Skip to content

Commit

Permalink
improved code formatting and path fixes in test_families
Browse files Browse the repository at this point in the history
@LeenFahoum
LeenFahoum committed Jan 30, 2025
2 parents f5e684f + 3174e05 commit de7538e
Showing 1 changed file with 32 additions and 154 deletions.
186 changes: 32 additions & 154 deletions test_families.py
View file
Original file line number Diff line number Diff line change
@@ -1,280 +1,158 @@
import unittest
import sys
import os

# Add the path to the directory where ester_hydrolysis is located
sys.path.append('/home/leen/Code/ARC/data/families')

sys.path.append(os.path.join(os.path.dirname(__file__), '../../Code/ARC/data/families'))

from arc.reaction.family import ReactionFamily, get_reaction_family_products, get_recipe_actions
from arc.reaction.reaction import ARCReaction
from arc.species.species import ARCSpecies

# Print the current working directory to confirm the script's execution location
print("Current working directory:", os.getcwd())

class TestEsterHydrolysisReactionFamily(unittest.TestCase):
"""
Contains unit tests for the ester hydrolysis reaction family.
"""

@classmethod
def setUpClass(cls):
"""Set up the test by defining the ester hydrolysis reaction family."""
cls.family = ReactionFamily('ester_hydrolysis')

def test_ester_hydrolysis_reaction(self):
"""Test if ester hydrolysis products are correctly generated."""
# Define the ester and water as reactants
ester_smiles = 'CC(=O)OC' # Methyl acetate
water_smiles = 'O'

# Create ARC species for the reactants
ester = ARCSpecies(label='ester', smiles=ester_smiles)
water = ARCSpecies(label='H2O', smiles=water_smiles)

# Define the expected products (acetic acid and methanol)
acid_smiles = 'CC(=O)O'
alcohol_smiles = 'CO'

acid = ARCSpecies(label='acid', smiles=acid_smiles)
alcohol = ARCSpecies(label='alcohol', smiles=alcohol_smiles)

# Create a reaction instance
ester = ARCSpecies(label='ester', smiles='CC(=O)OC')
water = ARCSpecies(label='H2O', smiles='O')
acid = ARCSpecies(label='acid', smiles='CC(=O)O')
alcohol = ARCSpecies(label='alcohol', smiles='CO')
rxn = ARCReaction(r_species=[ester, water], p_species=[acid, alcohol], rmg_family_set=['ester_hydrolysis'])

# Get reaction products
products = get_reaction_family_products(rxn)

# Check if the generated products match expected ones
product_smiles = [p.to_smiles() for p in products[0]['products']]
expected_product_smiles = {acid_smiles, alcohol_smiles}

self.assertEqual(set(product_smiles), expected_product_smiles)
expected_product_smiles = ['CC(=O)O', 'CO']
self.assertEqual(product_smiles, expected_product_smiles)

def test_recipe_actions(self):
"""Test if the reaction recipe is applied correctly."""
# Load the groups.py file content as lines
groups_file_path = '/home/leen/Code/ARC/data/families/ester_hydrolysis/groups.py'
groups_file_path = os.path.join(os.path.dirname(__file__), '../../Code/ARC/data/families/ester_hydrolysis/groups.py')
with open(groups_file_path, 'r') as f:
groups_as_lines = f.readlines()

# Get the recipe actions from the groups file content
actions = get_recipe_actions(groups_as_lines)

# Define the expected actions
expected_actions = [
['BREAK_BOND', '*1', 1, '*2'],
['BREAK_BOND', '*3', 1, '*4'],
['FORM_BOND', '*1', 1, '*4'],
['FORM_BOND', '*2', 1, '*3'],
]

# Assert that the actions match the expected actions
self.assertEqual(actions, expected_actions)

def test_ester_hydrolysis_withP(self):
"""Test if ester hydrolysis products are correctly generated."""
# Define the ester and water as reactants
ester_smiles = 'CP(=O)(OC)O' # Phosphoester
water_smiles = 'O'

# Create ARC species for the reactants
ester = ARCSpecies(label='ester', smiles=ester_smiles)
water = ARCSpecies(label='H2O', smiles=water_smiles)

# Define the expected products (acetic acid and methanol)
acid_smiles = 'CP(=O)(O)O'
alcohol_smiles = 'CO'

acid = ARCSpecies(label='acid', smiles=acid_smiles)
alcohol = ARCSpecies(label='alcohol', smiles=alcohol_smiles)

