def __init__(self, CompGraph):
self.graph = CompGraph
self.graph_info = {}
self.send = {} # {(iblock,token):output class}
self.requirements = ['pandas']
self.start_time = time.time()
self.block_time = 0
self.date = std_datetime_str('date')
self.time = std_datetime_str('time')
self.InputScript = ''
self.output_directory = '.'
self.log = []
def write(self, X, main_directory=''):
"""
Write DataFrame to a comma-seprated-values CSV) file.
Parameters
----------
X : array-like
This array like input should be a pandas dataframe or should be convertible to a dataframe.
main_directory : str, optional (default='')
if there is a main directory for entire chemml wrapper project
"""
try:
df = pd.DataFrame(X)
except:
msg = 'The input `X` must be convertible to a pandas dataframe.'
raise TypeError(msg)
# create final output dir
self.output_directory = os.path.join(main_directory,
self.output_directory)
if not os.path.exists(self.output_directory):
os.makedirs(self.output_directory)
# record time
if self.record_time:
self.file_path = '%s/%s_%s' % (self.output_directory,
self.filename, std_datetime_str())
else:
self.file_path = '%s/%s' % (self.output_directory, self.filename)
# store csv file
df.to_csv(self.file_path, index=self.index, header=self.header)
def write(self, X, main_directory=''):
"""
This function Write an input data X to a file as a string.
Parameters
----------
df : array-like
The input array
main_directory : str, optional (default='')
if there is a main directory for entire chemml wrapper project
"""
X = np.array(X)
# create final output dir
self.output_directory = os.path.join(main_directory,
self.output_directory)
if not os.path.exists(self.output_directory):
os.makedirs(self.output_directory)
if self.record_time:
self.file_path = '%s/%s_%s' % (self.output_directory,
self.filename, std_datetime_str())
else:
self.file_path = '%s/%s' % (self.output_directory, self.filename)
# store file
f = h5py.File(self.file_path)
dst = f.create_dataset('dataset', shape=X.shape, data=X)
def write(self, X, main_directory=''):
"""
This function Write an input data X to a file as a string.
Parameters
----------
X : array-like
The input in any format
main_directory : str, optional (default='')
if there is a main directory for entire chemml wrapper project
"""
# create final output dir
self.output_directory = os.path.join(main_directory,
self.output_directory)
if not os.path.exists(self.output_directory):
os.makedirs(self.output_directory)
if self.record_time:
self.file_path = '%s/%s_%s' % (self.output_directory,
self.filename, std_datetime_str())
else:
self.file_path = '%s/%s' % (self.output_directory, self.filename)
# store file
with open(self.file_path, 'a') as file:
file.write('%s\n' % str(X))
def test_std_datetime_str():
s = std_datetime_str(mode='datetime')
assert s[-3] == ':'
s = std_datetime_str(mode='date')
assert s[-3] == '-'
s = std_datetime_str(mode='time')
assert s[-3] == ':'
s = std_datetime_str(mode='datetime_ms')
assert s[4] == '-'
s = std_datetime_str(mode='time_ms')
assert s[2] == ':'
with pytest.raises(ValueError):
std_datetime_str(mode='hour')
def script_wizard(self, script='new', output_directory='./'):
"""
The script_wizard is designed to build a Dragon script file. The name and
the functionality of this function is the same as available Script wizard
in the Dragon Graphic User Interface.
Note: All reported nodes are mandatory, except the <EXTERNAL> tag
Note: Script for version 7 doesn't support fingerprints block
Parameters
----------
script : string, optional (default="new")
If "new" start creating a new script from scratch. If you want to load an existing script,
pass the filename with drs format.
output_directory : string, optional (default = './')
the path to the working directory to store output files.
dragon : xml element
Dragon script in xml format.
drs : string
Dragon script file name
data_path : string
The path+name of saved data file in any format. If saveType is 'block'
or 'subblock' data_path is just the path to the directory that all data
files have been saved.
