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General_converter.py
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General_converter.py
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#!/usr/bin/env python
# coding: utf-8
import os
import re
from rdkit import Chem
from rdkit.Chem.rdMolDescriptors import CalcMolFormula
from splash import Spectrum, SpectrumType, Splash
import time
import json
atom = {"H":1.008, "C": 12.011, "O":15.999, "N": 14.007, "P":30.976, "S": 32.065}
inputdir = "/Users/donghanli/Documents/GitHub/convert_MassBank_format/KI_GIAR/"
inputfile = "KI-GIAR_zic-HILIC_Pos_v0.90.msp"
outputdir ="/Users/donghanli/Documents/GitHub/convert_MassBank_format/KI_GIAR/KI_Gumma/"
with open(inputdir+inputfile, "r") as f:
readdata = f.read()
filelist = readdata.split("\n\n")
filelist = filelist[:-2]
with open(inputdir+"classlist.json","r") as f:
classlist =json.loads(f.read())
data = []
faillist = []
successlist=[]
finallist =[]
name, formula, smiles, mol, inchi, instrmt_type, msn="","","","","","",""
def dateformat(date):
date = date.replace("/",".")
date = date.replace("-",".")
y,m,d = date.split(".")
MBdate = y+"."+format(int(m),"02d")+"."+format(int(d),"02d")
return(MBdate)
def calculate_weight(chem): # <string> formula.
s = re.findall('([A-Z][a-z]?)([0-9]*)', chem)
compoundweight = 0
for element, count in s:
count = int(count or '1')
compoundweight += atom[element] * count
return compoundweight # <float> formula weight
def searchsingle(tokeyword,fromkeyword1, fromkeyword2="\n", search = "ON"):
temp = fromkeyword1
tempfield = ""
if search == "ON":
temp = data.split(fromkeyword1)[1].split(fromkeyword2)[0]
if temp.upper() == "POSITIVE" or temp.upper() =="NEGATIVE":
temp = temp.upper()
elif temp == "MS1":
temp = "MS"
tempfield = tokeyword+temp
elif search =="OFF":
tempfield = tokeyword+fromkeyword1
finallist.append(tempfield)
return temp
def searchmulti(tokeyword, fromkeyword, ignore = ""):
searchlen = len(fromkeyword)
ignorelen = len(ignore)
temp = [k for k in data.split("\n") if k[:searchlen] == fromkeyword]
temp = list(set(temp))
if ignore != "":
for j in reversed(range(len(temp))):
if temp[j][-ignorelen:]==ignore:
del temp[j]
tempfield = "\n".join(temp)
tempfield = tempfield.replace(fromkeyword, tokeyword)
finallist.append(tempfield)
return temp
def peakprocess(beginline, endline="END", annotation=""):
peakX=[]
peakY=[]
anno=[]
if endline =="END":
peakinfo = data.split(beginline)[1].split("\n")[1:]
else:
peakinfo1 = data.split(beginline)[1].split("\n")[1:]
peakinfo2 = "\n".join(peakinfo1).split(endline)[0]
peakinfo = peakinfo2.split("\n")[:-1]
if annotation != "":
tempinfo = [peakinfo[0]]
for i in range(1,len(peakinfo)):
if (peakinfo[i-1].split(annotation)[0] != peakinfo[i].split(annotation)[0]):
tempinfo.append(peakinfo[i])
peakinfo = tempinfo
for i in range(len(peakinfo)):
calpeakinfo = peakinfo[i].split(annotation)[0]
calpeakinfo = calpeakinfo.strip()
calpeakinfo = calpeakinfo.replace(" ","\t")
peakX.append(float(calpeakinfo.split("\t")[0]))
peakY.append(float(calpeakinfo.split("\t")[1]))
pairpeak = list(sorted(zip(peakX, peakY)))
spectrum = Spectrum(pairpeak, SpectrumType.MS)
