Source code for example_workflow

from obelix.run_workflow import *
import chemspax



[docs]
ligand_excel_file = os.path.join(os.getcwd(), 'test_mace.xlsx')




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ligand_df = pd.read_excel(ligand_excel_file).dropna()




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ligand_name = ligand_df['Name']




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ligand_smiles = ligand_df['smiles']





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auxiliary_ligands = ['CC#[N:1]', 'CC#[N:1]']




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substrate = ['CC#[N:1]']





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geom = 'SP'




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central_atom = '[Rh+]'





# MACE input 


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mace_input = {'bidentate_ligands': ligand_smiles, 
                'auxiliary_ligands': auxiliary_ligands, 
                'names_of_xyz': ligand_name, 
                'central_atom': central_atom, 
                'geom': geom, 
                'substrate': substrate}



# The data files packaged along withchemspax can be accessed by pointing to the path where chemspax is installed in the local mahcine


[docs]
chemspax_directory = os.path.dirname(chemspax.__file__)





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path_to_substituents = os.path.join(chemspax_directory, "substituents_xyz")




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path_to_database = os.path.join(path_to_substituents, "manually_generated", "central_atom_centroid_database.csv")




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substituent_df = pd.read_excel(os.path.join(os.getcwd(), 'test_chemspax.xlsx'), sheet_name='Sheet1').dropna()




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substituent_list = np.array(substituent_df[['R1', 'R2', 'R3', 'R4']])


# print(substituent_list)


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names = substituent_df['Name']




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func_list = substituent_df['Functionalization']


# print(skeleton_list)
# path_to_hand_drawn_skeletons = os.path.join(os.getcwd(), "skeletons")
# path_to_output = os.path.join(os.getcwd(), "complexes")



[docs]
chemspax_input = {'substituent_list' : substituent_list}


                # 'path_to_database' : path_to_database,
                # 'path_to_substituents' : path_to_substituents}



[docs]
workflow = Workflow(mace_input = mace_input, chemspax_input=chemspax_input, path_to_workflow = os.getcwd() + '/wf_test5', geom='BD')


workflow.prepare_folder_structure()
workflow.run_mace()
workflow.run_chemspax(names=names, functionalization_list=func_list)