"""
self.output_directory = output_directory
if not os.path.exists(self.output_directory):
os.makedirs(self.output_directory)
if script == 'new':
if self.version == 6:
self.dragon = objectify.Element(
"DRAGON",
version="%i.0.0" % self.version,
script_version="1",
generation_date=std_datetime_str('date').replace('-', '/'))
OPTIONS = objectify.SubElement(self.dragon, "OPTIONS")
OPTIONS.append(
objectify.Element("CheckUpdates",
value=bool_formatter(self.CheckUpdates)))
OPTIONS.append(
objectify.Element("SaveLayout",
value=bool_formatter(self.SaveLayout)))
OPTIONS.append(
objectify.Element("ShowWorksheet",
value=bool_formatter(
self.ShowWorksheet)))
OPTIONS.append(
objectify.Element("Decimal_Separator",
value=self.Decimal_Separator))
OPTIONS.append(
objectify.Element("Missing_String",
value=self.Missing_String))
OPTIONS.append(
objectify.Element("DefaultMolFormat",
value=self.DefaultMolFormat))
OPTIONS.append(
objectify.Element("HelpBrowser", value=self.HelpBrowser))
OPTIONS.append(
objectify.Element("RejectUnusualValence",
value=bool_formatter(
self.RejectUnusualValence)))
OPTIONS.append(
objectify.Element("Add2DHydrogens",
value=bool_formatter(
self.Add2DHydrogens)))
OPTIONS.append(
objectify.Element("MaxSRforAllCircuit",
value=self.MaxSRforAllCircuit))
OPTIONS.append(objectify.Element("MaxSR", value=self.MaxSR))
OPTIONS.append(
objectify.Element("MaxSRDetour", value=self.MaxSRDetour))
OPTIONS.append(
objectify.Element("MaxAtomWalkPath",
value=self.MaxAtomWalkPath))
OPTIONS.append(
objectify.Element("LogPathWalk",
value=bool_formatter(self.LogPathWalk)))
OPTIONS.append(
objectify.Element("LogEdge",
value=bool_formatter(self.LogEdge)))
Weights = objectify.SubElement(OPTIONS, "Weights")
for weight in self.Weights:
if weight not in [
"Mass", "VdWVolume", "Electronegativity",
"Polarizability", "Ionization", "I-State"
]:
msg = "'%s' is not a valid weight type." % weight
raise ValueError(msg)
Weights.append(objectify.Element('weight', name=weight))
OPTIONS.append(
objectify.Element("SaveOnlyData",
value=bool_formatter(self.SaveOnlyData)))
OPTIONS.append(
objectify.Element("SaveLabelsOnSeparateFile",
value=bool_formatter(
self.SaveLabelsOnSeparateFile)))
OPTIONS.append(
objectify.Element("SaveFormatBlock",
value=self.SaveFormatBlock))
OPTIONS.append(
objectify.Element("SaveFormatSubBlock",
value=self.SaveFormatSubBlock))
OPTIONS.append(
objectify.Element("SaveExcludeMisVal",
value=bool_formatter(
self.SaveExcludeMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeAllMisVal",
value=bool_formatter(
self.SaveExcludeAllMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeConst",
value=bool_formatter(
self.SaveExcludeConst)))
OPTIONS.append(
objectify.Element("SaveExcludeNearConst",
value=bool_formatter(
self.SaveExcludeNearConst)))
OPTIONS.append(
objectify.Element("SaveExcludeStdDev",
value=bool_formatter(
self.SaveExcludeStdDev)))
OPTIONS.append(
objectify.Element("SaveStdDevThreshold",
value=self.SaveStdDevThreshold))
OPTIONS.append(
objectify.Element("SaveExcludeCorrelated",
value=bool_formatter(
self.SaveExcludeCorrelated)))
OPTIONS.append(
objectify.Element("SaveCorrThreshold",
value=self.SaveCorrThreshold))
OPTIONS.append(
objectify.Element(
"SaveExclusionOptionsToVariables",
value=bool_formatter(
self.SaveExclusionOptionsToVariables)))
OPTIONS.append(
objectify.Element("SaveExcludeMisMolecules",
value=bool_formatter(
self.SaveExcludeMisMolecules)))
OPTIONS.append(
objectify.Element("SaveExcludeRejectedMolecules",
value=bool_formatter(
self.SaveExcludeRejectedMolecules)))
DESCRIPTORS = objectify.SubElement(self.dragon, "DESCRIPTORS")
for i in self.blocks:
if i < 1 or i > 29:
msg = "block id must be in range 1 to 29."
