diff --git a/phasecalculator/analysis/fgipanalysis.py b/phasecalculator/analysis/fgipanalysis.py
index 47f739fc67caebb08a820f897360112fb17c5178..fb1ebec73ed27247ec4e0ca108b3b0af08956e7b 100755
--- a/phasecalculator/analysis/fgipanalysis.py
+++ b/phasecalculator/analysis/fgipanalysis.py
@@ -139,7 +139,9 @@ def create_solvation_plots_from_poly_files(
plot_outputs = []
filename_list = []
directory = kwargs.get("directory", "")
- frac_occ_inf_dict = solvmapgen.fractionaloccupancycalculator.read_fractional_occupancy_information(frac_occ_filename)
+ frac_occ_inf_dict = solvmapgen.fractionaloccupancycalculator.read_fractional_occupancy_information(
+ frac_occ_filename
+ )
for polynomial_filename in polynomial_filename_list:
LOGGER.info("polynomial_filename:")
LOGGER.info(polynomial_filename)
diff --git a/phasecalculator/analysis/vleanalysis.py b/phasecalculator/analysis/vleanalysis.py
index a92e978bf6556862d80a7a7cbcbb187c2f7980e6..f521c539dbcfec5d6b6e53c94cb10964c78f9d1a 100755
--- a/phasecalculator/analysis/vleanalysis.py
+++ b/phasecalculator/analysis/vleanalysis.py
@@ -28,6 +28,7 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
+
def process_vle_data(phase_filename, csv_filename):
"""Process phase XML and write to csv file.
@@ -45,7 +46,8 @@ def process_vle_data(phase_filename, csv_filename):
"""
mixture_dict = read_data_from_mixtures(phase_filename)
mixture_info_list = convert_mixture_container_dict_to_list(mixture_dict)
- write_data_to_csv(mixture_info_list,csv_filename)
+ write_data_to_csv(mixture_info_list, csv_filename)
+
def write_data_to_csv(mixture_info_list, csv_filename):
"""Write data to csv file.
@@ -63,11 +65,17 @@ def write_data_to_csv(mixture_info_list, csv_filename):
"""
with open(csv_filename, "w") as outfile:
- csvwriter = csv.writer(outfile, delimiter="\t",lineterminator="\n")
- header_row = ['solvent_id', 'temperature', "phase type",'concentrations[name, value]']
+ csvwriter = csv.writer(outfile, delimiter="\t", lineterminator="\n")
+ header_row = [
+ "solvent_id",
+ "temperature",
+ "phase type",
+ "concentrations[name, value]",
+ ]
csvwriter.writerow(header_row)
csvwriter.writerows(mixture_info_list)
+
def convert_mixture_container_dict_to_list(mixture_container_dict):
"""Convert mixture dictionary to list of lists
@@ -87,8 +95,8 @@ def convert_mixture_container_dict_to_list(mixture_container_dict):
for phase_id, phase_dict in mixture.items():
phase_list_container.append(convert_phase_dict_to_list(phase_dict))
return phase_list_container
-
-
+
+
def convert_phase_dict_to_list(phase_dict):
"""Convert phase dictionary to list for output.
@@ -103,18 +111,18 @@ def convert_phase_dict_to_list(phase_dict):
List of information for output to file.
"""
- phase_list = [
+ phase_list = [
phase_dict["solvent_id"],
phase_dict["temperature_value"],
phase_dict["phase_type"],
- ]
-
- for inchikey, mol_dict in phase_dict['concentrations'].items():
- phase_list += [inchikey, "{:.10f}".format(mol_dict["concentration_value"]) ]
-
+ ]
+
+ for inchikey, mol_dict in phase_dict["concentrations"].items():
+ phase_list += [inchikey, "{:.10f}".format(mol_dict["concentration_value"])]
+
return phase_list
-
-
+
+
def read_data_from_mixtures(vle_filename):
"""Read Mixture XML.
@@ -129,4 +137,4 @@ def read_data_from_mixtures(vle_filename):
Summary of phase concentration information.
"""
- return mixparser.parse_mixture_file(vle_filename)
\ No newline at end of file
+ return mixparser.parse_mixture_file(vle_filename)
diff --git a/phasecalculator/classes/outputinformation.py b/phasecalculator/classes/outputinformation.py
index 92888b18a101f888f1bec2195b2499e571fe7ec6..d1a66117b36dd2fe64fe53debf7fbb68c3b0a6eb 100755
--- a/phasecalculator/classes/outputinformation.py
+++ b/phasecalculator/classes/outputinformation.py
@@ -104,9 +104,10 @@ class OutputInformation(object):
"""
fgip_output = OutputInformation.parse_fgip_output(output_xml)
- similarity_output, similarity_output_type = OutputInformation.parse_similarity_output(
- output_xml
- )
+ (
+ similarity_output,
+ similarity_output_type,
+ ) = OutputInformation.parse_similarity_output(output_xml)
vle_output = OutputInformation.parse_vle_output(output_xml)
return OutputInformation(
fgip_output, similarity_output, similarity_output_type, vle_output
diff --git a/phasecalculator/classes/phase.py b/phasecalculator/classes/phase.py
index 41ee8f2537c7cc0846425c6f04c352bbafd7483f..4f5cbecf2e1e555d69e2e444c7c07dd9a0b6d18a 100755
--- a/phasecalculator/classes/phase.py
+++ b/phasecalculator/classes/phase.py
@@ -160,7 +160,7 @@ class Phase(object):
molefraction_total = 0.0
for mole_frac in self.get_molefractions_by_molecule().values():
molefraction_total += mole_frac
- return (abs(1.0-molefraction_total) < 1e-5)
+ return abs(1.0 - molefraction_total) < 1e-5
def write_to_xml(self):
"""Write information to Etree representation of XML.
