def smiles_to_inchi_inchikey(smiles,verbose=0):
error_counter=0
warning_counter=0
inchis=[]
inchis2=[]
inchiKeys=[]
for elem in smiles:
mol=Chem.MolFromSmiles(elem)
if(mol!=None):
inchi, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchiKey=rdinchi.InchiToInchiKey(inchi)
inchis.append(inchi)
inchiKeys.append(inchiKey)
try:
mol, retcode, message, logs=rdinchi.InchiToMol(inchi)
if(mol!=None):
inchi2, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchis2.append(inchi2)
else:
inchis2.append("XXX")
if(verbose!=0):
print(elem+ ": InChI cannot converted to mol object, added XXX instead!")
except:
if(verbose!=0):
print(retcode)
print(message)
print("Smiles:"+elem)
inchis2.append("XXX")
else:
inchis.append("XXX")
inchiKeys.append("XXX")
inchis2.append("XXX")
if(verbose!=0):
print(elem+ ": can not converted added XXX instead! ")
error_counter=error_counter+1
for i1,i2 in zip(inchis,inchis2):
if(i1!=i2):
if(verbose!=0):
print("Warning:"+i1+" - "+i2)
warning_counter=warning_counter+1
print("\nGeneration of InChI and InChIKey from SMILES is completed.")
print("Total errors:"+str(error_counter))
print("Total warnings:"+str(warning_counter)+"\n")
return inchis,inchiKeys
def MolToInchiAndAuxInfo(mol,
options="",
logLevel=None,
treatWarningAsError=False):
"""Returns the standard InChI string and InChI auxInfo for a molecule
Keyword arguments:
logLevel -- the log level used for logging logs and messages from InChI
API. set to None to diable the logging completely
treatWarningAsError -- set to True to raise an exception in case of a
molecule that generates warning in calling InChI API. The resultant InChI
string and AuxInfo string as well as the error message are encoded in the
exception.
Returns:
a tuple of the standard InChI string and the auxInfo string returned by
InChI API, in that order, for the input molecule
"""
inchi, retcode, message, logs, aux = rdinchi.MolToInchi(mol, options)
if logLevel is not None:
if logLevel not in logLevelToLogFunctionLookup:
raise ValueError("Unsupported log level: %d" % logLevel)
log = logLevelToLogFunctionLookup[logLevel]
if retcode == 0:
log(message)
if retcode != 0:
if retcode == 1:
logger.warning(message)
else:
logger.error(message)
if treatWarningAsError and retcode != 0:
raise InchiReadWriteError(inchi, aux, message)
return inchi, aux
def sln_to_smiles(sln_list,verbose=0):
error_counter=0
warning_counter=0
smiles_list= []
inchis_from_sln=[]
inchis_from_smiles=[]
for elem in sln_list:
mol=rdSLNParse.MolFromQuerySLN(elem)
if(mol!=None):
smiles=Chem.MolToSmiles(mol)
smiles_list.append(smiles)
inchi, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchis_from_sln.append(inchi)
mol=Chem.MolFromSmiles(smiles)
if(mol!=None):
inchi, retcode, message, logs, aux =rdinchi.MolToInchi(mol)
inchis_from_smiles.append(inchi)
else:
inchis_from_smiles.append("XXX")
if(verbose!=0):
print(elem+ ": SMILES cannot converted to mol object, added XXX instead!")
else:
smiles_list.append("XXX")
print(elem+ ": SLN can not converted to mol object, added XXX instead!")
error_counter=error_counter+1
for i1,i2 in zip(inchis_from_sln,inchis_from_smiles):
if(i1!=i2):
if(verbose!=0):
print("Warning:"+i1+" - "+i2)
warning_counter=warning_counter+1
print("\nConversion from SLN to SMILES is completed.")
print("Total errors:"+str(error_counter))
print("Total warnings:"+str(warning_counter)+"\n")
return smiles_list
def parse_file(input_file, db_name):
""" takes all text from nanpdb database file and returns a list of lists
with NPs which is easy to use.