raise ValueError(msg)
DESCRIPTORS.append(
objectify.Element('block',
id="%i" % i,
SelectAll="true"))
MOLFILES = objectify.SubElement(self.dragon, "MOLFILES")
MOLFILES.append(
objectify.Element("molInput", value=self.molInput))
# if self.molInput == "stdin":
# if self.molInputFormat not in ['SYBYL', 'MDL', 'HYPERCHEM', 'SMILES', 'MACROMODEL']:
# msg = "'%s' is not a valid molInputFormat. Formats:['SYBYL','MDL','HYPERCHEM','SMILES','MACROMODEL']" % self.molInputFormat
# raise ValueError(msg)
# MOLFILES.append(objectify.Element("molInputFormat", value=self.molInputFormat))
if self.molInput == "file":
if isinstance(self.molFile, dict):
for f in range(1, len(self.molFile) + 1):
MOLFILES.append(
objectify.Element(
"molFile", value=self.molFile[f]['file']))
elif isinstance(self.molFile, str):
MOLFILES.append(
objectify.Element("molFile", value=self.molFile))
else:
msg = 'Variable molInput can be either a string or a list'
raise ValueError(msg)
else:
msg = "The molInput value must be 'file'. 'stdin' is not supported through ChemML"
raise ValueError(msg)
OUTPUT = objectify.SubElement(self.dragon, "OUTPUT")
OUTPUT.append(
objectify.Element("SaveStdOut",
value=bool_formatter(self.SaveStdOut)))
OUTPUT.append(
objectify.Element("SaveProject",
value=bool_formatter(self.SaveProject)))
if self.SaveProject:
OUTPUT.append(
objectify.Element("SaveProjectFile",
value=self.SaveProjectFile))
OUTPUT.append(
objectify.Element("SaveFile",
value=bool_formatter(self.SaveFile)))
if self.SaveFile:
OUTPUT.append(
objectify.Element("SaveType", value=self.SaveType)
) # value = "[singlefile/block/subblock]"
OUTPUT.append(
objectify.Element("SaveFilePath",
value=self.output_directory +
self.SaveFilePath)
) #Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.
OUTPUT.append(objectify.Element(
"logMode",
value=self.logMode)) # value = [none/stderr/file]
if self.logMode == "file":
OUTPUT.append(
objectify.Element("logFile",
value=self.output_directory +
self.logFile))
if self.external:
EXTERNAL = objectify.SubElement(self.dragon, "EXTERNAL")
EXTERNAL.append(
objectify.Element("fileName", value=self.fileName))
EXTERNAL.append(
objectify.Element("delimiter", value=self.delimiter))
EXTERNAL.append(
objectify.Element("consecutiveDelimiter",
value=bool_formatter(
self.consecutiveDelimiter)))
EXTERNAL.append(
objectify.Element("MissingValue",
value=self.MissingValue))
self._save_script()
elif self.version == 7:
self.dragon = objectify.Element(
"DRAGON",
version="%i.0.0" % self.version,
description="Dragon7 - FP1 - MD5270",
script_version="1",
generation_date=std_datetime_str('date').replace('-', '/'))
OPTIONS = objectify.SubElement(self.dragon, "OPTIONS")
OPTIONS.append(
objectify.Element("CheckUpdates",
value=bool_formatter(self.CheckUpdates)))
OPTIONS.append(
objectify.Element("PreserveTemporaryProjects",
value=bool_formatter(
self.PreserveTemporaryProjects)))
OPTIONS.append(
objectify.Element("SaveLayout",
value=bool_formatter(self.SaveLayout)))
# OPTIONS.append(objectify.Element("ShowWorksheet", value = bool_formatter(self.ShowWorksheet)))
OPTIONS.append(
objectify.Element("Decimal_Separator",
value=self.Decimal_Separator))
if self.Missing_String == "NaN": self.Missing_String = "na"
OPTIONS.append(
objectify.Element("Missing_String",
value=self.Missing_String))
OPTIONS.append(
objectify.Element("DefaultMolFormat",
value=self.DefaultMolFormat))