@@ -203,7 +203,7 @@ class Phase(object):
"""
return [molecule.ssip_file_loc for molecule in self.molecule_list]
-
+
def get_name_inchikey_map(self):
"""Get the name inchikey mapping for all molecules in the phases.
diff --git a/phasecalculator/classes/phases.py b/phasecalculator/classes/phases.py
index 6b04fed7c68a064ed1185fae9fb22f16f6af00e7..b5cbcb6065c2a265e6b268468dbe091bc69eddf9 100755
--- a/phasecalculator/classes/phases.py
+++ b/phasecalculator/classes/phases.py
@@ -181,7 +181,7 @@ class Phases(object):
for phase in self.phase_list:
ssip_file_locations.extend(phase.get_ssip_file_locations())
return set(ssip_file_locations)
-
+
def get_name_inchikey_map(self):
"""Get the name inchikey mapping for all molecules in the phases.
@@ -194,4 +194,4 @@ class Phases(object):
name_inchikey_map = {}
for phase in self.phase_list:
name_inchikey_map.update(phase.get_name_inchikey_map())
- return name_inchikey_map
\ No newline at end of file
+ return name_inchikey_map
diff --git a/phasecalculator/classes/system.py b/phasecalculator/classes/system.py
index a09412c6007221aaeab1555bd936cefecb054074..5242ee26b991d2684a3f82baaaa7b1a4a3352669 100755
--- a/phasecalculator/classes/system.py
+++ b/phasecalculator/classes/system.py
@@ -268,7 +268,7 @@ class System(object):
"""
return self.phases.get_ssip_file_locations()
-
+
def get_name_inchikey_map(self):
"""Get the name inchikey mapping for all molecules in the phases.
diff --git a/phasecalculator/io/phasecsvconverter.py b/phasecalculator/io/phasecsvconverter.py
index 3430acf865e03e4d8690a728db2876e161c734bd..a46ccb7257e7c2e58b23c508b86279e2e0f1c229 100755
--- a/phasecalculator/io/phasecsvconverter.py
+++ b/phasecalculator/io/phasecsvconverter.py
@@ -37,6 +37,7 @@ NAME_INCHIKEY_MAP = pureinf.get_name_inchikey_mapping()
INCHIKEY_POLARISED_SSIP_FILE_DICT = pureinf.get_ssip_file_dict()
INCHIKEY_UNPOLARISED_SSIP_FILE_DICT = pureinf.get_unpolarised_ssip_file_dict()
+
def convert_csv_file_to_phases(csv_filename, unpolarised_ssips):
"""Read CSV file and convert contents to Phases.
diff --git a/phasecalculator/phasecalculatorcli.py b/phasecalculator/phasecalculatorcli.py
index 643ca11fbd0d322bb30ccd82c4d0eb0d7b9619ec..6f5dd2e44cce0dea49133550622f6670e01ee428 100755
--- a/phasecalculator/phasecalculatorcli.py
+++ b/phasecalculator/phasecalculatorcli.py
@@ -254,6 +254,7 @@ def run_system_collection(system_collection, **kwargs):
for system_info in system_collection.system_list:
phasecrun.run_all_analysis(system_info, **kwargs)
+
def get_acceptable_solvent_names():
"""Get Acceptable solvent names.
@@ -265,7 +266,8 @@ def get_acceptable_solvent_names():
"""
solvent_names = pureinf.get_name_inchikey_mapping().keys()
return "\n".join(solvent_names)
-
+
+
def solvent_names(args):
"""Output solvent names by using a logger.
@@ -276,6 +278,7 @@ def solvent_names(args):
"""
INFO_LOGGER.info("Solvent names:\n%s", get_acceptable_solvent_names())
+
def create_phasecalculator_argparser():
"""Create Argument parser for Phasecalculator module.
@@ -296,11 +299,13 @@ similarity and VLE analysis for solvents."""
subparsers = phase_argparser.add_subparsers(title="commands", dest="command")
calc_description = """Calculation runner based on input System XML."""
- calc_epilog = textwrap.dedent("""Example Usage:
+ calc_epilog = textwrap.dedent(
+ """Example Usage:
python -m phasecalculator calculate -f systemcollection.xml
-Where systemcollection.xml was generated with inpgen. For large phase sets you need to set memreq to match your current hardware limit.""")
+Where systemcollection.xml was generated with inpgen. For large phase sets you need to set memreq to match your current hardware limit."""
+ )
calc_argparser = subparsers.add_parser(
"calculate",
@@ -326,13 +331,15 @@ Where systemcollection.xml was generated with inpgen. For large phase sets you n
calc_argparser.set_defaults(func=process_phasecalculator)
inpgen_description = """Input SystemCollection XML generation."""
- inpgen_epilog = textwrap.dedent("""\
+ inpgen_epilog = textwrap.dedent(
+ """\
Example usage:
python -m phasecalculator inpgen -p $CONDA_PREFIX/lib/python3.7/site-packages/phasecalculator/test/resources/examplephasecomp.csv -f -j PATH_TO_JAR
Where PATH_TO_JAR is replaced with the SSIP phasetransfer jar file location.
-""")
+"""
+ )
inpgen_argparser = subparsers.add_parser(
"inpgen",
@@ -372,17 +379,29 @@ Where systemcollection.xml was generated with inpgen. For large phase sets you n
"-v", "--vle", action="store_true", help="Calculate VLE for input solvents"
)
inpgen_argparser.add_argument(
- "--filename", type=str, default="systemcollection.xml",
+ "--filename",
+ type=str,
+ default="systemcollection.xml",
help="filename for XML file.",
)
ssip_desc = inpgen_argparser.add_mutually_exclusive_group(required=False)
- ssip_desc.add_argument("--polarised", action="store_false", dest="unpolarised_ssips",
- help="Use unpolarised SSIP descriptions in calculations")
- ssip_desc.add_argument("--unpolarised", action="store_true", dest="unpolarised_ssips",
- help="Use polarised SSIP descriptions in calculations")
+ ssip_desc.add_argument(
+ "--polarised",
+ action="store_false",
+ dest="unpolarised_ssips",
+ help="Use unpolarised SSIP descriptions in calculations",
+ )
+ ssip_desc.add_argument(
+ "--unpolarised",
+ action="store_true",
+ dest="unpolarised_ssips",
+ help="Use polarised SSIP descriptions in calculations",
+ )
inpgen_argparser.set_defaults(func=process_inputgen, unpolarised_ssips=False)
solvname_description = """Display acceptable solvent molecule names for inclusion in a phases csv file."""
