def test_with_sbnw_c_api(self):
sbml_model = sbnw.loadSBMLFile(self.sbml_fname)
layout_info = sbnw.processLayout(sbml_model)
sbnw.randomizeLayout(layout_info)
network = sbnw.getNetworkp(layout_info)
_layout_alg_options = sbnw.FrAlgOptions(
20.0, # k
1, #boundary
100, # magnatism
5.0, # grav, has to be > 5 for effect
500.0, # baryx
500.0, # baryy
1, # autobary
0, #enable compartments
1, #pre-randomize
20.0 # padding
)
comp = sbnw.nw_getCompartmentp(network, 0)
comp_height_before = sbnw.compartment_getHeight(comp)
print('comp_height_before', comp_height_before)
sbnw.doLayoutAlgorithm(_layout_alg_options, layout_info)
sbnw.doLayoutAlgorithm(_layout_alg_options, layout_info)
sbnw.doLayoutAlgorithm(_layout_alg_options, layout_info)
sbnw.doLayoutAlgorithm(_layout_alg_options, layout_info)
# sbnw.doLayoutAlgorithm(_layout_alg_options, layout_info)
comp_height_after = sbnw.compartment_getHeight(comp)
print('comp_height_after', comp_height_after)
# print(sbnw.getSBMLwithLayoutStr(sbml_model, layout_info))
print(sbnw.writeSBMLwithLayout(self.sbml_with_layout, sbml_model, layout_info))
def setUp(self) -> None:
self.sbml_fname = os.path.join(os.path.dirname(__file__),
'teusink2000.xml')
self.sbml_with_layout = os.path.join(
os.path.dirname(__file__), 'teusink2000WithLayoutFromPython.xml')
self.sbml_model = sbnw.loadSBMLString(teusink2000)
self.layout_info = sbnw.processLayout(self.sbml_model)
def test(self):
h_model = sbnw.loadSBMLString(self.sbml)
# returns a layout_info object which has only a `contents` attribute
layout_info = sbnw.processLayout(h_model)
network = sbnw.getNetworkp(layout_info)
print(h_model)
print(layout_info)
print(layout_info.contents)
print(network)
def test_with_sbnw_c_api2(self):
sbml_model = sbnw.loadSBMLFile(self.sbml_fname)
layout_info = sbnw.processLayout(sbml_model)
sbnw.randomizeLayout(layout_info)
network = sbnw.getNetworkp(layout_info)
_layout_alg_options = sbnw.FrAlgOptions(
20.0, # k
1, #boundary
100, # magnatism
0.0, # grav, has to be > 5 for effect
500.0, # baryx
500.0, # baryy
1, # autobary
0, #enable compartments
1, #pre-randomize
20.0 # padding
)
def test_processLayout(self):
actual = sbnw.processLayout(self.h_model)
self.eval_type_via_class_name('LP_LayoutInfo')
def setUp(self) -> None:
self.sbml = compartment_model
self.h_model = sbnw.loadSBMLString(self.sbml)
self.h_layout_info = sbnw.processLayout(self.h_model)
self.h_network = sbnw.getNetworkp(self.h_layout_info)
self.h_canvas = sbnw.getCanvasp(self.h_layout_info)