# OPTIONS.append(objectify.Element("HelpBrowser", value = self.HelpBrowser))
OPTIONS.append(
objectify.Element("RejectDisconnectedStrucuture",
value=bool_formatter(
self.RejectDisconnectedStrucuture)))
OPTIONS.append(
objectify.Element("RetainBiggestFragment",
value=bool_formatter(
self.RetainBiggestFragment)))
OPTIONS.append(
objectify.Element("RejectUnusualValence",
value=bool_formatter(
self.RejectUnusualValence)))
OPTIONS.append(
objectify.Element("Add2DHydrogens",
value=bool_formatter(
self.Add2DHydrogens)))
OPTIONS.append(
objectify.Element(
"DisconnectedCalculationOption",
value=self.DisconnectedCalculationOption))
OPTIONS.append(
objectify.Element("MaxSRforAllCircuit",
value=self.MaxSRforAllCircuit))
# OPTIONS.appendm(objectify.Element("MaxSR", value = self.MaxSR))
OPTIONS.append(
objectify.Element("MaxSRDetour", value=self.MaxSRDetour))
OPTIONS.append(
objectify.Element("MaxAtomWalkPath",
value=self.MaxAtomWalkPath))
OPTIONS.append(
objectify.Element("RoundCoordinates",
value=bool_formatter(
self.RoundCoordinates)))
OPTIONS.append(
objectify.Element("RoundWeights",
value=bool_formatter(self.RoundWeights)))
OPTIONS.append(
objectify.Element("LogPathWalk",
value=bool_formatter(self.LogPathWalk)))
OPTIONS.append(
objectify.Element("LogEdge",
value=bool_formatter(self.LogEdge)))
Weights = objectify.SubElement(OPTIONS, "Weights")
for weight in self.Weights:
if weight not in [
"Mass", "VdWVolume", "Electronegativity",
"Polarizability", "Ionization", "I-State"
]:
msg = "'%s' is not a valid weight type." % weight
raise ValueError(msg)
Weights.append(objectify.Element('weight', name=weight))
OPTIONS.append(
objectify.Element("SaveOnlyData",
value=bool_formatter(self.SaveOnlyData)))
OPTIONS.append(
objectify.Element("SaveLabelsOnSeparateFile",
value=bool_formatter(
self.SaveLabelsOnSeparateFile)))
OPTIONS.append(
objectify.Element("SaveFormatBlock",
value=self.SaveFormatBlock))
OPTIONS.append(
objectify.Element("SaveFormatSubBlock",
value=self.SaveFormatSubBlock))
OPTIONS.append(
objectify.Element("SaveExcludeMisVal",
value=bool_formatter(
self.SaveExcludeMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeAllMisVal",
value=bool_formatter(
self.SaveExcludeAllMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeConst",
value=bool_formatter(
self.SaveExcludeConst)))
OPTIONS.append(
objectify.Element("SaveExcludeNearConst",
value=bool_formatter(
self.SaveExcludeNearConst)))
OPTIONS.append(
objectify.Element("SaveExcludeStdDev",
value=bool_formatter(
self.SaveExcludeStdDev)))
OPTIONS.append(
objectify.Element("SaveStdDevThreshold",
value=self.SaveStdDevThreshold))
OPTIONS.append(
objectify.Element("SaveExcludeCorrelated",
value=bool_formatter(
self.SaveExcludeCorrelated)))
OPTIONS.append(
objectify.Element("SaveCorrThreshold",
value=self.SaveCorrThreshold))
OPTIONS.append(
objectify.Element(
"SaveExclusionOptionsToVariables",
value=bool_formatter(
self.SaveExclusionOptionsToVariables)))
OPTIONS.append(
objectify.Element("SaveExcludeMisMolecules",
value=bool_formatter(
self.SaveExcludeMisMolecules)))
OPTIONS.append(
objectify.Element("SaveExcludeRejectedMolecules",
value=bool_formatter(
self.SaveExcludeRejectedMolecules)))
OPTIONS.append(
objectify.Element("RoundDescriptorValues",
value=bool_formatter(
self.RoundDescriptorValues)))
DESCRIPTORS = objectify.SubElement(self.dragon, "DESCRIPTORS")
for i in self.blocks:
if i < 1 or i > 30:
msg = "block id must be in range 1 to 30."