- solvnames_epilog = "Solvent molecule names:\n" + get_acceptable_solvent_names() + "\n"
+ solvnames_epilog = (
+ "Solvent molecule names:\n" + get_acceptable_solvent_names() + "\n"
+ )
solvent_nameparser = subparsers.add_parser(
"solventnames",
description=solvname_description,
diff --git a/phasecalculator/runners/fgipanalysisrunner.py b/phasecalculator/runners/fgipanalysisrunner.py
index c0cd7ab92480c0f8443c7a31a927b03c62dbeb09..2fd402d82b05c3c54ab20ea40e931cb0a8df2fbb 100755
--- a/phasecalculator/runners/fgipanalysisrunner.py
+++ b/phasecalculator/runners/fgipanalysisrunner.py
@@ -34,7 +34,12 @@ LOGGER.setLevel(logging.WARN)
def calc_energies_and_fgips(
- jar_path, energy_xml_filename, frac_occ_filename, solvent_filename, directory_base, **kwargs
+ jar_path,
+ energy_xml_filename,
+ frac_occ_filename,
+ solvent_filename,
+ directory_base,
+ **kwargs
):
"""Run phasetransfer calculation and generate FGIPs for input solvent.
@@ -68,8 +73,7 @@ def calc_energies_and_fgips(
temperature = kwargs.get("temperature", 298.0)
temperature_unit = kwargs.get("temperature_unit", "KELVIN")
run_binding_energy_calculation(
- jar_path, energy_xml_filename, frac_occ_filename,
- solvent_filename, **kwargs
+ jar_path, energy_xml_filename, frac_occ_filename, solvent_filename, **kwargs
)
directory = generate_directory(directory_base, temperature, temperature_unit)
out_res, polynomial_filename_list = extract_solvents_and_generate_polynomials(
@@ -201,6 +205,5 @@ def run_binding_energy_calculation(
"""
return phaserun.run_phasetransfer_binding_energy(
- jar_path, output_filename, frac_occ_filename,
- solvent_filename, **kwargs
+ jar_path, output_filename, frac_occ_filename, solvent_filename, **kwargs
)
diff --git a/phasecalculator/runners/phasecalculatorrunner.py b/phasecalculator/runners/phasecalculatorrunner.py
index 1fd76f4aaa12f10589d41debddbaed9715065d3f..4d15429f1eefd677e044f07c1ade175dac2d15f8 100755
--- a/phasecalculator/runners/phasecalculatorrunner.py
+++ b/phasecalculator/runners/phasecalculatorrunner.py
@@ -189,12 +189,12 @@ def run_vle_analysis(system_info, phase_filename, **kwargs):
"""
jar_path = system_info.runtime_information.phasetransfer_jar
phase_output_filename = create_phase_output_filename(phase_filename)
- csv_filename = create_phase_summary_filename(system_info.runtime_information.output_dir,
- phase_filename)
+ csv_filename = create_phase_summary_filename(
+ system_info.runtime_information.output_dir, phase_filename
+ )
create_output_dir(system_info)
vlerun.calculate_and_process_vle_data(
- jar_path, phase_filename, phase_output_filename,
- csv_filename, **kwargs
+ jar_path, phase_filename, phase_output_filename, csv_filename, **kwargs
)
@@ -215,6 +215,7 @@ def create_output_dir(system_info):
output_path.mkdir(parents=True, exist_ok=True)
return output_path.as_posix()
+
def create_phase_summary_filename(output_dir, phase_filename):
"""Create phase summary CSV filename.
@@ -231,8 +232,11 @@ def create_phase_summary_filename(output_dir, phase_filename):
CSV filename.
"""
- summary_filename = phase_filename.split("/")[-1].replace(".xml", "calculation_summary.csv")
- return (pathlib.Path(output_dir) /summary_filename).as_posix()
+ summary_filename = phase_filename.split("/")[-1].replace(
+ ".xml", "calculation_summary.csv"
+ )
+ return (pathlib.Path(output_dir) / summary_filename).as_posix()
+
def create_free_energy_output_filename(solvent_filename):
"""Create free energy filename for solvent file.
@@ -284,6 +288,7 @@ def create_fractional_occupancy_filename(solvent_filename):
"""
return solvent_filename.replace(".xml", "_fracocc.xml")
+
def create_phase_output_filename(phase_filename):
"""Create phase output filename.
