def test_convert_er_mech_to_grasp_pattern_G6PD(self):
true_res_file = os.path.join(self.test_folder,
'true_res_G6PDH_mech_grasp.txt')
file_in = os.path.join(self.test_folder, 'G6PDH_mech_er.txt')
file_out = os.path.join(self.test_folder, 'G6PDH_mech_grasp.txt')
convert_er_mech_to_grasp_pattern(file_in, file_out, promiscuous=True)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
def test_convert_er_mech_to_grasp_pattern_orderedBiBi(self):
true_res_file = os.path.join(self.test_folder,
'true_res_orderedBiBi.txt')
file_in = os.path.join(self.test_folder, 'orderedBiBi_mech_er.txt')
file_out = os.path.join(self.test_folder, 'orderedBiBi_mech_grasp.txt')
convert_er_mech_to_grasp_pattern(file_in, file_out)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
def test_convert_er_mech_to_grasp_pattern_G6PDH2CompInhib(self):
true_res_file = os.path.join(self.test_folder,
'true_res_G6PDH2CompInhib.txt')
file_in = os.path.join(self.test_folder, 'G6PDH2CompInhib_mech_er.txt')
file_out = os.path.join(self.test_folder,
'G6PDH2CompInhib_mech_grasp.txt')
inhib_list = ['m_nadph_c', 'm_nadh_c']
convert_er_mech_to_grasp_pattern(file_in,
file_out,
promiscuous=True,
inhib_list=inhib_list)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
def test_convert_er_mech_to_grasp_pattern_randomBiBiCompInhib(self):
true_res_file = os.path.join(self.test_folder,
'true_res_randomBiBiCompInhib.txt')
file_in = os.path.join(self.test_folder,
'randomBiBiCompInhib_mech_er.txt')
file_out = os.path.join(self.test_folder,
'randomBiBiCompInhib_mech_grasp.txt')
inhib_list = ['pyr_c']
convert_er_mech_to_grasp_pattern(file_in,
file_out,
inhib_list=inhib_list)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
def test_convert_er_mech_to_grasp_pattern_orderedBiBiActivTwoTracks(self):
true_res_file = os.path.join(self.test_folder,
'true_res_orderedBiBiActivTwoTracks.txt')
file_in = os.path.join(self.test_folder,
'orderedBiBiActivTwoTracks_mech_er.txt')
file_out = os.path.join(self.test_folder,
'orderedBiBiActivTwoTracks_mech_grasp.txt')
activ_list = ['pyr_c']
convert_er_mech_to_grasp_pattern(file_in,
file_out,
activ_list=activ_list)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
def test_convert_er_mech_to_grasp_pattern_AANATCompInhibIndep(self):
true_res_file = os.path.join(self.test_folder,
'true_res_AANATCompInhibIndep.txt')
file_in = os.path.join(self.test_folder,
'AANATCompInhibIndep_mech_er.txt')
file_out = os.path.join(self.test_folder,
'AANATCompInhibIndep_mech_grasp.txt')
inhib_list = ['mltn_c']
convert_er_mech_to_grasp_pattern(file_in,
file_out,
promiscuous=True,
inhib_list=inhib_list)
with open(true_res_file, 'r') as f_in:
true_res = f_in.read()
with open(file_out, 'r') as f_in:
res = f_in.read()
self.assertEqual(true_res, res)
import os
from set_up_grasp_models.set_up_models.convert_mechanisms import convert_er_mech_to_grasp_pattern
# convert orderedBiBi
file_in = os.path.join('mechanisms', 'orderedBiBi_mech_er.txt')
file_out = os.path.join('mechanisms', 'orderedBiBi_pattern.txt')
convert_er_mech_to_grasp_pattern(file_in, file_out)
# convert orderedBiBi with activation
file_in = os.path.join('mechanisms', 'orderedBiBiActiv_mech_er.txt')
file_out = os.path.join('mechanisms', 'orderedBiBiActiv_pattern.txt')
activ_list = ['pyr_c']
convert_er_mech_to_grasp_pattern(file_in, file_out, activ_list=activ_list)
# convert orderedBiBi with activation, where the reaction can proceed both
# with and without the activator bound to the enzyme
file_in = os.path.join('mechanisms', 'orderedBiBiActivTwoTracks_mech_er.txt')
file_out = os.path.join('mechanisms', 'orderedBiBiActivTwoTracks_pattern.txt')
activ_list = ['pyr_c']
convert_er_mech_to_grasp_pattern(file_in, file_out, activ_list=activ_list)
# convert uniUniPromiscuous
file_in = os.path.join('mechanisms', 'uniUniPromiscuous_mech_er.txt')
file_out = os.path.join('mechanisms', 'uniUniPromiscuous_pattern.txt')
convert_er_mech_to_grasp_pattern(file_in, file_out, promiscuous=True)