raise ValueError(msg)
DESCRIPTORS.append(
objectify.Element('block',
id="%i" % i,
SelectAll="true"))
MOLFILES = objectify.SubElement(self.dragon, "MOLFILES")
MOLFILES.append(
objectify.Element("molInput", value=self.molInput))
# if self.molInput == "stdin":
# if self.molInputFormat not in [
# 'SYBYL', 'MDL', 'HYPERCHEM', 'SMILES', 'CML', 'MACROMODEL'
# ]:
# msg = "'%s' is not a valid molInputFormat. Formats:['SYBYL','MDL','HYPERCHEM','SMILES','CML','MACROMODEL']" % self.molInputFormat
# raise ValueError(msg)
# MOLFILES.append(objectify.Element("molInputFormat", value=self.molInputFormat))
if self.molInput == "file":
if isinstance(self.molFile, dict):
for f in range(1, len(self.molFile) + 1):
MOLFILES.append(
objectify.Element(
"molFile", value=self.molFile[f]['file']))
elif isinstance(self.molFile, str):
MOLFILES.append(
objectify.Element("molFile", value=self.molFile))
else:
msg = 'Variable molFile can be either a string or a list'
raise ValueError(msg)
else:
msg = "The molInput value must be 'file'. 'stdin' is not supported through ChemML"
raise ValueError(msg)
OUTPUT = objectify.SubElement(self.dragon, "OUTPUT")
OUTPUT.append(
objectify.Element("knimemode",
value=bool_formatter(self.knimemode)))
OUTPUT.append(
objectify.Element("SaveStdOut",
value=bool_formatter(self.SaveStdOut)))
OUTPUT.append(
objectify.Element("SaveProject",
value=bool_formatter(self.SaveProject)))
if self.SaveProject:
OUTPUT.append(
objectify.Element("SaveProjectFile",
value=self.SaveProjectFile))
OUTPUT.append(
objectify.Element("SaveFile",
value=bool_formatter(self.SaveFile)))
if self.SaveFile:
OUTPUT.append(
objectify.Element("SaveType", value=self.SaveType)
) # value = "[singlefile/block/subblock]"
OUTPUT.append(
objectify.Element("SaveFilePath",
value=self.output_directory +
self.SaveFilePath)
) #Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.
OUTPUT.append(objectify.Element(
"logMode",
value=self.logMode)) # value = [none/stderr/file]
if self.logMode == "file":
OUTPUT.append(
objectify.Element("logFile",
value=self.output_directory +
self.logFile))
if self.external:
EXTERNAL = objectify.SubElement(self.dragon, "EXTERNAL")
EXTERNAL.append(
objectify.Element("fileName", value=self.fileName))
EXTERNAL.append(
objectify.Element("delimiter", value=self.delimiter))
EXTERNAL.append(
objectify.Element("consecutiveDelimiter",
value=bool_formatter(
self.consecutiveDelimiter)))
EXTERNAL.append(
objectify.Element("MissingValue",
value=self.MissingValue))
self._save_script()
else:
doc = etree.parse(script)
self.dragon = etree.tostring(doc) # dragon script : dragon
self.dragon = objectify.fromstring(self.dragon)
objectify.deannotate(self.dragon)
etree.cleanup_namespaces(self.dragon)
if self.dragon.attrib['version'][0] not in ['6', '7']:
msg = "Dragon script is not labeled to the newest vesions of Dragon, 6 or 7. This may causes some problems."
