def molconvert_chemaxon(data):
"""
molconvert wrapper
:param data: buffer or string or path to file
:return: array of molecules of reactions
"""
if isinstance(data, Path):
with data.open('rb') as f:
data = f.read()
elif isinstance(data, StringIO):
data = data.read().encode()
elif isinstance(data, BytesIO):
data = data.read()
elif hasattr(data, 'read'): # check if data is open(filename, mode)
data = data.read()
if isinstance(data, str):
data = data.encode()
elif isinstance(data, str):
data = data.encode()
elif not isinstance(data, bytes):
raise ValueError('invalid input')
try:
p = run(['molconvert', '-g', 'mrv'], input=data, stdout=PIPE)
except FileNotFoundError as e:
raise ConfigurationError from e
if p.returncode != 0:
raise ConfigurationError(p.stderr.decode())
with BytesIO(p.stdout) as f, MRVRead(f) as r:
return iter2array(r)
def __processor_s(self, structure):
with StringIO() as f:
with MRVWrite(f) as w:
w.write(structure)
data = dict(
structure=f.getvalue(),
parameters='mrv',
filterChain=[
dict(filter='standardizer',
parameters=dict(standardizerDefinition=self.rules))
])
try:
q = post(f'{CHEMAXON_REST}/rest-v0/util/calculate/molExport',
json=data,
timeout=20)
except RequestException as e:
raise ConfigurationError from e
if q.status_code not in (201, 200):
raise ValueError('invalid data')
res = q.json()
if not res:
raise ValueError('invalid data')
with BytesIO(res['structure'].encode()) as f, MRVRead(f) as r:
return r.read()
def display_output(value):
if value: # data from `download` attr of widget
with BytesIO(value.encode()) as f, MRVRead(f) as i:
s = next(i)
s.standardize()
s.thiele()
with StringIO() as f:
with MRVWrite(f) as o:
o.write(s)
value = f.getvalue()
return value # send to `upload` attr of widget
def molconvert_chemaxon(data):
"""
ChemAxon molconvert wrapper.
Parameters
----------
data : Buffer or string or path to file
All supported by molconvert formats for chemical data storing.
Returns
-------
array : Array of molecules of reactions
CGRtools data types for Reactions and Molecules storing.
"""
if isinstance(data, Path):
with data.open('rb') as f:
data = f.read()
elif isinstance(data, StringIO):
data = data.read().encode()
elif isinstance(data, BytesIO):
data = data.read()
elif hasattr(data, 'read'): # check if data is open(filename, mode)
data = data.read()
if isinstance(data, str):
data = data.encode()
elif isinstance(data, str):
data = data.encode()
elif not isinstance(data, bytes):
raise ValueError('invalid input')
try:
p = run(['molconvert', '-g', 'mrv'], input=data, stdout=PIPE)
except FileNotFoundError as e:
raise ConfigurationError from e
if p.returncode != 0:
raise ConfigurationError(p.stderr.decode())
with BytesIO(p.stdout) as f, MRVRead(f) as r:
return iter2array(r)
def __processor_m(self, structures):
with StringIO() as f:
with MRVWrite(f) as w:
for s in structures:
w.write(s)
tmp = f.getvalue().encode()
try:
p = run(
['standardize', '-c',
str(self.__config), '-f', 'mrv', '-g'],
input=tmp,
stdout=PIPE,
stderr=PIPE)
except FileNotFoundError as e:
raise ConfigurationError from e
if p.returncode != 0:
raise ConfigurationError(p.stderr.decode())
with BytesIO(p.stdout) as f, MRVRead(f) as r:
res = r.read()
if len(res) != len(structures):
raise ValueError('invalid data')
return res