FilesExpand file tree

main

/

exercise_python_mol.py

Copy path

Blame

More file actions

Blame

More file actions

Latest commit

 

History

History

History

133 lines (120 loc) · 3.11 KB

main

/

exercise_python_mol.py

Copy path

Top

File metadata and controls

• Code
• Blame

133 lines (120 loc) · 3.11 KB

Raw

Copy raw file

Download raw file

Open symbols panel

Edit and raw actions

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

57

58

59

60

61

62

63

64

65

66

67

68

69

70

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

87

88

89

90

91

92

93

94

95

96

97

98

99

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

a_molecule = [

# a list of models

[ # a list of chains

["A",[

[1081,"","ASN",[

[[" O ",""],

[1.0,22.87," O"],

[0.287,20.822,40.742]],

[[" C ",""],

[1.0,22.17," C"],

[0.303,20.8649,39.5379]],

[[" ND2",""],

[1.0,29.17," N"],

[1.363,16.5869,37.908]],

[[" OD1",""],

[1.0,32.810001373291," O"],

[2.877,18.049,38.597]],

[[" CG ",""],

[1.0,27.4," C"],

[1.711,17.676,38.529]],

[[" CB ",""],

[1.0,24.58," C"],

[0.547,18.528,39.102]],

[[" CA ",""],

[1.0,23.18," C"],

[0.657,19.99,38.7]],

[[" N ",""],

[1.0,22.87," N"],

[0.531,20.0909,37.2929]]]

],

[1082,"","GLN",[

[[" O ",""],

[1.0,19.223," O"],

[0.419,24.068,39.868]],

[[" C ",""],

[1.0,20.54," C"],

[1.431,23.549,40.3401]],

[[" NE2",""],

[1.0,14.77," N"],

[5.637,22.1359,39.458]],

[[" OE1",""],

[1.0,25.2299," O"],

[5.2859,23.3729,41.34]],

[[" CD ",""],

[1.0,25.7," C"],

[5.08,23.136,40.01]],

[[" CG ",""],

[1.0,19.98," C"],

[4.176,24.007,39.253]],

[[" CB ",""],

[1.0,21.63," C"],

[3.038,23.178,38.604]],

[[" CA ",""],

[1.0,20.56," C"],

[2.118,22.47,39.593]],

[[" N ",""],

[1.0,21.99," N"],

[1.156,21.65,38.894]]]

]

] # end of chain A content

] # end of chain A

] # end of list of chains

] # end of list of models

# Return a python_mol

#

#

#

def jiggled_mol(reference_mol, current_mol, traj_frac):

def jiggle_random():

import random

return (random.random() - 0.5)

def jiggled_pos(ref_pos, current_pos):

if (traj_frac < 0): # magic value

# make a starting set of coords

return map(lambda x1:

jiggle_random() * 1.0 + x1,

ref_pos)

else:

q = 1 - traj_frac

return map(lambda x, x_ref:

traj_frac * x_ref + q * x +

0.4 * q * jiggle_random(),

current_pos, ref_pos)

def jiggled_atom(ref_atom, current_atom):

ref_pos = ref_atom[2]

cur_pos = current_atom[2]

ret = [ref_atom[0], ref_atom[1], jiggled_pos(ref_pos, cur_pos)]

return ret

def jiggled_residue(ref_res, cur_res):

ret = [ref_res[0], ref_res[1], ref_res[2], map(jiggled_atom, ref_res[3], cur_res[3])]

return ret

def jiggled_chain(ref_chain, cur_chain):

ret = [ref_chain[0],

map(jiggled_residue,

ref_chain[1],

cur_chain[1])]

return ret

def jiggled_model(ref_model, cur_model):

ret = map(jiggled_chain, ref_model, cur_model)

return ret

j_mod = map (jiggled_model, reference_mol, current_mol)

return j_mod

#

def disrupt(reference_mol, biggness):

ret = jiggled_mol(reference_mol, reference_mol, -1)

return ret

#

max_count = 5000.0

mol_no = add_molecule(a_molecule, "test molecule")

if (not mol_no == -1):

set_rotation_centre(*centre_of_mass(mol_no))

for count in range(int(max_count) + 1):

current_mol = disrupt(a_molecule,0.8)

new_mol = jiggled_mol(a_molecule, current_mol,

count / max_count)

#print "cycle ", count, count/max_count, max_count

clear_and_update_molecule(mol_no, new_mol)

# gtk stuff

if gtk.events_pending():

gtk.main_iteration(False)