make_cfg.py

#!/usr/bin/env python
from __future__ import print_function
from IMP.npctransport import *
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
    config.angular_D_factor.lower=0.3 #increased dynamic viscosity relative to water?
    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)