make_cfg.py

#!/usr/bin/env python
import IMP
from IMP.npctransport import create_range, Configuration
import sys

if len(sys.argv) > 1:
    outfile = sys.argv[1]
else:
    outfile = IMP.create_temporary_file_name("config", "pb")


def get_basic_config():
    config = Configuration()
    IMP.npctransport.set_default_configuration(config)
    config.statistics_fraction.lower = 0.9
    # config.dump_interval = 1
    config.interaction_k.lower = 10
    config.interaction_range.lower = 1
    # create_range(config.backbone_k, .2, 1, 10
    config.backbone_k.lower = 1
    # config.time_step_factor.lower = 0.3
    config.time_step_factor.lower = 3
    # create_range(config.rest_length_factor, .5, 1, 10)
    config.excluded_volume_k.lower = 20
    config.nonspecific_range.lower = 2
    config.nonspecific_k.lower = 0.01
    config.slack.lower = 8
    config.number_of_trials = 1
    config.dump_interval_ns = 0.1
    config.simulation_time_ns = 500
    # increased dynamic viscosity relative to water?
    config.angular_D_factor.lower = 0.3
    config.statistics_interval_ns = 0.05

    # simulation bounding volumes:
    config.box_is_on.lower = 1
    config.box_side.lower = 400
    config.slab_is_on.lower = 0
    config.slab_thickness.lower = 150
    config.tunnel_radius.lower = 75
    return config


def add_interactions_for_fg(fg_name,
                            k_kap_lower,
                            k_kap_upper=0,  # relevant only if k_kap_steps > 1
                            k_kap_steps=1):
    interactionFG_KAP = IMP.npctransport.add_interaction(
        config, name0=fg_name, name1="my_kap", interaction_k=k_kap_lower,
        interaction_range=2)
    if k_kap_steps > 1:
        create_range(interactionFG_KAP.interaction_k,
                     k_kap_lower, k_kap_upper,
                     steps=k_kap_steps)
    # interactionFG_CRAP = IMP.npctransport.add_interaction(
    #    config, name0=fg_name, name1="my_crap", interaction_k=0,
    #    interaction_range=0)


# ********* MAIN: *********
try:
    import google.protobuf
except ImportError:
    print('npctransport python module requires the python protobuf package.\n'
          'One way to install the protobuf python package is using pip '
          '- "pip install protobuf" on a local'
          ' python installation, see documentation of pip.')
    exit(-1)
config = get_basic_config()
config.dump_interval_ns = 1
config.simulation_time_ns = 0.01
config.box_is_on.lower = 1
config.box_side.lower = 200
config.slab_is_on.lower = 0
config.slab_thickness.lower = 150
config.tunnel_radius.lower = 90

fg = IMP.npctransport.add_fg_type(config,
                                  type_name="my_fg",
                                  number_of_beads=4,
                                  number=1,
                                  radius=6,
                                  interactions=1,
                                  rest_length_factor=1.5)
kap = IMP.npctransport.add_float_type(config,
                                      type_name="my_kap",
                                      number=1,
                                      radius=25,
                                      interactions=12)
nonspecifics = IMP.npctransport.add_float_type(config,
                                               type_name="my_crap",
                                               number=1,
                                               radius=25,
                                               interactions=0)
###########
# fg with kaps / craps
add_interactions_for_fg("my_fg",
                        k_kap_lower=1,
                        k_kap_upper=20,
                        k_kap_steps=15)
#############

# non-specific attraction
config.nonspecific_range.lower = 1.0
config.nonspecific_k.lower = 1.5
# create_range(config.nonspecific_range, 0.1, 2, steps=3)
# create_range(config.nonspecific_k, 0.1, 10, steps=5)

# internal FG-FG
interactionFG_FG = IMP.npctransport.add_interaction(config,
                                                    name0="my_fg",
                                                    name1="my_fg",
                                                    interaction_k=1.5,
                                                    interaction_range=2)
##############
create_range(interactionFG_FG.interaction_k, 1, 20, steps=15)
##############

# dump to file
f = open(outfile, "wb")
f.write(config.SerializeToString())
print(config)