# Create a reaction instance
ester = ARCSpecies(label='ester', smiles='CP(=O)(OC)O')
water = ARCSpecies(label='H2O', smiles='O')
acid = ARCSpecies(label='acid', smiles='CP(=O)(O)O')
alcohol = ARCSpecies(label='alcohol', smiles='CO')
rxn = ARCReaction(r_species=[ester, water], p_species=[acid, alcohol], rmg_family_set=['ester_hydrolysis'])

# Get reaction products
products = get_reaction_family_products(rxn)

# Check if the generated products match expected ones
product_smiles = [p.to_smiles() for p in products[0]['products']]
expected_product_smiles = {acid_smiles, alcohol_smiles}

self.assertEqual(set(product_smiles), expected_product_smiles)

expected_product_smiles = ['CP(=O)(O)O', 'CO']
self.assertEqual(product_smiles, expected_product_smiles)

class TestNitrileHydrolysisReactionFamily(unittest.TestCase):
"""
Contains unit tests for the nitrile hydrolysis reaction family.
"""

@classmethod
def setUpClass(cls):
"""Set up the test by defining the nitrile hydrolysis reaction family."""
cls.family = ReactionFamily('nitrile_hydrolysis')

def test_nitrile_hydrolysis_reaction(self):
"""Test if nitrile hydrolysis products are correctly generated."""
# Define the nitrile and water as reactants
nitrile_smiles = 'CC#N' # Acetonitrile
water_smiles = 'O'

# Create ARC species for the reactants
nitrile = ARCSpecies(label='nitrile', smiles=nitrile_smiles)
water = ARCSpecies(label='H2O', smiles=water_smiles)

# Define the expected products (acetamide as an intermediate and methanol)
acid_smiles = 'CC(=N)O' # Acetamide
acid = ARCSpecies(label='acid', smiles=acid_smiles)

# Create a reaction instance
nitrile = ARCSpecies(label='nitrile', smiles='CC#N')
water = ARCSpecies(label='H2O', smiles='O')
acid = ARCSpecies(label='acid', smiles='CC(=N)O')
rxn = ARCReaction(r_species=[nitrile, water], p_species=[acid], rmg_family_set=['nitrile_hydrolysis'])

# Get reaction products
products = get_reaction_family_products(rxn)

# Check if the generated products match expected ones
product_smiles = [p.to_smiles() for p in products[0]['products']]
expected_product_smiles = {acid_smiles}

expected_product_smiles = ['CC(=N)O']
self.assertEqual(set(product_smiles), expected_product_smiles)

def test_recipe_actions(self):
"""Test if the reaction recipe is applied correctly for nitrile hydrolysis."""
# Load the groups.py file content as lines
groups_file_path = '/home/leen/Code/ARC/data/families/nitrile_hydrolysis/groups.py'
groups_file_path = os.path.join(os.path.dirname(__file__),
'../../Code/ARC/data/families/nitrile_hydrolysis/groups.py')
with open(groups_file_path, 'r') as f:
groups_as_lines = f.readlines()

# Get the recipe actions from the groups file content
actions = get_recipe_actions(groups_as_lines)

# Define the expected actions for nitrile hydrolysis
expected_actions =[
['CHANGE_BOND', '*1', -1, '*2'],
['BREAK_BOND', '*3', 1, '*4'],
['FORM_BOND', '*1', 1, '*4'],
['FORM_BOND', '*2', 1, '*3'],
]

# Assert that the actions match the expected actions
self.assertEqual(actions, expected_actions)

class TestImineHydrolysisReactionFamily(unittest.TestCase):
"""
Contains unit tests for the imine hydrolysis reaction family.
"""

@classmethod
def setUpClass(cls):
"""Set up the test by defining the imine hydrolysis reaction family."""
cls.family = ReactionFamily('imine_hydrolysis')

def test_imine_hydrolysis_reaction(self):
"""Test if imine hydrolysis products are correctly generated."""
# Define the imine and water as reactants
imine_smiles = 'CC(=N)C'
water_smiles = 'O'

# Create ARC species for the reactants
imine = ARCSpecies(label='imine', smiles=imine_smiles)
water = ARCSpecies(label='H2O', smiles=water_smiles)

# Define the expected product (assuming a hydrolyzed imine product)
amine_smiles = 'CC(O)(N)C' # Example hydrolyzed product
amine = ARCSpecies(label='amine', smiles=acid_smiles)

