This is a network-based method written by Python to calculate the herb-herb ingredients in the PPI network. The structure of the whole project is like below:
help to set up protein-protein interaction network For instance, for a given file path with PPI edgelist pairs e.g. example/toy.sif, Construct_Network object will create by "network = Construct_Network("example/toy.sif")".
contains the key script that generates five different network distances, such as center, separation, closest, shortest and kernel.
the object named ‘Ingredients’ contains ingredient-related information, especially ingredient-target relationship. The object ‘Herb’ wraps herb-related information, especially ingredient pairs.
calculate the herb-herb network distance by "herb_herb_dis(self, herb_from, herb_to, distance_method, distance_method_herb_list)" and "herb_herb_dis_all(self, herb_from, herb_to)" for all the distance.
contain herb informtaion and TCM formulae information
generate key objects that will be used in the methods.