
RDKIT_MOLDRAW2D_EXPORT bool doLinesIntersect(const Point2D &l1s, const Point2D &l1f, const Point2D &l2s, const Point2D &l2f, Point2D *ip)
RDKit::MolDraw2D_detail::addBondIndices
RDKIT_MOLDRAW2D_EXPORT void addBondIndices(const ROMol &mol)
add annotations with bond indices.
Definition MolDraw2DDetails.h:78
RDKit::MolDraw2D_detail::calcArrowHead
RDKIT_MOLDRAW2D_EXPORT void calcArrowHead(Point2D &arrowEnd, Point2D &arrow1, Point2D &arrow2, const Point2D &arrowBegin, double frac, double lineWidth, double angle)
RDKit::MolDraw2D_detail::getBracketPoints
RDKIT_MOLDRAW2D_EXPORT std::vector< Point2D > getBracketPoints(const Point2D &p1, const Point2D &p2, const Point2D &refPt, const std::vector< std::pair< Point2D, Point2D > > &bondSegments, double bracketFrac=0.1)
RDKit::MolDraw2D_detail::handdrawnLine
RDKIT_MOLDRAW2D_EXPORT std::vector< Point2D > handdrawnLine(Point2D cds1, Point2D cds2, double scale, bool shiftBegin=false, bool shiftEnd=false, unsigned nSteps=4, double deviation=0.03, double endShift=0.5)
RDKit::MolDraw2D_detail::isPointInTriangle
RDKIT_MOLDRAW2D_EXPORT bool isPointInTriangle(const Point2D &pt, const Point2D &t1, const Point2D &t2, const Point2D &t3)
RDKit::MolDraw2D_detail::addAtomIndices
RDKIT_MOLDRAW2D_EXPORT void addAtomIndices(const ROMol &mol)
add annotations with atom indices.
Definition MolDraw2DDetails.h:60
RDKit::MolDraw2D_detail::char_widths
const int char_widths[]
Definition MolDraw2DDetails.h:33
RDKit::MolDraw2D_detail::doesTriangleIntersect
RDKIT_MOLDRAW2D_EXPORT bool doesTriangleIntersect(const StringRect &rect, const Point2D &pt1, const Point2D &pt2, const Point2D &pt3, double padding)
RDKit::MolDraw2D_detail::doesLineIntersectArc
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersectArc(const Point2D &centre, double xradius, double yradius, double start_ang, double stop_ang, double padding, const Point2D &end1, const Point2D &end2)
RDKit::MolDraw2D_detail::doesLineIntersectEllipse
RDKIT_MOLDRAW2D_EXPORT bool doesLineIntersectEllipse(const Point2D &centre, double xradius, double yradius, double padding, const Point2D &end1, const Point2D &end2)
RDKit::MolDraw2D_detail::formatDouble
std::string formatDouble(double val)
Definition MolDraw2DDetails.h:105
RDKit::MolDraw2D_detail::getWavyLineSegments
RDKIT_MOLDRAW2D_EXPORT std::vector< std::tuple< Point2D, Point2D, Point2D, Point2D > > getWavyLineSegments(const Point2D &p1, const Point2D &p2, unsigned int nSegments, double vertOffset)
RDKit::common_properties::bondNote
RDKIT_RDGENERAL_EXPORT const std::string bondNote
RDKit::common_properties::atomNote
RDKIT_RDGENERAL_EXPORT const std::string atomNote
RDKit
Std stuff.
Definition Abbreviations.h:19
point.h
RDKit::MolDraw2D_detail::StringRect
Definition StringRect.h:24