SimpleFastOpenAtomicVisualiser
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colour.h
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1#ifndef COLOUR_H
2#define COLOUR_H
3
4#include <map>
5#include <string>
6#include <filesystem>
7#include <sstream>
8#include <fstream>
9
10#include <glm/glm.hpp>
11
12#include <element.h>
13
18const std::map<Element, glm::vec4> CPK_COLOURS =
19{
20 { Element::Unknown, {1.0,0.5,0.5,1.0}},
21 { Element::H, {1.0,1.0,1.0,1.0}},
22 { Element::He, {1.0,0.753,0.796,1.0}},
23 { Element::Li, {0.698,0.133,0.133,1.0}},
24 { Element::Be, {1.0,0.078,0.576,1.0}},
25 { Element::B, {0.0,1.0,0.0,1.0}},
26 { Element::C, {0.784,0.784,0.784,1.0}},
27 { Element::N, {0.561,0.561,1.0,1.0}},
28 { Element::O, {0.941,0.0,0.0,1.0}},
29 { Element::F, {0.855,0.647,0.125,1.0}},
30 { Element::Ne, {1.0,0.078,0.576,1.0}},
31 { Element::Na, {0.0,0.0,1.0,1.0}},
32 { Element::Mg, {0.133,0.545,0.133,1.0}},
33 { Element::Al, {0.502,0.502,0.565,1.0}},
34 { Element::Si, {0.855,0.647,0.125,1.0}},
35 { Element::P, {1.0,0.647,0.0,1.0}},
36 { Element::S, {1.0,0.784,0.196,1.0}},
37 { Element::Cl, {0.0,1.0,0.0,1.0}},
38 { Element::Ar, {1.0,0.078,0.576,1.0}},
39 { Element::K, {1.0,0.078,0.576,1.0}},
40 { Element::Ca, {0.502,0.502,0.565,1.0}},
41 { Element::Sc, {1.0,0.078,0.576,1.0}},
42 { Element::Ti, {0.502,0.502,0.565,1.0}},
43 { Element::V, {1.0,0.078,0.576,1.0}},
44 { Element::Cr, {0.502,0.502,0.565,1.0}},
45 { Element::Mn, {0.502,0.502,0.565,1.0}},
46 { Element::Fe, {1.0,0.647,0.0,1.0}},
47 { Element::Co, {1.0,0.078,0.576,1.0}},
48 { Element::Ni, {0.647,0.165,0.165,1.0}},
49 { Element::Cu, {0.647,0.165,0.165,1.0}},
50 { Element::Zn, {0.647,0.165,0.165,1.0}},
51 { Element::Ga, {1.0,0.078,0.576,1.0}},
52 { Element::Ge, {1.0,0.078,0.576,1.0}},
53 { Element::As, {1.0,0.078,0.576,1.0}},
54 { Element::Se, {1.0,0.078,0.576,1.0}},
55 { Element::Br, {0.647,0.165,0.165,1.0}},
56 { Element::Kr, {1.0,0.078,0.576,1.0}},
57 { Element::Rb, {1.0,0.078,0.576,1.0}},
58 { Element::Sr, {1.0,0.078,0.576,1.0}},
59 { Element::Y, {1.0,0.078,0.576,1.0}},
60 { Element::Zr, {1.0,0.078,0.576,1.0}},
61 { Element::Nb, {1.0,0.078,0.576,1.0}},
62 { Element::Mo, {1.0,0.078,0.576,1.0}},
63 { Element::Tc, {1.0,0.078,0.576,1.0}},
64 { Element::Ru, {1.0,0.078,0.576,1.0}},
65 { Element::Rh, {1.0,0.078,0.576,1.0}},
66 { Element::Pd, {1.0,0.078,0.576,1.0}},
67 { Element::Ag, {0.502,0.502,0.565,1.0}},
68 { Element::Cd, {1.0,0.078,0.576,1.0}},
69 { Element::In, {1.0,0.078,0.576,1.0}},
70 { Element::Sn, {1.0,0.078,0.576,1.0}},
71 { Element::Sb, {1.0,0.078,0.576,1.0}},
72 { Element::Te, {1.0,0.078,0.576,1.0}},
73 { Element::I, {0.627,0.125,0.941,1.0}},
74 { Element::Xe, {1.0,0.078,0.576,1.0}},
75 { Element::Cs, {1.0,0.078,0.576,1.0}},
76 { Element::Ba, {1.0,0.647,0.0,1.0}},
77 { Element::La, {1.0,0.078,0.576,1.0}},
78 { Element::Ce, {1.0,0.078,0.576,1.0}},
79 { Element::Pr, {1.0,0.078,0.576,1.0}},
80 { Element::Nd, {1.0,0.078,0.576,1.0}},
81 { Element::Pm, {1.0,0.078,0.576,1.0}},
82 { Element::Sm, {1.0,0.078,0.576,1.0}},
83 { Element::Eu, {1.0,0.078,0.576,1.0}},
84 { Element::Gd, {1.0,0.078,0.576,1.0}},
85 { Element::Tb, {1.0,0.078,0.576,1.0}},
86 { Element::Dy, {1.0,0.078,0.576,1.0}},
87 { Element::Ho, {1.0,0.078,0.576,1.0}},
88 { Element::Er, {1.0,0.078,0.576,1.0}},
89 { Element::Tm, {1.0,0.078,0.576,1.0}},
90 { Element::Yb, {1.0,0.078,0.576,1.0}},
91 { Element::Lu, {1.0,0.078,0.576,1.0}},
92 { Element::Hf, {1.0,0.078,0.576,1.0}},
93 { Element::Ta, {1.0,0.078,0.576,1.0}},
94 { Element::W, {1.0,0.078,0.576,1.0}},
95 { Element::Re, {1.0,0.078,0.576,1.0}},
