Coverage for subcell_pipeline/visualization/display_data.py: 0%

1"""Methods for visualization display data.""" 

2 

3from simulariumio import DISPLAY_TYPE, DisplayData 

4 

5 

6def get_readdy_display_data() -> dict[str, DisplayData]: 

7 """ 

8 Get DisplayData for ReaDDy actin simulations. 

9 

10 Each actin monomer uses the `SPHERE` display type with the following colors: 

11 

12 ======================= ======= 

13 Label Color 

14 ======================= ======= 

15 actin #bf9b30 

16 actin#mid #bf9b30 

17 actin#fixed #bf9b30 

18 actin#mid_fixed #bf9b30 

19 actin#ATP #ffbf00 

20 actin#mid_ATP #ffbf00 

21 actin#fixed_ATP #ffbf00 

22 actin#mid_fixed_ATP #ffbf00 

23 actin#barbed #ffdc73 

24 actin#barbed_ATP #ffdc73 

25 actin#fixed_barbed #ffdc73 

26 actin#fixed_barbed_ATP #ffdc73 

27 actin#pointed #a67c00 

28 actin#pointed_ATP #a67c00 

29 actin#pointed_fixed #a67c00 

30 actin#pointed_fixed_ATP #a67c00 

31 ======================= ======= 

32 

33 Returns 

34 ------- 

35 : 

36 Map of names to DisplayData objects. 

37 """ 

38 

39 extra_radius = 1.5 

40 actin_radius = 2.0 + extra_radius 

41 n_polymer_numbers = 5 

42 result = {} 

43 for i in range(1, n_polymer_numbers + 1): 

44 result.update( 

45 { 

46 f"actin#{i}": DisplayData( 

47 name="actin", 

48 display_type=DISPLAY_TYPE.SPHERE, 

49 radius=actin_radius, 

50 color="#bf9b30", 

51 ), 

52 f"actin#mid_{i}": DisplayData( 

53 name="actin#mid", 

54 display_type=DISPLAY_TYPE.SPHERE, 

55 radius=actin_radius, 

56 color="#bf9b30", 

57 ), 

58 f"actin#fixed_{i}": DisplayData( 

59 name="actin#fixed", 

60 display_type=DISPLAY_TYPE.SPHERE, 

61 radius=actin_radius, 

62 color="#bf9b30", 

63 ), 

64 f"actin#mid_fixed_{i}": DisplayData( 

65 name="actin#mid_fixed", 

66 display_type=DISPLAY_TYPE.SPHERE, 

67 radius=actin_radius, 

68 color="#bf9b30", 

69 ), 

70 f"actin#ATP_{i}": DisplayData( 

71 name="actin#ATP", 

72 display_type=DISPLAY_TYPE.SPHERE, 

73 radius=actin_radius, 

74 color="#ffbf00", 

75 ), 

76 f"actin#mid_ATP_{i}": DisplayData( 

77 name="actin#mid_ATP", 

78 display_type=DISPLAY_TYPE.SPHERE, 

79 radius=actin_radius, 

80 color="#ffbf00", 

81 ), 

82 f"actin#fixed_ATP_{i}": DisplayData( 

83 name="actin#fixed_ATP", 

84 display_type=DISPLAY_TYPE.SPHERE, 

85 radius=actin_radius, 

86 color="#ffbf00", 

87 ), 

88 f"actin#mid_fixed_ATP_{i}": DisplayData( 

89 name="actin#mid_fixed_ATP", 

90 display_type=DISPLAY_TYPE.SPHERE, 

91 radius=actin_radius, 

92 color="#ffbf00", 

93 ), 

94 f"actin#barbed_{i}": DisplayData( 

95 name="actin#barbed", 

96 display_type=DISPLAY_TYPE.SPHERE, 

97 radius=actin_radius, 

98 color="#ffdc73", 

99 ), 

100 f"actin#barbed_ATP_{i}": DisplayData( 

101 name="actin#barbed_ATP", 

102 display_type=DISPLAY_TYPE.SPHERE, 

103 radius=actin_radius, 

104 color="#ffdc73", 

105 ), 

106 f"actin#fixed_barbed_{i}": DisplayData( 

107 name="actin#fixed_barbed", 

108 display_type=DISPLAY_TYPE.SPHERE, 

109 radius=actin_radius, 

110 color="#ffdc73", 

111 ), 

112 f"actin#fixed_barbed_ATP_{i}": DisplayData( 

113 name="actin#fixed_barbed_ATP", 

114 display_type=DISPLAY_TYPE.SPHERE, 

115 radius=actin_radius, 

116 color="#ffdc73", 

117 ), 

118 f"actin#pointed_{i}": DisplayData( 

119 name="actin#pointed", 

120 display_type=DISPLAY_TYPE.SPHERE, 

121 radius=actin_radius, 

122 color="#a67c00", 

123 ), 

124 f"actin#pointed_ATP_{i}": DisplayData( 

125 name="actin#pointed_ATP", 

126 display_type=DISPLAY_TYPE.SPHERE, 

127 radius=actin_radius, 

128 color="#a67c00", 

129 ), 

130 f"actin#pointed_fixed_{i}": DisplayData( 

131 name="actin#pointed_fixed", 

132 display_type=DISPLAY_TYPE.SPHERE, 

133 radius=actin_radius, 

134 color="#a67c00", 

135 ), 

136 f"actin#pointed_fixed_ATP_{i}": DisplayData( 

137 name="actin#pointed_fixed_ATP", 

138 display_type=DISPLAY_TYPE.SPHERE, 

139 radius=actin_radius, 

140 color="#a67c00", 

141 ), 

142 }, 

143 ) 

144 return result