Json formats

This article will present all the json formats needed during a typical execution of Smiles2Monomers.

All the files are lists of objects, so you have to use [ ] around the list.

Polymers (and learning base)

[ { "id":"1337", "name":"My_polymer_name", "smiles":"O1C(C)C(O)C(O)C(O)C1Oc2ccc(cc2)C(NC)C(=O)NC(C(c3ccc(O4)cc3)OC5C(O)C(O)C(O)C(CO)O5)(C=O)NC(c6ccc(O)cc6)C(=O)NC(c7cc4c(c8c7)OC9OC(CO)C(O)C(O)C9OC%10OC(C)C(O)C(N)C%10)C(=O)NC(C%11=O)c%12ccc(O)c(c%12)c%13c(O)cc(O)cc%13C(C(=O)O)N" } ]

Monomers

[ { "id":"Tyr", "name":"Tyrosine", "smiles":"c1cc(ccc1CC(C(=O)O)N)O" } ]

Rules

[ { "name" : "pepOH", "formula" : "C(=O)O[H]", "transformations" : ["C(=O).x"], "exclusion" : [], "weights" : [5], "alone" : true } ]

• name : Name of the binding rule.
• formula : Smiles formula for the binding site.
• transformations : List of the possible transformations after the binding. Put a '.' for the atom that will be replaced during the binding and 'x' for the atoms that will be lost.
• exclusion : The binding site must not be changed if it is part of an exclusion.
• weights : This is a kind of priority. During the execution of s2m, if we have to choose between a monomer weighted 3 and another weigthed 5, the second one will be selected in priority.
• alone : true if the binding can occur alone.