diff --git a/tests/random/test_io.py b/tests/random/test_io.py index b4edc53..4b4eb82 100644 --- a/tests/random/test_io.py +++ b/tests/random/test_io.py @@ -1,6 +1,5 @@ from wc_model_gen import prokaryote import unittest -import wc_lang import wc_kb_gen import wc_kb import unittest diff --git a/tests/random/test_kb_gen_core.py b/tests/random/test_kb_gen_core.py index 961d9ae..6569d7e 100644 --- a/tests/random/test_kb_gen_core.py +++ b/tests/random/test_kb_gen_core.py @@ -23,7 +23,7 @@ def test(self): 'component': { 'PropertiesGenerator': { 'mean_volume': 1e-15, - 'mean_cell_cycle_len': 100, + 'mean_doubling_time': 100, }, 'GenomeGenerator': { 'num_chromosomes': 10, diff --git a/tests/random/test_kb_gen_genome.py b/tests/random/test_kb_gen_genome.py index feceff7..ada649d 100644 --- a/tests/random/test_kb_gen_genome.py +++ b/tests/random/test_kb_gen_genome.py @@ -28,7 +28,7 @@ def setUp(self): 'component': { 'PropertiesGenerator': { 'mean_volume': 1e-15, - 'mean_cell_cycle_len': 1000., + 'mean_doubling_time': 1000., }, 'GenomeGenerator': { 'num_genes': 200., diff --git a/tests/random/test_kb_gen_properties.py b/tests/random/test_kb_gen_properties.py index 35d150b..c69f0e1 100644 --- a/tests/random/test_kb_gen_properties.py +++ b/tests/random/test_kb_gen_properties.py @@ -16,9 +16,9 @@ def test(self): kb = wc_kb.core.KnowledgeBase() cell = kb.cell = wc_kb.core.Cell() gen = properties.PropertiesGenerator(kb, options={ - 'mean_cell_cycle_len': 3600, + 'mean_doubling_time': 3600, }) gen.run() self.assertEqual(cell.properties.get_one( - id='cell_cycle_len').value, 3600) + id='mean_doubling_time').value, 3600) diff --git a/wc_kb_gen/random/complex.py b/wc_kb_gen/random/complex.py index 6c3a282..0aec560 100644 --- a/wc_kb_gen/random/complex.py +++ b/wc_kb_gen/random/complex.py @@ -40,7 +40,7 @@ def gen_components(self): cytosol = cell.compartments.get_one(id='c') assigned_complexes = self.options['assigned_complexes'] mean_complex_copy_number = self.options['mean_complex_copy_number'] - mean_volume = cell.properties.get_one(id='initial_volume').value + mean_volume = cell.properties.get_one(id='mean_volume').value for complex_name in assigned_complexes: cmplex_st = cell.species_types.get_or_create(id=complex_name, __type=wc_kb.core.ComplexSpeciesType) diff --git a/wc_kb_gen/random/genome.py b/wc_kb_gen/random/genome.py index c922f2d..185f10e 100644 --- a/wc_kb_gen/random/genome.py +++ b/wc_kb_gen/random/genome.py @@ -397,7 +397,7 @@ def gen_rnas_proteins(self): options = self.options mean_copy_number = options.get('mean_copy_number') mean_half_life = options.get('mean_half_life') - mean_volume = self.knowledge_base.cell.properties.get_one(id='initial_volume').value + mean_volume = self.knowledge_base.cell.properties.get_one(id='mean_volume').value for chromosome in self.knowledge_base.cell.species_types.get(__type=wc_kb.core.DnaSpeciesType): for i in range(len(chromosome.loci)): @@ -441,7 +441,7 @@ def gen_concentrations(self): options = self.options cell = self.knowledge_base.cell cytosol = cell.compartments.get_one(id='c') - mean_volume = cell.properties.get_one(id='initial_volume').value + mean_volume = cell.properties.get_one(id='mean_volume').value mean_rna_copy_number = options.get('mean_rna_copy_number') mean_protein_copy_number = options.get('mean_protein_copy_number') diff --git a/wc_kb_gen/random/properties.py b/wc_kb_gen/random/properties.py index 2667865..eeabd3e 100644 --- a/wc_kb_gen/random/properties.py +++ b/wc_kb_gen/random/properties.py @@ -16,7 +16,7 @@ class PropertiesGenerator(wc_kb_gen.KbComponentGenerator): Options: * mean_volume (:obj:`float`): mean volume in L - * mean_cell_cycle_len (:obj:`float`): mean doubling time in s + * mean_doubling_time (:obj:`float`): mean doubling time in s """ def clean_and_validate_options(self): @@ -27,13 +27,9 @@ def clean_and_validate_options(self): assert(mean_volume > 0) options['mean_volume'] = mean_volume - mean_fraction_dry_weight = options.get('mean_fraction_dry_weight', 0.3) - assert(mean_fraction_dry_weight > 0) - options['mean_fraction_dry_weight'] = mean_fraction_dry_weight - - mean_cell_cycle_len = options.get('mean_cell_cycle_len', 30 * 60) - assert(mean_cell_cycle_len > 0) - options['mean_cell_cycle_len'] = mean_cell_cycle_len + mean_doubling_time = options.get('mean_doubling_time', 30 * 60) + assert(mean_doubling_time > 0) + options['mean_doubling_time'] = mean_doubling_time mean_cell_density = options.get('mean_cell_density', 1e6) assert(mean_cell_density > 0) @@ -48,16 +44,12 @@ def gen_components(self): # generate properties cell = self.knowledge_base.cell - prop = cell.properties.get_or_create(id='initial_volume') + prop = cell.properties.get_or_create(id='mean_volume') prop.value = options.get('mean_volume') prop.units = 'L' - prop = cell.properties.get_or_create(id='fraction_dry_weight') - prop.value = options.get('mean_fraction_dry_weight') - prop.units = 'dimensionless' - - prop = cell.properties.get_or_create(id='cell_cycle_len') - prop.value = options.get('mean_cell_cycle_len') + prop = cell.properties.get_or_create(id='mean_doubling_time') + prop.value = options.get('mean_doubling_time') prop.units = 's' prop = cell.properties.get_or_create(id='cell_density')