diff --git a/phasecalculator/runners/phasetransferrunner.py b/phasecalculator/runners/phasetransferrunner.py
index d339996745a241515d2b6dcb899340d973b43400..a0bd752324f6822d05164127b0d42380b34935af 100755
--- a/phasecalculator/runners/phasetransferrunner.py
+++ b/phasecalculator/runners/phasetransferrunner.py
@@ -264,8 +264,7 @@ def generate_phasetransfer_binding_args(
"""
jar_args = make_java_arguments(jar_path, memory_req=kwargs.pop("memory_req", None))
- binding_args = ["--energies", "solvationbinding",
- "-f", frac_occ_filename ]
+ binding_args = ["--energies", "solvationbinding", "-f", frac_occ_filename]
solvent_args = generate_solvent_calc_args(
output_filename, solvent_filename, **kwargs
)
diff --git a/phasecalculator/runners/phasexmlcreatorrunner.py b/phasecalculator/runners/phasexmlcreatorrunner.py
index c6c4a5cd1085ed8e7d474ad923d72f8322f0e956..1d2cb7a9a88a043fa9e5679b89c934ab164e4e13 100755
--- a/phasecalculator/runners/phasexmlcreatorrunner.py
+++ b/phasecalculator/runners/phasexmlcreatorrunner.py
@@ -55,20 +55,32 @@ def create_phase_and_solvent_files(system_info, filestem="system", **kwargs):
"""
create_scratch_dir(system_info)
- name_inchikey_map = kwargs.pop("name_inchikey_map", system_info.get_name_inchikey_map())
+ name_inchikey_map = kwargs.pop(
+ "name_inchikey_map", system_info.get_name_inchikey_map()
+ )
phase_file = None
solvent_list = None
- LOGGER.info("System calcs: VLE: %s, FGIP: %s, SIM: %s", system_info.calc_vle(),
- system_info.calc_fgip(), system_info.calc_similarity())
+ LOGGER.info(
+ "System calcs: VLE: %s, FGIP: %s, SIM: %s",
+ system_info.calc_vle(),
+ system_info.calc_fgip(),
+ system_info.calc_similarity(),
+ )
if system_info.calc_vle():
- phase_file = create_phase_file(system_info, filestem + "phase",
- name_inchikey_map=name_inchikey_map,
- **kwargs)
+ phase_file = create_phase_file(
+ system_info,
+ filestem + "phase",
+ name_inchikey_map=name_inchikey_map,
+ **kwargs
+ )
if system_info.calc_fgip() or system_info.calc_similarity():
LOGGER.info("Creating solvents")
- solvent_list = create_solvent_files(system_info, filestem + "solvent",
- name_inchikey_map=name_inchikey_map,
- **kwargs)
+ solvent_list = create_solvent_files(
+ system_info,
+ filestem + "solvent",
+ name_inchikey_map=name_inchikey_map,
+ **kwargs
+ )
return phase_file, solvent_list
diff --git a/phasecalculator/runners/vleanalysisrunner.py b/phasecalculator/runners/vleanalysisrunner.py
index 801460a6a7ad9817d55e87a8f9ff05e5680e88ad..0d3a89cc200f70063c8fb0cf8ba28dfff07ee21c 100755
--- a/phasecalculator/runners/vleanalysisrunner.py
+++ b/phasecalculator/runners/vleanalysisrunner.py
@@ -28,7 +28,10 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def calculate_and_process_vle_data(jar_path, phase_filename, phase_output_filename, csv_filename, **kwargs):
+
+def calculate_and_process_vle_data(
+ jar_path, phase_filename, phase_output_filename, csv_filename, **kwargs
+):
"""Calculate and process VLE data.
Parameters
@@ -76,6 +79,7 @@ def process_vle_data(calculated_phase_filename, csv_filename):
"""
return vleanalysis.process_vle_data(calculated_phase_filename, csv_filename)
+
def run_vle_calculation(jar_path, phase_filename, output_filename, **kwargs):
"""Run VLE phase calculation.
diff --git a/phasecalculator/test/analysistest/fgipanalysis_test.py b/phasecalculator/test/analysistest/fgipanalysis_test.py
index e17048715fca69af19694cf7b6eb27e6e268c54b..a251fdc044fffb94910f844d9bbb1046fb4546f6 100755
--- a/phasecalculator/test/analysistest/fgipanalysis_test.py
+++ b/phasecalculator/test/analysistest/fgipanalysis_test.py
@@ -85,7 +85,10 @@ class FGIPAnalysisTestCase(unittest.TestCase):
\label{fig:1-butanol0_164528302water0_835471698solvationmap}
\end{figure}
"""
- self.frac_occ_inf_dict = fgipanalysis.solvmapgen.fractionaloccupancycalculator.read_fractional_occupancy_information(self.frac_occ_filename)
+ self.frac_occ_inf_dict = fgipanalysis.solvmapgen.fractionaloccupancycalculator.read_fractional_occupancy_information(
+ self.frac_occ_filename
+ )
+
def tearDown(self):
"""Clean up after tests.
@@ -156,7 +159,9 @@ class FGIPAnalysisTestCase(unittest.TestCase):
8,
)
self.assertListEqual([(0, 0)], plot_outputs)
- self.assertEqual(["1-butanol0.164528302water0.835471698_solv_map.svg"], filenames)
+ self.assertEqual(
+ ["1-butanol0.164528302water0.835471698_solv_map.svg"], filenames
+ )
self.assertTrue(pathlib.Path(self.matrix_file).is_file())
self.assertTrue(pathlib.Path(self.solvent_map).is_file())
diff --git a/phasecalculator/test/analysistest/vleanalysis_test.py b/phasecalculator/test/analysistest/vleanalysis_test.py
index d58e2692c6afd12c59463fb9c25210caaf9070ab..772265c3c561cc862300adbaf97761268c145665 100755
--- a/phasecalculator/test/analysistest/vleanalysis_test.py
+++ b/phasecalculator/test/analysistest/vleanalysis_test.py
@@ -33,6 +33,7 @@ LOGGER.setLevel(logging.WARN)
class VLEAnalysisTestCase(unittest.TestCase):
"""Test case for VLE analysis methods."""
+
def setUp(self):
"""Set up environment for tests.
@@ -41,7 +42,7 @@ class VLEAnalysisTestCase(unittest.TestCase):
None.
"""
- self.maxDiff=None
+ self.maxDiff = None
parent_directory = pathlib.Path(__file__).parents[1]
self.calculated_phase_file = (
(parent_directory / "resources" / "expected_phasecalculated.xml")
@@ -53,9 +54,14 @@ class VLEAnalysisTestCase(unittest.TestCase):
.absolute()
.as_posix()
)
- self.mixture_info_dict = vleanalysis.read_data_from_mixtures(self.calculated_phase_file)
- self.processed_list = vleanalysis.convert_mixture_container_dict_to_list(self.mixture_info_dict)
+ self.mixture_info_dict = vleanalysis.read_data_from_mixtures(
+ self.calculated_phase_file
+ )
+ self.processed_list = vleanalysis.convert_mixture_container_dict_to_list(
+ self.mixture_info_dict
+ )
self.output_file = "phase_summary.csv"
+
def tearDown(self):
"""Clean up after tests.
