RDKit
Open-source cheminformatics and machine learning.
MolDraw2DDetails.h
Go to the documentation of this file.
1//
2// Copyright (C) 2015-2020 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 RDKITMOLDRAW2DDETAILS_H
13#define RDKITMOLDRAW2DDETAILS_H
14
15#include <vector>
16
17#include <Geometry/point.h>
18#include <GraphMol/RDKitBase.h>
20
21#include <boost/tuple/tuple.hpp>
22#include <boost/format.hpp>
23
24// ****************************************************************************
25using RDGeom::Point2D;
26
27namespace RDKit {
28namespace MolDraw2D_detail {
29struct StringRect;
30
31// data taken from the helvetica font info in
32// $RDBASE/rdkit/sping/PDF/pdfmetrics.py
33const int char_widths[] = {
34 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
35 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
36 0, 0, 0, 0, 278, 278, 355, 556, 556, 889, 667, 222, 333, 333,
37 389, 584, 278, 333, 278, 278, 556, 556, 556, 556, 556, 556, 556, 556,
38 556, 556, 278, 278, 584, 584, 584, 556, 1015, 667, 667, 722, 722, 667,
39 611, 778, 722, 278, 500, 667, 556, 833, 722, 778, 667, 778, 722, 667,
40 611, 722, 667, 944, 667, 667, 611, 278, 278, 278, 469, 556, 222, 556,
41 556, 500, 556, 556, 278, 556, 556, 222, 222, 500, 222, 833, 556, 556,
42 556, 556, 333, 500, 278, 556, 500, 722, 500, 500, 500, 334, 260, 334,
43 584, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
44 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
45 0, 0, 0, 0, 0, 0, 0, 333, 556, 556, 167, 556, 556, 556,
46 556, 191, 333, 556, 333, 333, 500, 500, 0, 556, 556, 556, 278, 0,
47 537, 350, 222, 333, 333, 556, 1000, 1000, 0, 611, 0, 333, 333, 333,
48 333, 333, 333, 333, 333, 0, 333, 333, 0, 333, 333, 333, 1000, 0,
49 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
50 0, 1000, 0, 370, 0, 0, 0, 0, 556, 778, 1000, 365, 0, 0,
51 0, 0, 0, 889, 0, 0, 0, 278, 0, 0, 222, 611, 944, 611,
52 0, 0, 834};
53
54// angles in degrees.
55RDKIT_MOLDRAW2D_EXPORT void arcPoints(const Point2D &cds1, const Point2D &cds2,
56 std::vector<Point2D> &res,
57 float startAng = 0, float extent = 360);
58
59//! add R/S, relative stereo, and E/Z annotations to atoms and bonds
61 const ROMol &mol, bool includeRelativeCIP = false);
62
63//! add annotations with atom indices.
65 // we don't need this in the global set of tags since it will only be used
66 // here
67 if (mol.hasProp("_atomIndicesAdded")) {
68 return;
69 }
70 bool computed = true;
71 mol.setProp("_atomIndicesAdded", 1, computed);
72 for (auto atom : mol.atoms()) {
73 auto lab = std::to_string(atom->getIdx());
74 if (atom->hasProp(common_properties::atomNote)) {
75 lab += "," + atom->getProp<std::string>(common_properties::atomNote);
76 }
77 atom->setProp(common_properties::atomNote, lab);
78 }
79};
80
81//! add annotations with bond indices.
83 // we don't need this in the global set of tags since it will only be used
84 // here
85 if (mol.hasProp("_bondIndicesAdded")) {
86 return;
87 }
88 bool computed = true;
89 mol.setProp("_bondIndicesAdded", 1, computed);
90 for (auto bond : mol.bonds()) {
91 auto lab = std::to_string(bond->getIdx());
92 if (bond->hasProp(common_properties::bondNote)) {
93 lab += "," + bond->getProp<std::string>(common_properties::bondNote);
94 }
95 bond->setProp(common_properties::bondNote, lab);
96 }
97};
98
100 const Point2D &p1, const Point2D &p2, const Point2D &refPt,
101 const std::vector<std::pair<Point2D, Point2D>> &bondSegments,
102 double bracketFrac = 0.1);
103// there are a several empirically determined constants here.