warnings.warn(msg, RuntimeWarning)
mandatory_nodes = ['OPTIONS', 'DESCRIPTORS', 'MOLFILES', 'OUTPUT']
reported_nodes = [
element.tag for element in self.dragon.iterchildren()
]
if not set(reported_nodes).issuperset(set(mandatory_nodes)):
msg = "Dragon script doesn't contain all required nodes, which are:%s" % str(
mandatory_nodes)
raise ValueError(msg)
self.drs = script
self.data_path = self.dragon.OUTPUT.SaveFilePath.attrib['value']
return self
def call(self):
self.refs = {}
for iblock in self.ImpOrder:
task = self.cmls[iblock]['task']
parameters = self.cmls[iblock]['parameters']
host = parameters.pop('host')
function = parameters.pop('function')
start_time = time.time()
tmp_str = "======= block#%i: (%s, %s)" % (iblock + 1, host,
function)
print(tmp_str)
tmp_str = "| run ...\n"
print(tmp_str)
if host == 'sklearn':
# check methods
legal_functions = [
klass[0] for klass in inspect.getmembers(sklw)
]
if function in legal_functions:
self.references(host, function) # check references
self.Base.graph_info[iblock] = (host, function)
cml_interface = [
klass[1] for klass in inspect.getmembers(sklw)
if klass[0] == function
][0]
cmli = cml_interface(self.Base, parameters, iblock, task,
function, host)
cmli.run()
else:
self.references(host, function) # check references
self.Base.graph_info[iblock] = (host, function)
cml_interface = [
klass[1] for klass in inspect.getmembers(sklw)
if klass[0] == 'automatic_run'
][0]
cmli = cml_interface(self.Base, parameters, iblock, task,
function, host)
cmli.run()
elif host == 'chemml':
# check methods
legal_functions = [
klass[0] for klass in inspect.getmembers(cmlw)
]
# print("legal_functions: ", legal_functions)
if function not in legal_functions:
msg = "@function #%i: couldn't find function '%s' in the module '%s' wrapper" % (
iblock, function, host)
raise NameError(msg)
self.references(host, function) # check references
self.Base.graph_info[iblock] = (host, function)
cml_interface = [
klass[1] for klass in inspect.getmembers(cmlw)
if klass[0] == function
][0]
cmli = cml_interface(self.Base, parameters, iblock, task,
function, host)
cmli.run()
elif host == 'pandas':
# check methods
legal_functions = [
klass[0] for klass in inspect.getmembers(pdw)
]
if function not in legal_functions:
msg = "@function #%i: couldn't find function '%s' in the module '%s' wrarpper" % (
iblock, function, host)
raise NameError(msg)
self.references(host, function) # check references
self.Base.graph_info[iblock] = (host, function)
cml_interface = [
klass[1] for klass in inspect.getmembers(pdw)
if klass[0] == function
][0]
cmli = cml_interface(self.Base, parameters, iblock, task,
function, host)
cmli.run()
elif host == 'tensorflow':
# check methods
legal_functions = [
klass[0] for klass in inspect.getmembers(tfw)
]
if function not in legal_functions:
msg = "@function #%i: couldn't find function '%s' in the module '%s' wrarpper" % (
iblock, function, host)
raise NameError(msg)
self.references(host, function) # check references
self.Base.graph_info[iblock] = (host, function)
cml_interface = [
klass[1] for klass in inspect.getmembers(tfw)
if klass[0] == function
][0]
cmli = cml_interface(self.Base, parameters, iblock, task,
function, host)
cmli.run()
end_time = tot_exec_time_str(start_time)
tmp_str = "| ... done!"
print(tmp_str)
tmp_str = '| ' + end_time
print(tmp_str)
tmp_str = "=======\n\n"
print(tmp_str)
self._save_references()
tmp_str = "Total " + tot_exec_time_str(self.Base.start_time)
print(tmp_str)
tmp_str = std_datetime_str() + '\n'
print(tmp_str)
def _script_wizard(self, input_mol_list, input_mol_type):
"""
The script_wizard is designed to build a Dragon script file. The name and
the functionality of this function is the same as available Script wizard
in the Dragon Graphic User Interface.
Note: All reported nodes are mandatory, except the <EXTERNAL> tag
Note: Script for version 7 doesn't support fingerprints block
Parameters
----------
input_mol_list : list
if SMILES, list contains only 1 element -- path to one SMILES file
if mol2, list of '.mol2' file paths
input_mol_type: str
Input molecule type: either 'mol2' or 'smiles'
output_directory : string, optional (default = './')
the path to the working directory to store output files.