SPNO = "PK$SPLASH: "+ Splash().splash(spectrum)
pknum= "PK$NUM_PEAK: " + str(len(pairpeak))
maxY=max(peakY)
pklist="PK$PEAK: m/z int. rel.int.\n"
for i in range(len(pairpeak)):
pklist+=(" "+str(pairpeak[i][0])+" "+str(pairpeak[i][1])+" "+str(round(pairpeak[i][1]/maxY*999))+"\n")
pklist+="//"
pkanno ="PK$ANNOTATION: m/z annotation\n"
for i in range(len(peakinfo)):
anno= peakinfo[i].split("\"")[1]
anno = anno.replace(";", "\\")
anno = anno.replace(" ","_")
anno = anno.replace("\\_","\\")
pkanno +=(" "+str(pairpeak[i][0])+" "+anno+"\n")
pkanno = pkanno[:-2]
finallist.extend([SPNO,pkanno,pknum,pklist])
return None
elif annotation == "":
for i in range(len(peakinfo)):
calpeakinfo = peakinfo[i].strip()
calpeakinfo = calpeakinfo.replace(" ","\t")
peakX.append(float(calpeakinfo.split("\t")[0]))
peakY.append(float(calpeakinfo.split("\t")[1]))
pairpeak = list(sorted(zip(peakX, peakY)))
spectrum = Spectrum(pairpeak, SpectrumType.MS)
SPNO = "PK$SPLASH: "+ Splash().splash(spectrum)
pknum= "PK$NUM_PEAK: " + str(len(pairpeak))
maxY=max(peakY)
pklist="PK$PEAK: m/z int. rel.int.\n"
for i in range(len(pairpeak)):
pklist+=(" "+str(pairpeak[i][0])+" "+str(pairpeak[i][1])+" "+str(round(pairpeak[i][1]/maxY*999))+"\n")
pklist+="//"
finallist.extend([SPNO,pknum,pklist])
return None
def inserttitle(n,i,m):
title="RECORD_TITLE: "+n+"; "+i+"; "+m
finallist.insert(1,title)
return None
def standardASCii(finallist):
newstring = "\n".join(finallist)
newstring = newstring.replace("á","a")
newstring = newstring.replace("‐","-")
newstring = newstring.replace("™","")
newstring = newstring.replace(" "," ")
newstring = newstring.replace("′","'")
newstring = newstring.replace(" ","")
newstring = newstring.replace(" ","")
newstring = newstring.replace("フジッコ,","")
newstring = newstring.replace("α","alpha")
newstring = newstring.replace("µm","um")
return newstring
def adjustor2(base = "SMILES"):
if base == "SMILES":
s = smiles
m = Chem.MolFromSmiles(s)
i = Chem.MolToInchi(m)
ik= Chem.inchi.MolToInchiKey(m)
f = Chem.rdMolDescriptors.CalcMolFormula(mol)
if f[-1]=="+" or f[-1]=="-":
f = "["+f[:-1]+"]"+f[-1]
w = str(round(calculate_weight(f),4))
elif base == "INCHI":
i = inchi
m = Chem.MolFromInchi(i)
s = Chem.MolToSmiles(m)
ik= Chem.inchi.MolToInchiKey(m)
f = Chem.rdMolDescriptors.CalcMolFormula(mol)
if f[-1]=="+" or f[-1]=="-":
f = "["+f[:-1]+"]"+f[-1]
w = str(round(calculate_weight(f),4))
templist =["CH$SMILES: "+s if item.find("CH$SMILES: ")==0 else item for item in finallist]
templist =["CH$IUPAC: "+i if item.find("CH$IUPAC: ")==0 else item for item in templist]
templist =["CH$LINK: INCHIKEY "+ik if item.find("CH$LINK: INCHIKEY ")==0 else item for item in templist]
templist =["CH$FORMULA: "+f if item.find("CH$FORMULA:")==0 else item for item in templist]
templist =["CH$EXACT_MASS: "+w if item.find("CH$EXACT_MASS: ")==0 else item for item in templist]
return templist
def adjustor():
tempf = formula
mol = Chem.MolFromSmiles(smiles)
f2 = Chem.rdMolDescriptors.CalcMolFormula(mol)
if f2[:-1] == formula:
tempf= "["+f2[:-1]+"]"+f2[-1]
elif f2 != formula and formula != f2[:-1]:
faillist.append(name + " Bad SMILES/formula: ")
print("Fail: Bad SMILES/Formula.")