105 Point2D cds1, Point2D cds2, double scale, bool shiftBegin = false,
106 bool shiftEnd = false, unsigned nSteps = 4, double deviation = 0.03,
107 double endShift = 0.5);
108
109inline std::string formatDouble(double val) {
110 return boost::str(boost::format("%.1f") % val);
111}
112
113bool doesLineIntersect(const StringRect &rect, const Point2D &end1,
114 const Point2D &end2, double padding);
115// returns true if any corner of triangle is inside the rectangle.
116bool doesTriangleIntersect(const StringRect &rect, const Point2D &pt1,
117 const Point2D &pt2, const Point2D &pt3,
118 double padding);
119bool doesLineIntersectEllipse(const Point2D &centre, double xradius,
120 double yradius, double padding,
121 const Point2D &end1, const Point2D &end2);
122// angles expected in degrees, between 0 and 360.
123bool doesLineIntersectArc(const Point2D &centre, double xradius, double yradius,
124 double start_ang, double stop_ang, double padding,
125 const Point2D &end1, const Point2D &end2);
126bool doLinesIntersect(const Point2D &l1s, const Point2D &l1f,
127 const Point2D &l2s, const Point2D &l2f, Point2D *ip);
128// This uses the barycentric coordinate system method from
129// http://totologic.blogspot.com/2014/01/accurate-point-in-triangle-test.html
130// where it notes and provides a solution for instabilities when the point
131// in exactly on one of the edges of the triangle. That refinement is not
132// implemented because it seems a bit of overkill for most uses. It is an
133// issue when, for example, two triangles share an edge and the point is on that
134// edge, when it might give the disappointing result that the point is in
135// neither triangle.
136bool isPointInTriangle(const Point2D &pt, const Point2D &t1, const Point2D &t2,
137 const Point2D &t3);
138
139} // namespace MolDraw2D_detail
140} // namespace RDKit
141
142#endif
pulls in the core RDKit functionality
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
void setProp(const std::string &key, T val, bool computed=false) const
sets a property value
Definition: RDProps.h:77
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Definition: ROMol.h:257
CXXBondIterator< MolGraph, Bond * > bonds()
Definition: ROMol.h:296
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:273
static std::string to_string(const Descriptor &desc)
Definition: Descriptor.h:54
RDKIT_MOLDRAW2D_EXPORT void arcPoints(const Point2D &cds1, const Point2D &cds2, std::vector< Point2D > &res, float startAng=0, float extent=360)
bool doesLineIntersectArc(const Point2D &centre, double xradius, double yradius, double start_ang, double stop_ang, double padding, const Point2D &end1, const Point2D &end2)
bool doesLineIntersect(const StringRect &rect, const Point2D &end1, const Point2D &end2, double padding)
RDKIT_MOLDRAW2D_EXPORT void addBondIndices(const ROMol &mol)
add annotations with bond indices.
bool doesLineIntersectEllipse(const Point2D &centre, double xradius, double yradius, double padding, const Point2D &end1, const Point2D &end2)
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_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)
bool doLinesIntersect(const Point2D &l1s, const Point2D &l1f, const Point2D &l2s, const Point2D &l2f, Point2D *ip)
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::string formatDouble(double val)
bool doesTriangleIntersect(const StringRect &rect, const Point2D &pt1, const Point2D &pt2, const Point2D &pt3, double padding)
bool isPointInTriangle(const Point2D &pt, const Point2D &t1, const Point2D &t2, const Point2D &t3)
RDKIT_RDGENERAL_EXPORT const std::string bondNote
RDKIT_RDGENERAL_EXPORT const std::string atomNote
Std stuff.
Definition: Abbreviations.h:18