input_file: nanpdb database txt file
db_name: database name
"""
all_lines = input_file.split('\n')
all_lines = all_lines[:-1]
all_info_list = []
for line in all_lines:
line = line.split('\t')
info_per_row_list = []
for value in line:
my_string = ""
if len(value) == 0:
value = "NA"
my_string += value
info_per_row_list += [my_string]
info_per_row_list += [db_name]
all_info_list += [info_per_row_list]
attribute_names = ['MonoisotopicMass', 'InChI', 'SMILES', 'Identifier',\
'InChIKey2', 'InChIKey1', 'MolecularFormula', 'kingdom_name',\
'superclass_name', 'class_name', 'subclass_name']
mol_mass_list = []
inchi_list = []
SMILES_list = []
identifier_list = []
inchi_key1_list = []
inchi_key2_list = []
mol_formula_list = []
NA_list = []
for line in all_info_list:
# generate molecules
m = Chem.MolFromSmiles(line[0])
# MonoisotopicMass
mol_mass = str(Descriptors.ExactMolWt(m))[:-5]
mol_mass_list += [mol_mass]
# InChI
inchi = rdinchi.MolToInchi(m)
inchi_list += [inchi[0]]
# SMILES
SMILES_list += [line[0]]
# Identifier
identifier_list += [line[1]]
# MolecularFormula
mol_formula = rdMolDescriptors.CalcMolFormula(m)
mol_formula_list += [mol_formula]
# NA list
nr_of_structures = len(all_info_list)
NA_list += ['NA'] * nr_of_structures
# InChIKey
inchi_key_list = []
inchi_key_list2 = []
for inchi in inchi_list:
inchi_key = rdinchi.InchiToInchiKey(inchi)
inchi_key_list2 += [inchi_key]
inchi_key_list += inchi_key_list2
# InChiKey1 and InChiKey2
for inchikey in inchi_key_list:
inchikey = inchikey.split('-')
inchikey1 = inchikey[0]
inchikey2 = inchikey[1]
inchi_key1_list += [inchikey1]
inchi_key2_list += [inchikey2]
overall_list = [mol_mass_list]+[inchi_list]+[SMILES_list]+\
[identifier_list]+[inchi_key2_list]+[inchi_key1_list]+[mol_formula_list]+\
[NA_list]+[NA_list]+[NA_list]+[NA_list]
return attribute_names, overall_list
def parse_data(input_file):
""" takes all text from norine database file and returns a list of lists
with all CLASS data and an attribute list.
input_file: norine database txt file
"""
attribute_names = ['MonoisotopicMass', 'InChI', 'SMILES', 'Identifier',\
'InChIKey2', 'InChIKey1', 'MolecularFormula', 'kingdom_name',\
'superclass_name', 'class_name', 'subclass_name']
mol_mass_list = []
inchi_list = []
SMILES_list = []
identifier_list = []
inchi_key1_list = []
inchi_key2_list = []
mol_formula_list = []
NA_list = []
pre_SMILES_list = []
identifier_list = []
all_lines = input_file.split('\n')
all_lines = all_lines[2:]
for line in all_lines:
line = line.split('\t')
#Convert to mol and remove invalid structures
smile_string = ''
id_string = ''
m = line[2]
id_name = line[0]
mol = Chem.MolFromSmiles(m)
if mol != None:
smile_string += m
id_string += id_name
pre_SMILES_list += [smile_string]
#Source identifiers
identifier_list += [id_string]
pre_inchi_list = []
for smile in pre_SMILES_list:
#Generate mol
m = Chem.MolFromSmiles(smile)
#SMILES
sm = Chem.MolToSmiles(m)
SMILES_list += [sm]
#Monoisotopic mass
mol_weigth = Descriptors.ExactMolWt(m)
mol_mass_list += [mol_weigth]
#Mol Forumula
mol_formula = rdMolDescriptors.CalcMolFormula(m)
mol_formula_list += [mol_formula]
# InChI
inchi = rdinchi.MolToInchi(m)
pre_inchi_list += [inchi[0]]
# InChIKey1 and InChIKey2
for inchi in pre_inchi_list:
if not str(inchi).startswith('InCh'):
inchi = 'NA'
inchi_list += [inchi]
pre_inchi_key_list = []
for inchi2 in inchi_list:
if inchi2 == 'NA':
inchi_key = "NA-NA"
pre_inchi_key_list += [inchi_key]
if inchi2 != 'NA':
inchi_key = rdinchi.InchiToInchiKey(inchi2)
pre_inchi_key_list += [inchi_key]
for inchi_key in pre_inchi_key_list:
inchi_key = inchi_key.split('-')
inchi_key2 = inchi_key[1]
inchi_key2_list += [inchi_key2]
inchi_key1 = inchi_key[0]
inchi_key1_list += [inchi_key1]
# NA list
nr_of_structures = len(SMILES_list)
NA_list += ['NA'] * nr_of_structures
overall_list = [mol_mass_list]+[inchi_list]+[SMILES_list]+\
[identifier_list]+[inchi_key2_list]+[inchi_key1_list]+[mol_formula_list]+\
[NA_list]+[NA_list]+[NA_list]+[NA_list]
return attribute_names, overall_list
def create_CLASS_data(data_dict):
""" Generates CLASS data for the strepto data present in the strep_dict.
