4. utilities; Overview

.ipynb files in directiry “utirities” are tools to imprementing the rules of monomer extraction-cllasification , polymerization reaction definition and polymer generation.

By using the files in ‘./utilities’ directory, one can modify or add the definition of monomers, the rules of polymerization reactions and polymer classes.
To apply the new rule(s), replace the old ‘./smipoly/rules’ directory by the new one. The files must be run according to the number assigned the head of the each filename.

• 1_MonomerDefiner.ipynb: definitions of monomers

• 2_Ps_rxnL.ipynb: rules of polymerization reactions

• 3_Ps_GenL.ipynb: definitions of polymer classes with combinations of starting monomer(s) and polymerization reaction

Each definations were written by SMARTS (SMiles ARbitrary Target Specification) strings.

The difined monomer classificatin, polymerization reaction and the polymer genration rules were located in src/smipoly/rulse as pickle or json file.
These were genarated by using utilities/1_MonomerDefiner.ipynb, 2_Ps_rxnL.ipynb and 3_Ps_GenL.ipynb.

Generator .ipynb file name	Valiable name	Saved file name	Defined rule
1_MonomerDefiner.ipynb	mon_vals	mon_vals	Clategorization of monomer classes
	mon_dic, mon_dic_inv	mon_dic.json, mon_dic_inv.json	The defination of monomer
	monL	mon_lst.json	The definition of the polymerization site
	exclL	excl_lst.json	The definition of functional groups that should not coexist in a monomer molecule
2_Ps_rxnL.ipynb	Ps_rxnL	ps_rxn.pkl	polymerization reaction
3_Ps_GenL.ipynb	Ps_classL	ps_class.json	Polymer classes
	Ps_GenL	ps_gen.pkl	Polymer classes with applied polymerization reactions and starting monomer(s)