updating for removing specific parameters from wc-sim/models

KarrLab · Dec 23, 2018 · a14fff4 · a14fff4
1 parent 64bef0a
commit a14fff4
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Showing 7 changed files with 14 additions and 23 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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')