return False
templist =["CH$FORMULA: "+tempf if item.find("CH$FORMULA:")==0 else item for item in finallist]
templist =["CH$EXACT_MASS: "+str(round(calculate_weight(tempf),4)) if item.find("CH$EXACT_MASS: ")==0 else item for item in templist]
return templist
k1=time.time()
smilelist=[]
for i, data in enumerate(filelist):
finallist =[]
name, formula, smiles, mol, inchi, instrmt_type, msn="","","","","","",""
#data = filelist[i]
print("i=",i)
prefix = "TMP"
accession = searchsingle("ACCESSION: "+prefix, format(i+1, "0"+str(8-len(prefix))+"d"), search="OFF")
searchsingle("DATE: ","2019.06.10", search = "OFF")
searchsingle("AUTHORS: ","AUTHORS: ")
searchsingle("LICENSE: ","LICENSE: ")
searchsingle("COMMENT: ","COMMENT: ")
name = searchsingle("CH$NAME: ","NAME: ",";")
inchikey = searchsingle("inchikey:", "INCHIKEY: ")
inchikey = "InChIKey="+inchikey
finallist.pop()
try:
class1 = classlist[inchikey]
except KeyError:
print("No such class")
continue
else:
searchsingle("CH$COMPOUND_CLASS: ",class1, search = "OFF")
#class1 = classlist[inchikey]
#searchsingle("CH$COMPOUND_CLASS: ",class1, search = "OFF")
formula = searchsingle("CH$FORMULA: ","FORMULA: ")
searchsingle("CH$EXACT_MASS: ",str(round(calculate_weight(formula),4)),search = "OFF")
smiles = searchsingle("CH$SMILES: ","SMILES: ")
print(smiles)
mol = Chem.MolFromSmiles(smiles)
inchi = searchsingle("CH$IUPAC: ", "INCHI: ")
searchsingle("CH$LINK: INCHIKEY ","INCHIKEY: ")
searchsingle("AC$INSTRUMENT: ", "INSTRUMENT: ")
instrmt_type = searchsingle("AC$INSTRUMENT_TYPE: ", "INSTRUMENTTYPE: ")
msn = searchsingle("AC$MASS_SPECTROMETRY: MS_TYPE ", "MSLEVEL: ")
searchsingle("AC$MASS_SPECTROMETRY: ION_MODE ","IONMODE: ")
searchsingle("AC$MASS_SPECTROMETRY: IONIZATION ", "IONISATION: ")
searchsingle("AC$MASS_SPECTROMETRY: COLLISION_ENERGY ", "COLLISIONENERGY: ")
searchsingle("AC$CHROMATOGRAPHY: COLUMN_NAME ","COLUMN: ")
searchsingle("AC$CHROMATOGRAPHY: FLOW_GRADIENT ", "FlowGradient: ")
searchsingle("AC$CHROMATOGRAPHY: FLOW_RATE ","FlowRate: ")
searchsingle("AC$CHROMATOGRAPHY: RETENTION_TIME ", "RETENTIONTIME: ")
searchsingle("AC$CHROMATOGRAPHY: SOLVENT A ", "SolventA: ")
searchsingle("AC$CHROMATOGRAPHY: SOLVENT B ", "SolventB: ")
searchsingle("MS$FOCUSED_ION: PRECURSOR_TYPE ", "PRECURSORTYPE: ")
searchsingle("MS$FOCUSED_ION: PRECURSOR_M/Z ", "PRECURSORMZ: ")
peakprocess("Num Peaks", annotation="\"")
inserttitle(name,instrmt_type,msn)
finallist = adjustor()
#finallist = adjustor2("INCHI")
if finallist != False:
finalstr = standardASCii(finallist)
print(prefix+accession+" success.")
smilelist.append(smiles)
with open(outputdir+prefix+accession+".txt", "w") as f:
f.write(finalstr)
k2=time.time()
print(k2-k1)
with open(outputdir+"faillist.txt", "w") as f:
f.writelines(faillist)