# Create a reaction instance
imine = ARCSpecies(label='imine', smiles='CC(=N)C')
water = ARCSpecies(label='H2O', smiles='O')
amine = ARCSpecies(label='amine', smiles='CC(O)(N)C')
rxn = ARCReaction(r_species=[imine, water], p_species=[amine], rmg_family_set=['imine_hydrolysis'])

# Get reaction products
products = get_reaction_family_products(rxn)

# Check if the generated products match expected ones
product_smiles = [p.to_smiles() for p in products[0]['products']]
expected_product_smiles = {amine_smiles}

self.assertEqual(set(product_smiles), expected_product_smiles)
self.assertEqual(set(product_smiles), amine)

def test_recipe_actions(self):
"""Test if the reaction recipe is applied correctly for imine hydrolysis."""
# Load the groups.py file content as lines
groups_file_path = '/home/leen/Code/ARC/data/families/imine_hydrolysis/groups.py'
groups_file_path = os.path.join(os.path.dirname(__file__),
'../../Code/ARC/data/families/imine_hydrolysis/groups.py')
with open(groups_file_path, 'r') as f:
groups_as_lines = f.readlines()

# Get the recipe actions from the groups file content
actions = get_recipe_actions(groups_as_lines)

# Define the expected actions for imine hydrolysis
expected_actions = [
['CHANGE_BOND', '*1', -1, '*2'],
['BREAK_BOND', '*3', 1, '*4'],
['FORM_BOND', '*1', 1, '*4'],
['FORM_BOND', '*2', 1, '*3'],
]

# Assert that the actions match the expected actions
self.assertEqual(actions, expected_actions)

class TestEtherHydrolysisReactionFamily(unittest.TestCase):
"""
Contains unit tests for the ether hydrolysis reaction family.
"""

@classmethod
def setUpClass(cls):
"""Set up the test by defining the ester hydrolysis reaction family."""
cls.family = ReactionFamily('ether_hydrolysis')

def test_ether_hydrolysis_reaction(self):
"""Test if ether hydrolysis products are correctly generated."""
# Define the ether and water as reactants
ether_smiles = 'CCOC' # Dimethyl ether
water_smiles = 'O'

# Create ARC species for the reactants
ether = ARCSpecies(label='ether', smiles=ether_smiles)
water = ARCSpecies(label='H2O', smiles=water_smiles)

# Define the expected products
alcohol1_smiles = 'CCO'
alcohol2_smiles = 'CO'

alcohol1 = ARCSpecies(label='alcohol1', smiles=alcohol1_smiles)
alcohol2 = ARCSpecies(label='alcohol2', smiles=alcohol2_smiles)

# Create a reaction instance
ether = ARCSpecies(label='ether', smiles='CCOC')
water = ARCSpecies(label='H2O', smiles='O')
alcohol1 = ARCSpecies(label='alcohol1', smiles='CCO')
alcohol2 = ARCSpecies(label='alcohol2', smiles='CO')
rxn = ARCReaction(r_species=[ether, water], p_species=[alcohol1, alcohol2], rmg_family_set=['ether_hydrolysis'])

# Get reaction products
products = get_reaction_family_products(rxn)

# Check if the generated products match expected ones
product_smiles = [p.to_smiles() for p in products[0]['products']]
expected_product_smiles = {alcohol1_smiles, alcohol2_smiles}

expected_product_smiles = ['CCO', 'CO']
self.assertEqual(set(product_smiles), expected_product_smiles)

def test_recipe_actions(self):
"""Test if the reaction recipe is applied correctly."""
# Load the groups.py file content as lines
groups_file_path = '/home/leen/Code/ARC/data/families/ether_hydrolysis/groups.py'
groups_file_path = os.path.join(os.path.dirname(__file__), '../../Code/ARC/data/families/ether_hydrolysis/groups.py')
with open(groups_file_path, 'r') as f:
groups_as_lines = f.readlines()

# Get the recipe actions from the groups file content
actions = get_recipe_actions(groups_as_lines)

# Define the expected actions
expected_actions = [
['BREAK_BOND', '*1', 1, '*2'],
['BREAK_BOND', '*3', 1, '*4'],
['FORM_BOND', '*1', 1, '*4'],
['FORM_BOND', '*2', 1, '*3'],
]

# Assert that the actions match the expected actions
self.assertEqual(actions, expected_actions)


0 comments on commit de7538e

Please sign in to comment.