@@ -66,6 +72,7 @@ class VLEAnalysisTestCase(unittest.TestCase):
"""
if os.path.isfile(self.output_file):
os.remove(self.output_file)
+
def test_process_vle_data(self):
"""Test expected file is produced.
@@ -80,6 +87,7 @@ class VLEAnalysisTestCase(unittest.TestCase):
with open(self.expected_phas_csv, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
+
def test_write_data_to_csv(self):
"""Test Expected file is produced.
@@ -94,6 +102,7 @@ class VLEAnalysisTestCase(unittest.TestCase):
with open(self.expected_phas_csv, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
+
def test_convert_mixture_container_dict_to_list(self):
"""Test expected list created.
@@ -102,20 +111,29 @@ class VLEAnalysisTestCase(unittest.TestCase):
None.
"""
- expected_list = [['1-butanol0.165water0.835298.000KELVIN',
- 298.0, 'GAS',
- 'LRHPLDYGYMQRHN-UHFFFAOYSA-N',
- '0.0000021914',
- 'XLYOFNOQVPJJNP-UHFFFAOYSA-N',
- '0.0008190888'],
- ['1-butanol0.165water0.835298.000KELVIN',
- 298.0,'CONDENSED',
- 'LRHPLDYGYMQRHN-UHFFFAOYSA-N',
- '4.4440094829',
- 'XLYOFNOQVPJJNP-UHFFFAOYSA-N',
- '30.7036536932']]
+ expected_list = [
+ [
+ "1-butanol0.165water0.835298.000KELVIN",
+ 298.0,
+ "GAS",
+ "LRHPLDYGYMQRHN-UHFFFAOYSA-N",
+ "0.0000021914",
+ "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+ "0.0008190888",
+ ],
+ [
+ "1-butanol0.165water0.835298.000KELVIN",
+ 298.0,
+ "CONDENSED",
+ "LRHPLDYGYMQRHN-UHFFFAOYSA-N",
+ "4.4440094829",
+ "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+ "30.7036536932",
+ ],
+ ]
actual_list = self.processed_list
self.assertListEqual(expected_list, actual_list)
+
def test_convert_phase_dict_to_list(self):
"""Test conversion of phase information.
@@ -124,14 +142,22 @@ class VLEAnalysisTestCase(unittest.TestCase):
None.
"""
- expected_list = ['1-butanol0.165water0.835298.000KELVIN',
- 298.0, 'GAS',
- 'LRHPLDYGYMQRHN-UHFFFAOYSA-N',
- '0.0000021914',
- 'XLYOFNOQVPJJNP-UHFFFAOYSA-N',
- '0.0008190888']
- actual_list = vleanalysis.convert_phase_dict_to_list(self.mixture_info_dict['1-butanol0.165water0.835298.000KELVIN']['1-butanol0.165water0.835298.000KELVINGAS'])
+ expected_list = [
+ "1-butanol0.165water0.835298.000KELVIN",
+ 298.0,
+ "GAS",
+ "LRHPLDYGYMQRHN-UHFFFAOYSA-N",
+ "0.0000021914",
+ "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+ "0.0008190888",
+ ]
+ actual_list = vleanalysis.convert_phase_dict_to_list(
+ self.mixture_info_dict["1-butanol0.165water0.835298.000KELVIN"][
+ "1-butanol0.165water0.835298.000KELVINGAS"
+ ]
+ )
self.assertEqual(expected_list, actual_list)
+
def test_read_data_from_mixtures(self):
"""Test data is read in as expected.
@@ -140,8 +166,42 @@ class VLEAnalysisTestCase(unittest.TestCase):
None.
"""
- expected_dict = {'1-butanol0.165water0.835298.000KELVIN':{'1-butanol0.165water0.835298.000KELVINGAS': {'phase_type': 'GAS', 'temperature_value': 298.0, 'temperature_unit': 'KELVIN', 'solvent_id': '1-butanol0.165water0.835298.000KELVIN', 'concentrations': {'LRHPLDYGYMQRHN-UHFFFAOYSA-N': {'concentration_value': 2.1914464984900333e-06, 'concentration_unit': 'MOLAR'}, 'XLYOFNOQVPJJNP-UHFFFAOYSA-N': {'concentration_value': 0.0008190888071552708, 'concentration_unit': 'MOLAR'}}},
- '1-butanol0.165water0.835298.000KELVINCONDENSED': {'phase_type': 'CONDENSED', 'temperature_value': 298.0, 'temperature_unit': 'KELVIN', 'solvent_id': '1-butanol0.165water0.835298.000KELVIN', 'concentrations': {'LRHPLDYGYMQRHN-UHFFFAOYSA-N': {'concentration_value': 4.444009482942443, 'concentration_unit': 'MOLAR'}, 'XLYOFNOQVPJJNP-UHFFFAOYSA-N': {'concentration_value': 30.70365369323062, 'concentration_unit': 'MOLAR'}}}}}
+ expected_dict = {
+ "1-butanol0.165water0.835298.000KELVIN": {
+ "1-butanol0.165water0.835298.000KELVINGAS": {
+ "phase_type": "GAS",
+ "temperature_value": 298.0,
+ "temperature_unit": "KELVIN",
+ "solvent_id": "1-butanol0.165water0.835298.000KELVIN",
+ "concentrations": {
+ "LRHPLDYGYMQRHN-UHFFFAOYSA-N": {
+ "concentration_value": 2.1914464984900333e-06,
+ "concentration_unit": "MOLAR",
+ },
+ "XLYOFNOQVPJJNP-UHFFFAOYSA-N": {
+ "concentration_value": 0.0008190888071552708,
+ "concentration_unit": "MOLAR",
+ },
+ },
+ },
+ "1-butanol0.165water0.835298.000KELVINCONDENSED": {
+ "phase_type": "CONDENSED",
+ "temperature_value": 298.0,
+ "temperature_unit": "KELVIN",
+ "solvent_id": "1-butanol0.165water0.835298.000KELVIN",
+ "concentrations": {
+ "LRHPLDYGYMQRHN-UHFFFAOYSA-N": {
+ "concentration_value": 4.444009482942443,
+ "concentration_unit": "MOLAR",
+ },
+ "XLYOFNOQVPJJNP-UHFFFAOYSA-N": {
+ "concentration_value": 30.70365369323062,
+ "concentration_unit": "MOLAR",
+ },
+ },
+ },
+ }
+ }
actual_dict = self.mixture_info_dict
LOGGER.debug(actual_dict)
- self.assertDictEqual(expected_dict, actual_dict)
\ No newline at end of file
+ self.assertDictEqual(expected_dict, actual_dict)
diff --git a/phasecalculator/test/classestest/phase_test.py b/phasecalculator/test/classestest/phase_test.py
index f650ece3c85dec8ceffb58b19013c6ea85aec852..1c52cf3a02f7cede71b02b6e0a92e28bda2b15fa 100755
--- a/phasecalculator/test/classestest/phase_test.py
+++ b/phasecalculator/test/classestest/phase_test.py
@@ -138,6 +138,7 @@ class PhaseTestCase(unittest.TestCase):
expected_list = [self.molecule.ssip_file_loc]
actual_list = self.phase.get_ssip_file_locations()
self.assertListEqual(expected_list, actual_list)
+
def test_get_name_inchikey_map(self):
"""Test expected name: inchikey mapping is returned.