input_file: streptodb dictionary
"""
attribute_names = ['MonoisotopicMass', 'InChI', 'SMILES', 'Identifier',\
'InChIKey2', 'InChIKey1', 'MolecularFormula', 'kingdom_name',\
'superclass_name', 'class_name', 'subclass_name']
mol_mass_list = []
inchi_list = []
SMILES_list = []
identifier_list = []
inchi_key1_list = []
inchi_key2_list = []
mol_formula_list = []
NA_list = []
# Identifier
identifier_list = data_dict['compound_id']
# SMILES
SMILES_list = data_dict['canonical_smiles']
for SMILE in SMILES_list:
# generate molecules
m = Chem.MolFromSmiles(SMILE)
# MonoisotopicMass
mol_mass = str(Descriptors.ExactMolWt(m))[:-3]
mol_mass_list += [mol_mass]
# InChI
inchi = rdinchi.MolToInchi(m)
inchi_list += [inchi[0]]
# MolecularFormula
mol_formula = rdMolDescriptors.CalcMolFormula(m)
mol_formula_list += [mol_formula]
# NA list
nr_of_structures = len(data_dict['canonical_smiles'])
NA_list += ['NA'] * nr_of_structures
# InChIKey
inchi_key_list = []
inchi_key_list2 = []
for inchi in inchi_list:
inchi_key = rdinchi.InchiToInchiKey(inchi)
inchi_key_list2 += [inchi_key]
inchi_key_list += inchi_key_list2
# InChiKey1 and InChiKey2
for inchikey in inchi_key_list:
inchikey = inchikey.split('-')
inchikey1 = inchikey[0]
inchikey2 = inchikey[1]
inchi_key1_list += [inchikey1]
inchi_key2_list += [inchikey2]
overall_list = [mol_mass_list]+[inchi_list]+[SMILES_list]+\
[identifier_list]+[inchi_key2_list]+[inchi_key1_list]+[mol_formula_list]+\
[NA_list]+[NA_list]+[NA_list]+[NA_list]
return attribute_names, overall_list
def diff_mol_pdb(mol, pdbfile, logfile=devnull):
with stdout_redirected(to=logfile, stdout=sys_stderr):
with stdout_redirected(to=logfile, stdout=sys_stdout):
remove_isotopes(mol, sanitize=True)
nhmol = Chem.RemoveHs(mol,
implicitOnly=False,
updateExplicitCount=True,
sanitize=True)
try:
Chem.Kekulize(nhmol)
except:
pass
checkconnect = True
pdbmol = None
try:
pdbmol = Chem.MolFromPDBFile(pdbfile,
removeHs=False,
sanitize=True)
except:
pass
if pdbmol is None:
pdbmol = Chem.MolFromPDBFile(pdbfile,
removeHs=False,
sanitize=False)
if pdbmol is None:
raise ParsingError("Cannot open PDB molecule.")
pdbmol = disconnect(pdbmol)
Chem.SanitizeMol(pdbmol, catchErrors=True)
nhpdbmol = Chem.RemoveHs(pdbmol,
implicitOnly=False,
updateExplicitCount=True,
sanitize=False)
Chem.SanitizeMol(nhpdbmol, catchErrors=True)
try:
print(
'Applying bond orders and formal charges from molecule file to PDB molecule ... '
)
nhpdbmol = AssignBondOrdersFromTemplate(nhmol, nhpdbmol)
newpdbmol = Chem.AddHs(nhpdbmol,
addCoords=True,
explicitOnly=True)
newpdbmol.UpdatePropertyCache()
newpdbmol = correct_hydrogen_num_from_pdbmol(pdbmol, newpdbmol)
newpdbmol = set_hydrogen_coor_from_pdbmol(pdbmol,
newpdbmol,
refconfId=-1,
confId=-1)
except Exception:
print(
"WARNING: Cannot assign bond orders from molecule file template. Checking only non-hydrogen connectivity."
)
checkconnect = False
newpdbmol = nhpdbmol
pass
#Stoichiometric formula check
impnum = count_implicit_hydrogens(newpdbmol)
failnum = 0
result = 'OK'
unformula = remove_charge_formula(
rdMolDescriptors.CalcMolFormula(mol))
pdbunformula = remove_charge_formula(
rdMolDescriptors.CalcMolFormula(newpdbmol))
#print(pdbunformula)
pdbunformula = fix_formula(pdbunformula, impnum)
if unformula != pdbunformula:
failnum += 1
result = 'FAIL: Molecules have different Stoichiometric formulas ' + unformula + ' ' + pdbunformula + '.'
