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tri_inputs.py
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tri_inputs.py
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import os
import subprocess
# Input smiles string
# Adds smiles string depending on if theres a BBA or BBD or both in the string
# Depending on whether there is a BBA or BBD place the file in the directory
#name = input('What is name of chemdraw stucture without the Kr and Ar: ')
#smile = input('What is the smile string from Chemdraw (Place Ar for electron acceptor connection and Kr for electron donor connection): ')
#inchlkey = input('Copy and paste the inchlkey with the Ar and Kr: ')
def arkysmiconv(smile):
'''
converts Ar and Kr to BBA and BBD
'''
a = smile
#print(type(smile))
a = a.replace('[Ar]','(BBA)')
a = a.replace('[Kr]','(BBD)')
if a[0:5] == '(BBA)' or a[0:5] == '(BBD)':
a = a[5] + a[0:5] + a[6:]
#print(a)
#print(a)
return a
def typeofstruct(pa,pd,pb,smi):
'''
Places Smiles in file and inputs in correct directory
'''
# smi = arkysmiconv(smile)
print(smi)
if 'BBA' in smi and 'BBD' not in smi:
# print('acceptor')
#print(len(os.listdir(os.getcwd())))
numoffiles = 0
for x in list(os.scandir(pa)):
if x.is_file():
numoffiles += 1
os.chdir(pa)
print(numoffiles)
os.chdir('..')
x = 'acceptor'
print('This structure is an acceptor')
elif 'BBD' in smi and 'BBA' not in smi:
numoffiles = 0
for x in list(os.scandir(pd)):
if x.is_file():
numoffiles += 1
os.chdir(pd)
print(numoffiles)
x = 'donor'
print('This structure is an donor')
elif 'BBD' in smi and 'BBA' in smi:
numoffiles = 0
for x in list(os.scandir(pb)):
print('help'+str(x))
if x.is_file():
numoffiles += 1
os.chdir(pb)
print(numoffiles)
print('This structure is an backbone')
x = 'backbone'
else:
print('Error')
return x,numoffiles
#typeofstruct()
def CreatesInchlKey(smile):
print(smile)
filename = open('creator.smi','w+')
filename.write(str(smile))
filename.close()
key = 'obabel creator.smi -oinchikey'
carts = subprocess.check_output(key, shell=True)
#subprocess.call(cmd, shell=True)
carts = str(carts)
l = []
for i in carts:
#print(i)
l.append(i)
l.remove('b')
l.remove("'")
l.remove("'")
l.remove('n')
l.remove("\\")
inchlkey = ''
for i in l:
inchlkey += str(i)
os.remove('creator.smi')
return inchlkey
def InchlKeyDicBackbone(pb):
InchlKeyBackboneDict = {}
for h in os.listdir(pb):
if '.smi' in h:
with open(pb+'/' + str(h)) as f:
data = f.readlines()[2].rstrip('\n')
#print(data)
InchlKeyBackboneDict[data] = data
return InchlKeyBackboneDict
def InchlKeyDicAcceptor(pa):
InchlKeyAcceptorDict = {}
for h in os.listdir(pa):
if '.smi' in h:
with open(pa+ '/' +str(h)) as f:
# print(f)
# data = f.readlines()[2].rstrip('\n')
data = f.readlines()
smiles = data[0].rstrip('\n')
key = data[2].rstrip('\n')
# data = f.readlines()
# print(data[2])
InchlKeyAcceptorDict[key] = key
return InchlKeyAcceptorDict
def InchlKeyDicDonor(pd):
InchlKeyDonorsDict = {}
for h in os.listdir(pd):
if '.smi' in h:
with open(pd+'/' + str(h)) as f:
data = f.readlines()[2].rstrip('\n')
#print(data)
InchlKeyDonorsDict[data] = data
return InchlKeyDonorsDict
def inchlkeychecker(pb,pa,pd,struct,smi,bb,aa,dd,inchlkey,name):
'''
Checks whether the backbone,acceptor or donor has been made before
'''
if struct == 'backbone':
BackboneDict = bb
