def __init__(self,
biochem_root='../../Biochemistry/',
rxns_file='reactions.tsv'):
self.BiochemRoot = biochem_root
self.RxnsFile = biochem_root + rxns_file
self.AliasFile = biochem_root + "Aliases/Reactions_Aliases.tsv"
reader = DictReader(open(self.RxnsFile), dialect='excel-tab')
self.Headers = reader.fieldnames
from BiochemPy import Compounds
self.CompoundsHelper = Compounds()
self.Compounds_Dict = self.CompoundsHelper.loadCompounds()
def __init__(self,
biochem_root='../../../Biochemistry/',
rxns_file='reactions.tsv'):
self.BiochemRoot = os.path.dirname(__file__) + '/' + biochem_root
self.RxnsFile = self.BiochemRoot + rxns_file
self.AliasFile = self.BiochemRoot + "Aliases/Unique_ModelSEED_Reaction_Aliases.txt"
self.NameFile = self.BiochemRoot + "Aliases/Unique_ModelSEED_Reaction_Names.txt"
self.PwyFile = self.BiochemRoot + "Aliases/Unique_ModelSEED_Reaction_Pathways.txt"
self.ECFile = self.BiochemRoot + "Aliases/Unique_ModelSEED_Reaction_ECs.txt"
reader = DictReader(open(self.RxnsFile), dialect='excel-tab')
self.Headers = reader.fieldnames
from BiochemPy import Compounds
self.CompoundsHelper = Compounds()
self.Compounds_Dict = self.CompoundsHelper.loadCompounds()
if (inchikey not in mnx_inchikey_dict):
mnx_inchikey_dict[inchikey] = mnx
inchikey = "-".join(inchikey.split('-')[0:2])
if (inchikey not in mnx_inchikey_dict):
mnx_inchikey_dict[inchikey] = mnx
inchikey = inchikey.split('-')[0]
if (inchikey not in mnx_inchikey_dict):
mnx_inchikey_dict[inchikey] = mnx
file_handle.close()
#Here we can cross-check the structures that are in ModelSEED to find ones where
#there is a match in eQuilibrator
compounds_helper = Compounds()
structures_dict = compounds_helper.loadStructures(["InChIKey"], ["ModelSEED"])
seed_mnx_structural_map = dict()
for cpd in structures_dict:
structure_type = 'InChIKey'
if (structure_type not in structures_dict[cpd]):
#The load structures function will return all compounds, so have to
#Check that the structure is there
continue
#As these are unique structures, i.e. 1-1 mapping with compound id,
#there's only ever one in each list for each compound
structure = list(structures_dict[cpd][structure_type].keys())[0]
#Here we check on three levels, we check the full string
#Then the deprotonated string, then the structure alone
#!/usr/bin/env python
import os, sys, re
temp = list()
header = 1
from BiochemPy import Compounds
import pybel
from rdkit.Chem import AllChem
from rdkit import RDLogger
lg = RDLogger.logger()
lg.setLevel(RDLogger.ERROR)
#Load Structures and Aliases
CompoundsHelper = Compounds()
Structures_Dict = CompoundsHelper.loadStructures(["SMILE", "InChI"],
["KEGG", "MetaCyc"])
Structures_Root = os.path.dirname(__file__) + "/../../Biochemistry/Structures/"
file_handle_dict = dict()
for source in "KEGG", "MetaCyc":
for struct_type in "InChI", "SMILE":
for struct_stage in "Charged", "Original":
file_string = "_".join((source, struct_type, struct_stage))
file_name = Structures_Root + source + "/" + struct_type + "_" + struct_stage + "_Formulas_Charges.txt"
file_handle_dict[file_string] = open(file_name, "w")
resolved_structures = open('Resolved_Structures.txt', 'w')
unresolved_structures = open('Unresolved_Structures.txt', 'w')
for struct_type in sorted(Structures_Dict.keys()):