@@ -146,6 +147,6 @@ class PhaseTestCase(unittest.TestCase):
None.
"""
- expected_dict = {'water': 'XLYOFNOQVPJJNP-UHFFFAOYSA-N'}
+ expected_dict = {"water": "XLYOFNOQVPJJNP-UHFFFAOYSA-N"}
actual_dict = self.phase.get_name_inchikey_map()
- self.assertDictEqual(expected_dict, actual_dict)
\ No newline at end of file
+ self.assertDictEqual(expected_dict, actual_dict)
diff --git a/phasecalculator/test/classestest/phases_test.py b/phasecalculator/test/classestest/phases_test.py
index 6eb885040bfef44181bf61712e0259acb0b1b373..260a3fb2e38adb66e2ba24f32bce74a0e685ee16 100755
--- a/phasecalculator/test/classestest/phases_test.py
+++ b/phasecalculator/test/classestest/phases_test.py
@@ -145,6 +145,7 @@ class PhasesTestCase(unittest.TestCase):
expected_set = {self.molecule.ssip_file_loc}
actual_set = self.phases.get_ssip_file_locations()
self.assertSetEqual(expected_set, actual_set)
+
def test_get_name_inchikey_map(self):
"""Test expected name: inchikey mapping is returned.
@@ -153,6 +154,6 @@ class PhasesTestCase(unittest.TestCase):
None.
"""
- expected_dict = {'water': 'XLYOFNOQVPJJNP-UHFFFAOYSA-N'}
+ expected_dict = {"water": "XLYOFNOQVPJJNP-UHFFFAOYSA-N"}
actual_dict = self.phases.get_name_inchikey_map()
self.assertDictEqual(expected_dict, actual_dict)
diff --git a/phasecalculator/test/classestest/system_test.py b/phasecalculator/test/classestest/system_test.py
index e02dbeb7e0d42690cb94964c6fae71209700c78e..05cdc35089fb5a7b0fd2335486219e2322e5df84 100755
--- a/phasecalculator/test/classestest/system_test.py
+++ b/phasecalculator/test/classestest/system_test.py
@@ -222,7 +222,7 @@ class SystemTestCase(unittest.TestCase):
expected_set = {self.molecule.ssip_file_loc}
actual_set = self.system.get_ssip_file_locations()
self.assertSetEqual(expected_set, actual_set)
-
+
def test_get_name_inchikey_map(self):
"""Test expected name: inchikey mapping is returned.
@@ -231,7 +231,7 @@ class SystemTestCase(unittest.TestCase):
None.
"""
- expected_dict = {'water': 'XLYOFNOQVPJJNP-UHFFFAOYSA-N'}
+ expected_dict = {"water": "XLYOFNOQVPJJNP-UHFFFAOYSA-N"}
actual_dict = self.system.get_name_inchikey_map()
self.assertDictEqual(expected_dict, actual_dict)
diff --git a/phasecalculator/test/iotest/phasecsvconverter_test.py b/phasecalculator/test/iotest/phasecsvconverter_test.py
index e24798f4f3f495867e104385b1c8aed10504be14..26561972c696b1858c51fdf9dc43ac23a5050b6e 100755
--- a/phasecalculator/test/iotest/phasecsvconverter_test.py
+++ b/phasecalculator/test/iotest/phasecsvconverter_test.py
@@ -77,7 +77,7 @@ class PhaseCSVConverterTestCase(unittest.TestCase):
None.
