RDKit
Open-source cheminformatics and machine learning.
MolDraw2DDetails.h
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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 // ****************************************************************************
25 using RDGeom::Point2D;
26 
27 namespace RDKit {
28 namespace MolDraw2D_detail {
29 // data taken from the helvetica font info in
30 // $RDBASE/rdkit/sping/PDF/pdfmetrics.py
31 const int char_widths[] = {
32  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
33  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
34  0, 0, 0, 0, 278, 278, 355, 556, 556, 889, 667, 222, 333, 333,
35  389, 584, 278, 333, 278, 278, 556, 556, 556, 556, 556, 556, 556, 556,
36  556, 556, 278, 278, 584, 584, 584, 556, 1015, 667, 667, 722, 722, 667,
37  611, 778, 722, 278, 500, 667, 556, 833, 722, 778, 667, 778, 722, 667,
38  611, 722, 667, 944, 667, 667, 611, 278, 278, 278, 469, 556, 222, 556,
39  556, 500, 556, 556, 278, 556, 556, 222, 222, 500, 222, 833, 556, 556,
40  556, 556, 333, 500, 278, 556, 500, 722, 500, 500, 500, 334, 260, 334,
41  584, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
42  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
43  0, 0, 0, 0, 0, 0, 0, 333, 556, 556, 167, 556, 556, 556,
44  556, 191, 333, 556, 333, 333, 500, 500, 0, 556, 556, 556, 278, 0,
45  537, 350, 222, 333, 333, 556, 1000, 1000, 0, 611, 0, 333, 333, 333,
46  333, 333, 333, 333, 333, 0, 333, 333, 0, 333, 333, 333, 1000, 0,
47  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
48  0, 1000, 0, 370, 0, 0, 0, 0, 556, 778, 1000, 365, 0, 0,
49  0, 0, 0, 889, 0, 0, 0, 278, 0, 0, 222, 611, 944, 611,
50  0, 0, 834};
51 
52 // angles in degrees.
53 RDKIT_MOLDRAW2D_EXPORT void arcPoints(const Point2D &cds1, const Point2D &cds2,
54  std::vector<Point2D> &res,
55  float startAng = 0, float extent = 360);
56 
57 //! add R/S, relative stereo, and E/Z annotations to atoms and bonds
59  const ROMol &mol, bool includeRelativeCIP = false);
60 
61 //! add annotations with atom indices.
62 RDKIT_MOLDRAW2D_EXPORT inline void addAtomIndices(const ROMol &mol) {
63  // we don't need this in the global set of tags since it will only be used
64  // here
65  if (mol.hasProp("_atomIndicesAdded")) return;
66  bool computed = true;
67  mol.setProp("_atomIndicesAdded", 1, computed);
68  for (auto atom : mol.atoms()) {
69  auto lab = std::to_string(atom->getIdx());
70  if (atom->hasProp(common_properties::atomNote)) {
71  lab += "," + atom->getProp<std::string>(common_properties::atomNote);
72  }
73  atom->setProp(common_properties::atomNote, lab);
74  }
75 };
76 
77 //! add annotations with bond indices.
78 RDKIT_MOLDRAW2D_EXPORT inline void addBondIndices(const ROMol &mol) {
79  // we don't need this in the global set of tags since it will only be used
80  // here
81  if (mol.hasProp("_bondIndicesAdded")) return;
82  bool computed = true;
83  mol.setProp("_bondIndicesAdded", 1, computed);
84  for (auto bond : mol.bonds()) {
85  auto lab = std::to_string(bond->getIdx());
86  if (bond->hasProp(common_properties::bondNote)) {
87  lab += "," + bond->getProp<std::string>(common_properties::bondNote);
88  }
89  bond->setProp(common_properties::bondNote, lab);
90  }
91 };
92 
94  const Point2D &p1, const Point2D &p2, const Point2D &refPt,
95  const std::vector<std::pair<Point2D, Point2D>> &bondSegments,
96  double bracketFrac = 0.1);
98  const std::vector<MolDrawShape> &shapes);
99 
100 // there are a several empirically determined constants here.
102  Point2D cds1, Point2D cds2, double scale, bool shiftBegin = false,
103  bool shiftEnd = false, unsigned nSteps = 4, double deviation = 0.03,
104  double endShift = 0.5);
105 
106 inline std::string formatDouble(double val) {
107  return boost::str(boost::format("%.1f") % val);
108 }
109 
110 } // namespace MolDraw2D_detail
111 } // namespace RDKit
112 
113 #endif
pulls in the core RDKit functionality
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition: MolDraw2D.h:337
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:121
void setProp(const std::string &key, T val, bool computed=false) const
sets a property value
Definition: RDProps.h:72
CXXBondIterator< MolGraph, Bond * > bonds()
Definition: ROMol.h:295
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Definition: ROMol.h:256
#define RDKIT_MOLDRAW2D_EXPORT
Definition: export.h:265
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)
RDKIT_MOLDRAW2D_EXPORT void drawShapes(MolDraw2D &drawer, const std::vector< MolDrawShape > &shapes)
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
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)
std::string formatDouble(double val)
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_RDGENERAL_EXPORT const std::string bondNote
RDKIT_RDGENERAL_EXPORT const std::string atomNote
Std stuff.
Definition: Abbreviations.h:18