96 { Element::Os, {1.0,0.078,0.576,1.0}},
97 { Element::Ir, {1.0,0.078,0.576,1.0}},
98 { Element::Pt, {1.0,0.078,0.576,1.0}},
99 { Element::Au, {0.855,0.647,0.125,1.0}},
100 { Element::Hg, {1.0,0.078,0.576,1.0}},
101 { Element::Tl, {1.0,0.078,0.576,1.0}},
102 { Element::Pb, {1.0,0.078,0.576,1.0}},
103 { Element::Bi, {1.0,0.078,0.576,1.0}},
104 { Element::Po, {1.0,0.078,0.576,1.0}},
105 { Element::At, {1.0,0.078,0.576,1.0}},
106 { Element::Rn, {1.0,1.0,1.0,1.0}},
107 { Element::Fr, {1.0,1.0,1.0,1.0}},
108 { Element::Ra, {1.0,1.0,1.0,1.0}},
109 { Element::Ac, {1.0,1.0,1.0,1.0}},
110 { Element::Th, {1.0,0.078,0.576,1.0}},
111 { Element::Pa, {1.0,1.0,1.0,1.0}},
112 { Element::U, {1.0,0.078,0.576,1.0}},
113 { Element::Np, {1.0,1.0,1.0,1.0}},
114 { Element::Pu, {1.0,1.0,1.0,1.0}},
115 { Element::Am, {1.0,1.0,1.0,1.0}},
116 { Element::Cm, {1.0,1.0,1.0,1.0}},
117 { Element::Bk, {1.0,1.0,1.0,1.0}},
118 { Element::Cf, {1.0,1.0,1.0,1.0}},
119 { Element::Es, {1.0,1.0,1.0,1.0}},
120 { Element::Fm, {1.0,1.0,1.0,1.0}},
121 { Element::Md, {1.0,1.0,1.0,1.0}},
122 { Element::No, {1.0,1.0,1.0,1.0}},
123 { Element::Lw, {1.0,1.0,1.0,1.0}}
124};
125
132glm::vec4 elementToColour(Element & e)
133{
134 return CPK_COLOURS.at(e);
135}
136
143glm::vec4 stringSymbolToColour(std::string & s)
144{
145 return CPK_COLOURS.at(stringSymbolToElement(s));
146}
147
157std::map<Element, glm::vec4> coloursFromFile(std::filesystem::path path)
158{
159 if (std::filesystem::exists(path))
160 {
161 std::map<Element, glm::vec4> colours(CPK_COLOURS);
162 std::ifstream in(path);
163 std::string line;
164 std::stringstream ss;
165 std::string name;
166 Element element;
167 float r, g, b, a;
168 while (std::getline(in, line))
169 {
170 ss = std::stringstream(line);
171 ss >> name >> r >> g >> b >> a;
172 element = stringSymbolToElement(name);
173 if (!ss.fail() && element != Element::Unknown)
174 {
175 colours[element] = glm::vec4(r, g, b, a);
176 }
177 }
178
179 return colours;
180 }
181 else
182 {
183 std::cout << "Could not find colourmap file " << path << " defaulting to CPK\n";
184 return CPK_COLOURS;
185 }
186}
187
197std::map<uint64_t, glm::vec4> atomColoursFromFile(std::filesystem::path path)
198{
199 std::map<uint64_t, glm::vec4> colours;
200 if (std::filesystem::exists(path))
201 {
202 std::ifstream in(path);
203 std::string line;
204 std::stringstream ss;
205 std::string name;
206 uint64_t atom;
207 float r, g, b, a;
208 while (std::getline(in, line))
209 {
210 ss = std::stringstream(line);
211 ss >> atom >> r >> g >> b >> a;
212 if (!ss.fail())
213 {
214 colours[atom] = glm::vec4(r, g, b, a);
215 }
216 }
217 }
218 return colours;
219}
220
221#endif /* COLOUR_H */
CPK_COLOURS
const std::map< Element, glm::vec4 > CPK_COLOURS
Corey–Pauling–Koltun colourings.
Definition colour.h:18
elementToColour
glm::vec4 elementToColour(Element &e)
Map an Element to a CPK colour.
Definition colour.h:132
coloursFromFile
std::map< Element, glm::vec4 > coloursFromFile(std::filesystem::path path)
Read an Element colour map from a file.
Definition colour.h:157
atomColoursFromFile
std::map< uint64_t, glm::vec4 > atomColoursFromFile(std::filesystem::path path)
Read an atom index colour map from a file.
Definition colour.h:197
stringSymbolToColour
glm::vec4 stringSymbolToColour(std::string &s)
Map a string symbol to a CPK colour.
Definition colour.h:143
Element
Element
Representable elements.
Definition element.h:13
stringSymbolToElement
Element stringSymbolToElement(const std::string &s)
Map a string symbol to an Element.
Definition element.h:681
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