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process_TECRDB_compounds.py
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process_TECRDB_compounds.py
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import pandas as pd
class TECRDB_compounds_data(object):
def __init__(self):
"""
A module that processes information of compounds in TECRDB
"""
self.TECRDB_compounds_data_dict = {}
self.TECRDB_compounds_pH7_species_id_dict = {}
self.TECRDB_compounds_least_H_sid_dict = {}
self.get_TECRDB_compounds_data()
def get_TECRDB_compounds_data(self):
"""
reads in data for compounds in TECRDB
:return: a dictionary with keys being different ion bound states of the compound (we call it species_id here, e.g CHB_15422_-1 refers to -1 charged form of
compound_id CHB_15422), values being a dictionary storing the thermodynamic information and molecular properties of the species_id
"""
TECRDB_compounds_data_table = pd.read_csv('data/TECRDB_compounds_data.csv')
#all possible information that the particular ion bound state can have
data_entry_list = ['Cp', 'H_number', 'binding_constant', 'charge', 'dG_f', 'dH_f', 'dS_f', 'groups', 'metal_type','smiles_form','metal_number']
for i, row in TECRDB_compounds_data_table.iterrows():
cur_sid = row['species_id']
cur_cid = row['compound_id']
self.TECRDB_compounds_data_dict[cur_sid] = {'compound_id':cur_cid}
if row['is_pH7_species'] == True:
self.TECRDB_compounds_pH7_species_id_dict[cur_cid] = cur_sid
if row['is_least_protonated_species'] == True:
self.TECRDB_compounds_least_H_sid_dict[cur_cid] = cur_sid
for data_entry in data_entry_list:
if not pd.isnull(row[data_entry]):
if data_entry == 'groups':
#convert the text form of groups to python list
cur_sid_groups = map(float,row['groups'].strip('[').strip(']').split(','))
self.TECRDB_compounds_data_dict[cur_sid]['groups'] = cur_sid_groups
else:
try:
#convert value from string to float
self.TECRDB_compounds_data_dict[cur_sid][data_entry] = float(row[data_entry])
except ValueError:
self.TECRDB_compounds_data_dict[cur_sid][data_entry] = row[data_entry]
if __name__ == '__main__':
TECRDB_cpd_data = TECRDB_compounds_data()