print('Stoichiometric formula check (without charge): ' + result)
print('Generating Fixed H InChI for molecule file ... ')
inchi, code, msg, log, aux = rdinchi.MolToInchi(
mol, options='-FixedH -DoNotAddH')
if code == 0:
#print(inchi)
pass
if code == 1:
# print(inchi)
print(msg)
else:
print(msg)
print('Generating Standard InChI for molecule file ... ')
sinchi, code, msg, log, aux = rdinchi.MolToInchi(
mol, options=' -DoNotAddH')
if code == 0:
#print(sinchi)
pass
if code == 1:
#print(sinchi)
print(msg)
else:
print(msg)
maininchi = truncate_inchi(inchi, ['connect'])
print('Generating Fixed H InChI for PDB molecule ... ')
pdbinchi, code, msg, log, aux = rdinchi.MolToInchi(
newpdbmol, options='-FixedH -DoNotAddH')
if code == 0:
pass
if code == 1:
print(msg)
else:
print(msg)
print('Generating Standard InChI for PDB molecule ... ')
pdbsinchi, code, msg, log, aux = rdinchi.MolToInchi(
newpdbmol, options=' -DoNotAddH')
if code == 0:
pass
if code == 1:
print(msg)
else:
print(msg)
pdbmaininchi = truncate_inchi(pdbinchi, ['connect'])
result = 'OK'
if maininchi != pdbmaininchi:
result = 'FAIL: Molecules have diferent scaffolds\n' + maininchi + ' ' + pdbmaininchi + '.'
failnum += 1
print('Main chain InChI check: ' + result)
else:
print('Main chain InChI check: ' + result)
result = 'OK'
if checkconnect:
if sinchi != pdbsinchi:
result = 'FAIL: Molecules are not the same compound or have different net charge.\n' + sinchi + '\n' + pdbsinchi + '.'
failnum += 1
print('Standard InChI check: ' + result)
else:
print('Standard InChI check: ' + result)
result = 'OK'
if inchi != pdbinchi:
result = 'FAIL: Molecules have different protonation/tautomery\n' + inchi + '\n' + pdbinchi + '.'
failnum += 1
print('Fixed H InChI check: ' + result)
print('OK')
return failnum, newpdbmol, nhpdbmol
def generate_data(input_file):
""" takes all text from the input structure data file and returns a list of
lists with all generated data needed for the sqlite database.
input_file: input structure txt file
"""
mol_mass_list = []
inchi_list = []
SMILES_list = []
identifier_list = []
inchi_key1_list = []
inchi_key2_list = []
mol_formula_list = []
NA_list = []
pre_SMILES_list = []
identifier_list = []
all_lines = input_file.split('\n')
if all_lines[-1] == '':
all_lines = all_lines[:-1]
for line in all_lines:
line = line.split('\t')
#Convert to mol and remove invalid structures
smile_string = ''
id_string = ''
m = line[0]
id_name = line[1]
mol = Chem.MolFromSmiles(m)
if mol != None:
smile_string += m
id_string += id_name
pre_SMILES_list += [smile_string]
#Source identifiers
identifier_list += [id_string]
pre_inchi_list = []
for smile in pre_SMILES_list:
#Generate mol
m = Chem.MolFromSmiles(smile)
#SMILES, canonical
sm = Chem.MolToSmiles(m)
SMILES_list += [sm]
#Monoisotopic mass
mol_weigth = Descriptors.ExactMolWt(m)
mol_mass_list += [mol_weigth]
#Mol Forumula
mol_formula = rdMolDescriptors.CalcMolFormula(m)
mol_formula_list += [mol_formula]
# InChI
inchi = rdinchi.MolToInchi(m)
pre_inchi_list += [inchi[0]]
# InChIKey1 and InChIKey2
for inchi in pre_inchi_list:
if not str(inchi).startswith('InCh'):
inchi = 'NA'
inchi_list += [inchi]
pre_inchi_key_list = []
for inchi2 in inchi_list:
if inchi2 == 'NA':
inchi_key = "NA-NA"
pre_inchi_key_list += [inchi_key]
if inchi2 != 'NA':
inchi_key = rdinchi.InchiToInchiKey(inchi2)
pre_inchi_key_list += [inchi_key]
for inchi_key in pre_inchi_key_list:
inchi_key = inchi_key.split('-')
inchi_key2 = inchi_key[1]
inchi_key2_list += [inchi_key2]
inchi_key1 = inchi_key[0]
inchi_key1_list += [inchi_key1]
# NA list
nr_of_structures = len(SMILES_list)
NA_list += ['NA'] * nr_of_structures
overall_list = [mol_mass_list]+[inchi_list]+[SMILES_list]+\
[identifier_list]+[inchi_key2_list]+[inchi_key1_list]+[mol_formula_list]+\
[NA_list]+[NA_list]+[NA_list]+[NA_list]
return overall_list