"""
self.dragon = objectify.Element(
"DRAGON",
version="%i.0.0" % self.version,
description="Dragon7 - FP1 - MD5270",
script_version="1",
generation_date=std_datetime_str('date').replace('-', '/'))
OPTIONS = objectify.SubElement(self.dragon, "OPTIONS")
OPTIONS.append(
objectify.Element("CheckUpdates",
value=bool_formatter(self.CheckUpdates)))
OPTIONS.append(
objectify.Element("PreserveTemporaryProjects",
value=bool_formatter(
self.PreserveTemporaryProjects)))
OPTIONS.append(
objectify.Element("SaveLayout",
value=bool_formatter(self.SaveLayout)))
# OPTIONS.append(objectify.Element("ShowWorksheet", value = bool_formatter(self.ShowWorksheet)))
OPTIONS.append(
objectify.Element("Decimal_Separator",
value=self.Decimal_Separator))
if self.Missing_String == "NaN": self.Missing_String = "na"
OPTIONS.append(
objectify.Element("Missing_String", value=self.Missing_String))
OPTIONS.append(
objectify.Element("DefaultMolFormat", value=self.DefaultMolFormat))
# OPTIONS.append(objectify.Element("HelpBrowser", value = self.HelpBrowser))
OPTIONS.append(
objectify.Element("RejectDisconnectedStrucuture",
value=bool_formatter(
self.RejectDisconnectedStrucuture)))
OPTIONS.append(
objectify.Element("RetainBiggestFragment",
value=bool_formatter(
self.RetainBiggestFragment)))
OPTIONS.append(
objectify.Element("RejectUnusualValence",
value=bool_formatter(self.RejectUnusualValence)))
OPTIONS.append(
objectify.Element("Add2DHydrogens",
value=bool_formatter(self.Add2DHydrogens)))
OPTIONS.append(
objectify.Element("DisconnectedCalculationOption",
value=self.DisconnectedCalculationOption))
OPTIONS.append(
objectify.Element("MaxSRforAllCircuit",
value=self.MaxSRforAllCircuit))
# OPTIONS.appendm(objectify.Element("MaxSR", value = self.MaxSR))
OPTIONS.append(objectify.Element("MaxSRDetour",
value=self.MaxSRDetour))
OPTIONS.append(
objectify.Element("MaxAtomWalkPath", value=self.MaxAtomWalkPath))
OPTIONS.append(
objectify.Element("RoundCoordinates",
value=bool_formatter(self.RoundCoordinates)))
OPTIONS.append(
objectify.Element("RoundWeights",
value=bool_formatter(self.RoundWeights)))
OPTIONS.append(
objectify.Element("LogPathWalk",
value=bool_formatter(self.LogPathWalk)))
OPTIONS.append(
objectify.Element("LogEdge", value=bool_formatter(self.LogEdge)))
Weights = objectify.SubElement(OPTIONS, "Weights")
for weight in self.Weights:
if weight not in [
"Mass", "VdWVolume", "Electronegativity", "Polarizability",
"Ionization", "I-State"
]:
msg = "'%s' is not a valid weight type." % weight
raise ValueError(msg)
Weights.append(objectify.Element('weight', name=weight))
OPTIONS.append(
objectify.Element("SaveOnlyData",
value=bool_formatter(self.SaveOnlyData)))
OPTIONS.append(
objectify.Element("SaveLabelsOnSeparateFile",
value=bool_formatter(
self.SaveLabelsOnSeparateFile)))
OPTIONS.append(
objectify.Element("SaveFormatBlock", value=self.SaveFormatBlock))
OPTIONS.append(
objectify.Element("SaveFormatSubBlock",
value=self.SaveFormatSubBlock))
OPTIONS.append(
objectify.Element("SaveExcludeMisVal",
value=bool_formatter(self.SaveExcludeMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeAllMisVal",
value=bool_formatter(self.SaveExcludeAllMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeConst",
value=bool_formatter(self.SaveExcludeConst)))
OPTIONS.append(
objectify.Element("SaveExcludeNearConst",
value=bool_formatter(self.SaveExcludeNearConst)))
OPTIONS.append(
objectify.Element("SaveExcludeStdDev",
value=bool_formatter(self.SaveExcludeStdDev)))
OPTIONS.append(
objectify.Element("SaveStdDevThreshold",
value=self.SaveStdDevThreshold))
OPTIONS.append(
objectify.Element("SaveExcludeCorrelated",
value=bool_formatter(
self.SaveExcludeCorrelated)))
OPTIONS.append(
objectify.Element("SaveCorrThreshold",
value=self.SaveCorrThreshold))
OPTIONS.append(
objectify.Element("SaveExclusionOptionsToVariables",
value=bool_formatter(
self.SaveExclusionOptionsToVariables)))
OPTIONS.append(
objectify.Element("SaveExcludeMisMolecules",
value=bool_formatter(
self.SaveExcludeMisMolecules)))
OPTIONS.append(
objectify.Element("SaveExcludeRejectedMolecules",
value=bool_formatter(
self.SaveExcludeRejectedMolecules)))
OPTIONS.append(
objectify.Element("RoundDescriptorValues",
value=bool_formatter(
self.RoundDescriptorValues)))
DESCRIPTORS = objectify.SubElement(self.dragon, "DESCRIPTORS")
for i in self.blocks:
if i < 1 or i > 30:
msg = "block id must be in range 1 to 30."
