#!/usr/bin/env python3
# based on pymcell4_positive/2030_rule_eq
import sys
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
sys.path.append(os.path.join(MCELL_PATH, 'lib'))
else:
print(
"Error: variable MCELL_PATH that is used to find the mcell library was not set."
)
sys.exit(1)
import mcell as m
# must not print a warning
s1 = m.Subsystem()
s1.load_bngl_molecule_types_and_reaction_rules('test1.bngl')
assert len(s1.reaction_rules) == 2
# must not cause an error
s2 = m.Subsystem()
s2.load_bngl_molecule_types_and_reaction_rules('test2.bngl')
import mcell as m
params = m.bngl_utils.load_bngl_parameters('test.bngl')
MCELL_NO_COMPARTMENT_SIZE = params['MCELL_NO_COMPARTMENT_SIZE']
assert(float(MCELL_NO_COMPARTMENT_SIZE) == 0.0625)
ITERATIONS = int(params['ITERATIONS'])
assert(ITERATIONS == 10)
SEED = 1
TIME_STEP = 1e-6 # mcell3r converter does not handle this yet
subsystem = m.Subsystem()
subsystem.load_bngl_molecule_types_and_reaction_rules('test.bngl')
box_no_compartment = m.geometry_utils.create_box(
'box_no_compartment', MCELL_NO_COMPARTMENT_SIZE
)
instantiation = m.Instantiation()
instantiation.load_bngl_compartments_and_seed_species('test.bngl', box_no_compartment)
instantiation.add_geometry_object(box_no_compartment)
assert(len(instantiation.release_sites) == 2)
viz_output = m.VizOutput(
mode = m.VizMode.ASCII,
output_files_prefix = './viz_data/seed_' + str(SEED).zfill(5) + '/Scene',
"Error: variable MCELL_PATH that is used to find the mcell library was not set."
)
sys.exit(1)
import mcell as m
# single property
sc1 = m.SurfaceClass('sc',
type=m.SurfacePropertyType.REFLECTIVE,
affected_complex_pattern=m.Complex('X(y!1).Y(x!1)'))
sc2 = m.SurfaceClass('sc',
type=m.SurfacePropertyType.TRANSPARENT,
affected_complex_pattern=m.Complex('X(y!1).Y(x!1)'))
sub1 = m.Subsystem()
sub1.add_surface_class(sc1)
# error
try:
sub1.add_surface_class(sc2)
assert False
except ValueError as err:
print(err)
sc3 = m.SurfaceClass('sc',
type=m.SurfacePropertyType.TRANSPARENT,
affected_complex_pattern=m.Complex('Y(x!1).X(y!1)'))
sub2 = m.Subsystem()
sub2.add_surface_class(sc2)
# warning