"""
- actual_phases = phasecsv.convert_csv_file_to_phases(self.example_csv,False)
+ actual_phases = phasecsv.convert_csv_file_to_phases(self.example_csv, False)
self.assertEqual(self.phases, actual_phases)
def test_read_csv_file(self):
diff --git a/phasecalculator/test/iotest/phasetransferxmlcreator_test.py b/phasecalculator/test/iotest/phasetransferxmlcreator_test.py
index d5757df143d5778374feb9c212dab9e8bc5b3bc4..f982f18ba743511e10c3e137a6b4de9497d0e54c 100755
--- a/phasecalculator/test/iotest/phasetransferxmlcreator_test.py
+++ b/phasecalculator/test/iotest/phasetransferxmlcreator_test.py
@@ -277,8 +277,12 @@ class PhasetransferXMLCreatorTestCase(unittest.TestCase):
actual_info_list = self.solvent_info_list
self.assertEqual(1, len(actual_info_list))
actual_information = actual_info_list[0]
- self.assertEqual("1-butanol0.164528302water0.835471698", actual_information["solvent_name"])
- self.assertEqual("1-butanol0.164528302water0.835471698", actual_information["solvent_id"])
+ self.assertEqual(
+ "1-butanol0.164528302water0.835471698", actual_information["solvent_name"]
+ )
+ self.assertEqual(
+ "1-butanol0.164528302water0.835471698", actual_information["solvent_id"]
+ )
actual_list = actual_information["ssip_info_list"]
for entry, information_dict in enumerate(actual_list):
with self.subTest(entry=entry):
diff --git a/phasecalculator/test/runnerstest/fgipanalysisrunner_test.py b/phasecalculator/test/runnerstest/fgipanalysisrunner_test.py
index e305745b8c803235e9e64294db72a1d611a96b11..9a8cf182061ec5a776df9f9eaa4bb7398f5cfdf0 100755
--- a/phasecalculator/test/runnerstest/fgipanalysisrunner_test.py
+++ b/phasecalculator/test/runnerstest/fgipanalysisrunner_test.py
@@ -66,7 +66,7 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase):
(self.parent_directory / "resources/expected_solvent_fracocc.xml")
.absolute()
.as_posix()
- )
+ )
self.example_jar = (
(self.parent_directory / "resources" / "example.jar").absolute().as_posix()
)
@@ -79,15 +79,24 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase):
self.directory = fgiprunner.generate_directory(
self.directory_base, 298.0, "KELVIN"
)
- self.out_res, self.filename_list = fgiprunner.extract_solvents_and_generate_polynomials(
+ (
+ self.out_res,
+ self.filename_list,
+ ) = fgiprunner.extract_solvents_and_generate_polynomials(
self.solvent_filename, self.binding_output_filename, self.directory
)
- self.energy_xmlfile = "fgip/298_0K/1-butanol0.164528302water0.835471698binding.xml"
+ self.energy_xmlfile = (
+ "fgip/298_0K/1-butanol0.164528302water0.835471698binding.xml"
+ )
self.poly_file = (
"fgip/298_0K/1-butanol0.164528302water0.835471698binding_poly_fit_split.csv"
)
- self.matrix_file = "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.csv"
- self.solvent_map = "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.svg"
+ self.matrix_file = (
+ "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.csv"
+ )
+ self.solvent_map = (
+ "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.svg"
+ )
self.fgip_file = "fgip/298_0K/1-butanol0_164528302water0_835471698_FGIP.svg"
self.expected_latex = r"""
\begin{figure}[H]
@@ -149,6 +158,7 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase):
"""
self.assertTrue(pathlib.Path(self.directory).is_dir())
+
@pytest.mark.xfail
def test_run_fgip_analysis(self):
"""Test FGIP analysis is run.
@@ -208,7 +218,9 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase):
"298.0",
]
process = fgiprunner.run_binding_energy_calculation(
- self.example_jar, self.binding_output_filename,
- self.frac_occ_filename, self.solvent_filename
+ self.example_jar,
+ self.binding_output_filename,
+ self.frac_occ_filename,
+ self.solvent_filename,
)
self.assertListEqual(expected_args, process.args)
diff --git a/phasecalculator/test/runnerstest/phasecalculatorrunner_test.py b/phasecalculator/test/runnerstest/phasecalculatorrunner_test.py
index 760805a03aaf2947a7ccb70fc44c3dcbcd3e49a9..192b3b5cf0c9d42aa5b910dc0312465cba5423ae 100755
--- a/phasecalculator/test/runnerstest/phasecalculatorrunner_test.py
+++ b/phasecalculator/test/runnerstest/phasecalculatorrunner_test.py
@@ -137,8 +137,12 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
self.poly_file = (
"fgip/298_0K/1-butanol0.1645water0.8355binding_poly_fit_split.csv"
)
- self.matrix_file = "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.csv"
- self.solvent_map = "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.svg"
+ self.matrix_file = (
+ "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.csv"
+ )
+ self.solvent_map = (
+ "fgip/298_0K/1-butanol0.164528302water0.835471698_solv_map.svg"
+ )
self.fgip_file = "fgip/298_0K/1-butanol0_164528302water0_835471698_FGIP.svg"
self.similarity_file = "fgip/similaritymatrix.csv"
self.expected_latex = r"""
@@ -183,8 +187,11 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
self.expected_binding_file, "scratch/systemsolvent_298.0Kbinding.xml"
)
shutil.copyfile(self.expected_free_file, "scratch/systemsolvent_298.0Kfree.xml")
- shutil.copyfile(self.frac_occ_filename, "scratch/systemsolvent_298.0K_fracocc.xml")
+ shutil.copyfile(
+ self.frac_occ_filename, "scratch/systemsolvent_298.0K_fracocc.xml"
+ )
shutil.copyfile(self.expected_phase_output_filename, self.phase_out_file)
+
@pytest.mark.xfail
def test_run_all_analysis(self):
"""Test
@@ -271,8 +278,11 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
"""
expected_filename = "output/systemphasecalculation_summary.csv"
- actual_filename = pcalcrun.create_phase_summary_filename("output", "scratch/systemphase.xml")
+ actual_filename = pcalcrun.create_phase_summary_filename(
+ "output", "scratch/systemphase.xml"
+ )
self.assertEqual(expected_filename, actual_filename)
+
def test_create_free_energy_output_filename(self):
"""Test expected filename produced.
@@ -310,8 +320,11 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
"""
expected_filename = "solvent_filename_fracocc.xml"
- actual_filename = pcalcrun.create_fractional_occupancy_filename("solvent_filename.xml")
+ actual_filename = pcalcrun.create_fractional_occupancy_filename(
+ "solvent_filename.xml"
+ )
self.assertEqual(expected_filename, actual_filename)
+
def test_create_phase_output_filename(self):
"""Test expected filename produced.
@@ -332,9 +345,10 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
None.