raise ValueError(msg)
DESCRIPTORS.append(
objectify.Element('block', id="%i" % i, SelectAll="true"))
MOLFILES = objectify.SubElement(self.dragon, "MOLFILES")
MOLFILES.append(objectify.Element("molInput", value="file"))
# if self.molInput == "stdin":
# if self.molInputFormat not in [
# 'SYBYL', 'MDL', 'HYPERCHEM', 'SMILES', 'CML', 'MACROMODEL'
# ]:
# msg = "'%s' is not a valid molInputFormat. Formats:['SYBYL','MDL','HYPERCHEM','SMILES','CML','MACROMODEL']" % self.molInputFormat
# raise ValueError(msg)
# MOLFILES.append(objectify.Element("molInputFormat", value=self.molInputFormat))
if input_mol_type == 'mol2':
for mol2 in input_mol_list:
MOLFILES.append(objectify.Element("molFile", value=mol2))
else:
MOLFILES.append(
objectify.Element("molFile", value=input_mol_list[0]))
# if isinstance(self.molFile, dict):
# for f in range(1, len(self.molFile) + 1):
# if os.path.exists(self.molFile[f]['file']):
# MOLFILES.append(objectify.Element("molFile", value=self.molFile[f]['file']))
# else:
# msg = "file not found at "+ self.molFile[f]['file']
# raise FileNotFoundError(msg)
# elif isinstance(self.molFile, str):
# MOLFILES.append(objectify.Element("molFile", value=self.molFile))
# else:
# msg = 'Variable molFile can be either a string or a list'
# raise ValueError(msg)
OUTPUT = objectify.SubElement(self.dragon, "OUTPUT")
OUTPUT.append(
objectify.Element("knimemode",
value=bool_formatter(self.knimemode)))
OUTPUT.append(
objectify.Element("SaveStdOut",
value=bool_formatter(self.SaveStdOut)))
OUTPUT.append(
objectify.Element("SaveProject",
value=bool_formatter(self.SaveProject)))
if self.SaveProject:
OUTPUT.append(
objectify.Element("SaveProjectFile",
value=self.SaveProjectFile))
OUTPUT.append(
objectify.Element("SaveFile", value=bool_formatter(self.SaveFile)))
if self.SaveFile:
OUTPUT.append(objectify.Element(
"SaveType",
value=self.SaveType)) # value = "[singlefile/block/subblock]"
OUTPUT.append(
objectify.Element("SaveFilePath",
value=self.output_directory +
self.SaveFilePath)
) #Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.
OUTPUT.append(objectify.Element(
"logMode", value=self.logMode)) # value = [none/stderr/file]
if self.logMode == "file":
OUTPUT.append(
objectify.Element("logFile",
value=self.output_directory + self.logFile))
if self.external:
EXTERNAL = objectify.SubElement(self.dragon, "EXTERNAL")
EXTERNAL.append(objectify.Element("fileName", value=self.fileName))
EXTERNAL.append(
objectify.Element("delimiter", value=self.delimiter))
EXTERNAL.append(
objectify.Element("consecutiveDelimiter",
value=bool_formatter(
self.consecutiveDelimiter)))
EXTERNAL.append(
objectify.Element("MissingValue", value=self.MissingValue))
# objectify.deannotate(self.dragon)
etree.cleanup_namespaces(self.dragon)
self.drs_name = 'Dragon_script.drs'
with open(os.path.join(self.output_directory, self.drs_name),
'w') as outfile:
outfile.write(
etree.tostring(self.dragon, pretty_print=True).decode())
self.data_path = self.dragon.OUTPUT.SaveFilePath.attrib['value']
return self
