2 from __future__
import print_function
13 def get_basic_config():
14 config = Configuration()
15 IMP.npctransport.set_default_configuration(config)
16 config.statistics_fraction.lower = 0.9
18 config.interaction_k.lower = 10
19 config.interaction_range.lower = 1
21 config.backbone_k.lower = 1
23 config.time_step_factor.lower = 3
25 config.excluded_volume_k.lower = 20
26 config.nonspecific_range.lower = 2
27 config.nonspecific_k.lower = 0.01
28 config.slack.lower = 8
29 config.number_of_trials = 1
30 config.dump_interval_ns = 0.1
31 config.simulation_time_ns = 500
33 config.angular_D_factor.lower = 0.3
34 config.statistics_interval_ns = 0.05
37 config.box_is_on.lower = 1
38 config.box_side.lower = 400
39 config.slab_is_on.lower = 0
40 config.slab_thickness.lower = 150
41 config.tunnel_radius.lower = 75
45 def add_interactions_for_fg(fg_name,
49 interactionFG_KAP = IMP.npctransport.add_interaction(
50 config, name0=fg_name, name1=
"my_kap", interaction_k=k_kap_lower,
53 create_range(interactionFG_KAP.interaction_k,
54 k_kap_lower, k_kap_upper,
63 import google.protobuf
65 print(
'npctransport python module requires the python protobuf package.\n'
66 'One way to install the protobuf python package is using pip '
67 '- "pip install protobuf" on a local'
68 ' python installation, see documentation of pip.')
70 config = get_basic_config()
71 config.dump_interval_ns = 1
72 config.simulation_time_ns = 0.01
73 config.box_is_on.lower = 1
74 config.box_side.lower = 200
75 config.slab_is_on.lower = 0
76 config.slab_thickness.lower = 150
77 config.tunnel_radius.lower = 90
79 fg = IMP.npctransport.add_fg_type(config,
85 rest_length_factor=1.5)
86 kap = IMP.npctransport.add_float_type(config,
91 nonspecifics = IMP.npctransport.add_float_type(config,
98 add_interactions_for_fg(
"my_fg",
105 config.nonspecific_range.lower = 1.0
106 config.nonspecific_k.lower = 1.5
111 interactionFG_FG = IMP.npctransport.add_interaction(config,
117 create_range(interactionFG_FG.interaction_k, 1, 20, steps=15)
121 f = open(outfile,
"wb")
122 f.write(config.SerializeToString())
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.