"""
- phase_filename, solvent_filename_list = pcalcrun.create_phase_and_solvent_xml_files(
- self.system
- )
+ (
+ phase_filename,
+ solvent_filename_list,
+ ) = pcalcrun.create_phase_and_solvent_xml_files(self.system)
self.assertEqual("scratch/systemphase.xml", phase_filename)
with open(phase_filename, "r") as act_file:
actual_contents = act_file.read()
diff --git a/phasecalculator/test/runnerstest/phasetransferrunner_test.py b/phasecalculator/test/runnerstest/phasetransferrunner_test.py
index d4020b3dd8705a5c086687074fe06128f873740e..5333c2f8d7423df07a246f6b6e71411779cdf8de 100755
--- a/phasecalculator/test/runnerstest/phasetransferrunner_test.py
+++ b/phasecalculator/test/runnerstest/phasetransferrunner_test.py
@@ -49,7 +49,7 @@ class PhasetransferRunnerTestCase(unittest.TestCase):
self.r.replace(
"phasecalculator.runners.phasetransferrunner.run_calculation", self.Popen
)
-
+
self.addCleanup(self.r.restore)
parent_directory = pathlib.Path(__file__).parents[1]
self.example_jar = (
@@ -158,8 +158,10 @@ class PhasetransferRunnerTestCase(unittest.TestCase):
"298.0",
]
process = phaserun.run_phasetransfer_binding_energy(
- self.example_jar, self.binding_output_filename,
- self.frac_occ_filename, self.solvent_filename
+ self.example_jar,
+ self.binding_output_filename,
+ self.frac_occ_filename,
+ self.solvent_filename,
)
self.assertListEqual(expected_args, process.args)
@@ -299,8 +301,10 @@ class PhasetransferRunnerTestCase(unittest.TestCase):
"298.0",
]
actual_args = phaserun.generate_phasetransfer_binding_args(
- self.example_jar, self.binding_output_filename,
- self.frac_occ_filename, self.solvent_filename
+ self.example_jar,
+ self.binding_output_filename,
+ self.frac_occ_filename,
+ self.solvent_filename,
)
self.assertListEqual(expected_args, actual_args)
diff --git a/phasecalculator/test/runnerstest/phasexmlcreatorrunner_test.py b/phasecalculator/test/runnerstest/phasexmlcreatorrunner_test.py
index 717bd019256eb976856fa2008a85f368b63c38f5..9613834cbd5afd60a0c7205b5b333c1f30418e3a 100755
--- a/phasecalculator/test/runnerstest/phasexmlcreatorrunner_test.py
+++ b/phasecalculator/test/runnerstest/phasexmlcreatorrunner_test.py
@@ -114,9 +114,10 @@ class PhaseXMLCreatorRunnerTestCase(unittest.TestCase):
None.
"""
- phase_filename, solvent_filename_list = phasecreaterun.create_phase_and_solvent_files(
- self.system
- )
+ (
+ phase_filename,
+ solvent_filename_list,
+ ) = phasecreaterun.create_phase_and_solvent_files(self.system)
self.assertEqual("scratch/systemphase.xml", phase_filename)
with open(phase_filename, "r") as act_file:
actual_contents = act_file.read()
diff --git a/phasecalculator/test/runnerstest/similarityanalysisrunner_test.py b/phasecalculator/test/runnerstest/similarityanalysisrunner_test.py
index 452ccf7b07ec23134f2b49a5331554521be9f13a..0a3b649eb5599cf3b5cc00c8f307f69b89eae425 100755
--- a/phasecalculator/test/runnerstest/similarityanalysisrunner_test.py
+++ b/phasecalculator/test/runnerstest/similarityanalysisrunner_test.py
@@ -76,8 +76,13 @@ class SimilarityAnalysisRunnerTestCase(unittest.TestCase):
)
self.directory = simrun.generate_directory("sim", 298.0, "KELVIN")
self.energy_xmlfile = "sim/298_0K/1-butanol0.164528302water0.835471698free.xml"
- self.poly_file = "sim/298_0K/1-butanol0.164528302water0.835471698free_poly_fit_split.csv"
- self.out_res, self.filename_list = simrun.extract_solvents_and_generate_polynomials(
+ self.poly_file = (
+ "sim/298_0K/1-butanol0.164528302water0.835471698free_poly_fit_split.csv"
+ )
+ (
+ self.out_res,
+ self.filename_list,
+ ) = simrun.extract_solvents_and_generate_polynomials(
self.solvent_filename, self.free_output_filename, self.directory
)
self.solv_energy_dict = {
diff --git a/phasecalculator/test/runnerstest/vleanalysisrunner_test.py b/phasecalculator/test/runnerstest/vleanalysisrunner_test.py
index b5b0e1608da7214cafdb05314b462ab6d2422b95..b5d1522a5cb994af26f00ca71c5140debc3a58ae 100755
--- a/phasecalculator/test/runnerstest/vleanalysisrunner_test.py
+++ b/phasecalculator/test/runnerstest/vleanalysisrunner_test.py
@@ -72,6 +72,7 @@ class VLEAnalysisRunnerTestCase(unittest.TestCase):
.as_posix()
)
self.output_file = "phase_summary.csv"
+
def tearDown(self):
"""Clean up after tests.
@@ -82,6 +83,7 @@ class VLEAnalysisRunnerTestCase(unittest.TestCase):
"""
if os.path.isfile(self.output_file):
os.remove(self.output_file)
+
def test_calculate_and_process_vle_data(self):
"""Test expected output produced.
@@ -90,15 +92,18 @@ class VLEAnalysisRunnerTestCase(unittest.TestCase):
None.
"""
- vlerun.calculate_and_process_vle_data(self.example_jar,
- self.phase_filename,
- self.phase_output_filename,
- self.output_file)
+ vlerun.calculate_and_process_vle_data(
+ self.example_jar,
+ self.phase_filename,
+ self.phase_output_filename,
+ self.output_file,
+ )
with open(self.output_file, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_phas_csv, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
+
def test_process_vle_data(self):
"""Test expected output produced.
@@ -113,6 +118,7 @@ class VLEAnalysisRunnerTestCase(unittest.TestCase):
with open(self.expected_phas_csv, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
+
def test_run_vle_calculation(self):
"""Test expected system call is made.