if inchlkey in BackboneDict.keys():
for i in BackboneDict.keys():
print(i)
print('exists')
elif inchlkey not in BackboneDict.keys():
for i in BackboneDict.keys():
print(i)
numoffiles = []
for x in list(os.listdir(pb)):
if '.smi' in x:
numoffiles.append(int(x.replace('b.smi','')))
print(x)
numoffiles.sort()
print(numoffiles)
# print(numoffiles[-1])
# if x.is_file():
# print(x[11])
# numoffiles += 1
os.chdir(pb)
filename = open(str(numoffiles[-1]+1)+'b.smi','x+')
filename.write(str(smi))
filename.write('\n')
filename.write(str(name))
filename.write('\n')
filename.write(str(inchlkey))
filename.close()
if struct == 'acceptor':
AcceptorDict = aa
if inchlkey in AcceptorDict.keys():
for i in AcceptorDict.keys():
print(i)
print('exists')
elif inchlkey not in AcceptorDict.keys():
for i in AcceptorDict.keys():
print(i)
numoffiles2 = []
for x in list(os.listdir(pa)):
print(x)
if '.smi' in x:
#print(x)
numoffiles2.append(int(x.replace('ea.smi','')))
#print(x)
numoffiles2.sort()
print(numoffiles2[-1])
# if x.is_file():
# print(x[11])
# numoffiles += 1
os.chdir(pa)
filename = open(str(numoffiles2[-1]+1)+'ea.smi','x+')
filename.write(str(smi))
filename.write('\n')
filename.write(str(name))
filename.write('\n')
filename.write(str(inchlkey))
filename.close()
if struct == 'donor':
DonorDict = dd
if inchlkey in DonorDict.keys():
for i in DonorDict.keys():
print(i)
print('exists')
elif inchlkey not in DonorDict.keys():
for i in DonorDict.keys():
print(i)
numoffiles3 = []
for x in list(os.listdir(pd)):
#print(x)
if '.smi' in x:
#print(x)
numoffiles3.append(int(x.replace('ed.smi','')))
#print(x)
numoffiles3.sort()
print(numoffiles3[-1])
# if x.is_file():
# print(x[11])
# numoffiles += 1
os.chdir(pd)
filename = open(str(numoffiles3[-1]+1)+'ed.smi','x+')
filename.write(str(smi))
filename.write('\n')
filename.write(str(name))
filename.write('\n')
filename.write(str(inchlkey))
filename.close()
return
def filemaker(filename,smi,inchlkey,name,type):
if type == 'backbone':
with open(str(filename+1)+'b.smi','w+') as fp:
fp.write(str(smi))
fp.write('\n')
fp.write(str(name))
fp.write('\n')
fp.write(str(inchlkey))
fp.close()
if type == 'donor':
with open(str(filename+1)+'ed.smi','w+') as fp:
fp.write(str(smi))
fp.write('\n')
fp.write(str(name))
fp.write('\n')
fp.write(str(inchlkey))
fp.close()
if type=='acceptor':
with open(str(filename+1)+'ea.smi','w+') as fp:
fp.write(str(smi))
fp.write('\n')
fp.write(str(name))
fp.write('\n')
fp.write(str(inchlkey))
fp.close()
return
def main():
path_to_acceptors = 'eAcceptors'
path_to_donors = 'trieDonors'
path_to_backbone = 'tribackbones'
name = input('What is name of chemdraw stucture without the Kr and Ar: ')
# name = 'ffff'
smile = input('What is the smile string from Chemdraw (Place Ar for electron acceptor connection and Kr for electron donor connection): ')
# smile = 'CCC[Kr]CCC[Ar]'
inchlkey = CreatesInchlKey(smile)
smi = arkysmiconv(smile)
struct,numoffiles = typeofstruct(path_to_acceptors,path_to_donors,path_to_backbone,smi)
print((struct,'AAAAA'))
filemaker(numoffiles,smi,inchlkey,name,struct)
'''
inchlkeychecker(path_to_backbone,path_to_acceptors,path_to_donors,struct,smi,InchlKeyDicBackbone(path_to_backbone),InchlKeyDicAcceptor(path_to_acceptors),InchlKeyDicDonor(path_to_donors),CreatesInchlKey(smile),name)
'''
return
main()