diff --git a/phasecalculator/analysis/fgipanalysis.py b/phasecalculator/analysis/fgipanalysis.py index 40cbdc6da5f4b8122bfa234f645f127e9b7d4630..47f739fc67caebb08a820f897360112fb17c5178 100755 --- a/phasecalculator/analysis/fgipanalysis.py +++ b/phasecalculator/analysis/fgipanalysis.py @@ -28,7 +28,7 @@ import solventmapcreator.solvationcalculation.fgipmaker as fgipmaker logging.basicConfig() LOGGER = logging.getLogger(__name__) -LOGGER.setLevel(logging.WARN) +LOGGER.setLevel(logging.DEBUG) EPSILON_I_LIST = np.array([(float(x) / 10.0) - 10.0 for x in range(101)]) @@ -36,7 +36,7 @@ EPSILON_J_LIST = np.array([(float(x) / 10.0) for x in range(51)]) def create_solv_map_and_fgips_from_files( - solvent_filename, polynomial_filename_list, directory, **kwargs + frac_occ_filename, polynomial_filename_list, directory, **kwargs ): """Creates solvent map and FGIPs and output matrix of numerical values. @@ -45,8 +45,8 @@ def create_solv_map_and_fgips_from_files( Parameters ---------- - solvent_filename : str - solvent XML filename. + frac_occ_filename: str + Filename for fractional Occupancy XML. polynomial_filename_list : list of str solvation binding energy polynomial filenames. directory : str @@ -66,7 +66,7 @@ def create_solv_map_and_fgips_from_files( results, filenames = create_solvation_plots_from_poly_files( EPSILON_I_LIST, EPSILON_J_LIST, - solvent_filename, + frac_occ_filename, polynomial_filename_list, 8, directory=directory, @@ -106,7 +106,7 @@ def create_fgips_from_file_list(filename_list, **kwargs): def create_solvation_plots_from_poly_files( epsilon_i_list, epsilon_j_list, - solvent_filename, + frac_occ_filename, polynomial_filename_list, polynomial_order, **kwargs @@ -119,8 +119,8 @@ def create_solvation_plots_from_poly_files( epsilon values (x direction). epsilon_j_list : list of float epsilon values (y direction). - solvent_filename : str - solvent XML filename. + frac_occ_filename: str + fractional occupancy information filename. polynomial_filename_list : list of str solvation binding energy polynomial filenames. polynomial_order : int @@ -139,6 +139,7 @@ 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) for polynomial_filename in polynomial_filename_list: LOGGER.info("polynomial_filename:") LOGGER.info(polynomial_filename) @@ -150,7 +151,7 @@ def create_solvation_plots_from_poly_files( create_solvation_plot( epsilon_i_list, epsilon_j_list, - solvent_filename, + frac_occ_inf_dict, solvent_id, polynomial_filename, polynomial_order, @@ -191,7 +192,7 @@ def get_solvent_id_from_poly_filename( def create_solvation_plot( epsilon_i_list, epsilon_j_list, - solvent_filename, + frac_occ_inf_dict, solvent_id, polynomial_filename, polynomial_order, @@ -205,8 +206,8 @@ def create_solvation_plot( epsilon values (x direction). epsilon_j_list : list of float epsilon values (y direction). - solvent_filename : str - solvent XML filename. + frac_occ_inf_dict: dict + solvent_id : str solvent ID. polynomial_filename : str @@ -225,7 +226,7 @@ def create_solvation_plot( return solvmapgen.create_solvation_plot( epsilon_i_list, epsilon_j_list, - solvent_filename, + frac_occ_inf_dict, solvent_id, polynomial_filename, polynomial_order, diff --git a/phasecalculator/runners/fgipanalysisrunner.py b/phasecalculator/runners/fgipanalysisrunner.py index d75e999378d3fe8fbda04eb4361ac21e5cb82380..c0cd7ab92480c0f8443c7a31a927b03c62dbeb09 100755 --- a/phasecalculator/runners/fgipanalysisrunner.py +++ b/phasecalculator/runners/fgipanalysisrunner.py @@ -34,7 +34,7 @@ LOGGER.setLevel(logging.WARN) def calc_energies_and_fgips( - jar_path, energy_xml_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. @@ -44,6 +44,8 @@ def calc_energies_and_fgips( path to jar file. energy_xml_filename : str energy XML filename. + frac_occ_filename: str + Filename for fractional Occupancy XML. solvent_filename : str Solvent XML filename. directory_base : str @@ -66,14 +68,15 @@ 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, 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( solvent_filename, energy_xml_filename, directory ) return run_fgip_analysis( - solvent_filename, polynomial_filename_list, directory, **kwargs + frac_occ_filename, polynomial_filename_list, directory, **kwargs ) @@ -107,13 +110,13 @@ def generate_directory(directory_base, temperature, temperature_unit): return dir_path.as_posix() -def run_fgip_analysis(solvent_filename, polynomial_filename_list, directory, **kwargs): +def run_fgip_analysis(frac_occ_filename, polynomial_filename_list, directory, **kwargs): """Run FGIP analysis for all solvents included in solvent file. Parameters ---------- - solvent_filename : str - Filename for solvent XML. + frac_occ_filename: str + Filename for fractional occupancy XML. polynomial_filename_list : list of str list of polynomial files to read. directory : str @@ -128,7 +131,7 @@ def run_fgip_analysis(solvent_filename, polynomial_filename_list, directory, **k """ return fgipanalysis.create_solv_map_and_fgips_from_files( - solvent_filename, polynomial_filename_list, directory, **kwargs + frac_occ_filename, polynomial_filename_list, directory, **kwargs ) @@ -162,7 +165,7 @@ def extract_solvents_and_generate_polynomials( def run_binding_energy_calculation( - jar_path, output_filename, solvent_filename, **kwargs + jar_path, output_filename, frac_occ_filename, solvent_filename, **kwargs ): """Run solute solvation binding energy calculation. @@ -172,6 +175,8 @@ def run_binding_energy_calculation( path to jar executable. output_filename : str Output filename for result output. + frac_occ_filename: str + Filename for fractional Occupancy XML. solvent_filename : str filename for solvent XML. memory_req : str, optional @@ -196,5 +201,6 @@ def run_binding_energy_calculation( """ return phaserun.run_phasetransfer_binding_energy( - jar_path, output_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 0fca2c0e2a70e70611d13e7ece88c7efb048b3ed..8b6d61d6eb8ee2e468e3ec7c44cf2b579b9251f4 100755 --- a/phasecalculator/runners/phasecalculatorrunner.py +++ b/phasecalculator/runners/phasecalculatorrunner.py @@ -98,12 +98,14 @@ def run_fgip_analysis(system_info, solvent_filename_dict_list, **kwargs): for solvent_filename_dict in solvent_filename_dict_list: solvent_filename = solvent_filename_dict["solvent_filename"] energy_xml_filename = create_binding_energy_output_filename(solvent_filename) + frac_occ_filename = create_fractional_occupancy_filename(solvent_filename) directory_base = system_info.runtime_information.output_dir temperature = solvent_filename_dict["temperature_value"] temperature_unit = solvent_filename_dict["temperature_units"] results, latex_blocks = fgiprun.calc_energies_and_fgips( jar_path, energy_xml_filename, + frac_occ_filename, solvent_filename, directory_base, temperature=temperature, @@ -244,6 +246,22 @@ def create_binding_energy_output_filename(solvent_filename): return solvent_filename.replace(".xml", "binding.xml") +def create_fractional_occupancy_filename(solvent_filename): + """Create fractional occupancy filename for solvent file. + + Parameters + ---------- + solvent_filename : str + Input solvent filename. + + Returns + ------- + str + Fractional occupancy filename. + + """ + return solvent_filename.replace(".xml", "_fracocc.xml") + def create_phase_output_filename(phase_filename): """ diff --git a/phasecalculator/runners/phasetransferrunner.py b/phasecalculator/runners/phasetransferrunner.py index e707120e569996285271bf595008764120cceb93..e7f48cbf28de06c275a7abb7824efb2127249aca 100755 --- a/phasecalculator/runners/phasetransferrunner.py +++ b/phasecalculator/runners/phasetransferrunner.py @@ -65,7 +65,7 @@ def run_vle_calculation(jar_path, phase_filename, output_filename, **kwargs): def run_phasetransfer_binding_energy( - jar_path, output_filename, solvent_filename, **kwargs + jar_path, output_filename, frac_occ_filename, solvent_filename, **kwargs ): """Run solute solvation binding energy calculation. @@ -75,6 +75,8 @@ def run_phasetransfer_binding_energy( path to jar executable. output_filename : str Output filename for result output. + frac_occ_filename: str + Filename for fractional Occupancy XML. solvent_filename : str filename for solvent XML. memory_req : str, optional @@ -100,7 +102,7 @@ def run_phasetransfer_binding_energy( """ if check_jar_exists(jar_path): phase_binding_args = generate_phasetransfer_binding_args( - jar_path, output_filename, solvent_filename, **kwargs + jar_path, output_filename, frac_occ_filename, solvent_filename, **kwargs ) return run_calculation(phase_binding_args) else: @@ -228,7 +230,7 @@ def generate_phasetransfer_free_args( def generate_phasetransfer_binding_args( - jar_path, output_filename, solvent_filename, **kwargs + jar_path, output_filename, frac_occ_filename, solvent_filename, **kwargs ): """Generate full argument list for solute solvation binding energy calculation call. @@ -237,7 +239,9 @@ def generate_phasetransfer_binding_args( jar_path : str path to jar executable. output_filename : str - Output filename for result output. + Output filename for binding energy XML. + frac_occ_filename: str + Filename for fractional Occupancy XML. solvent_filename : str filename for solvent XML. memory_req : str, optional @@ -256,7 +260,8 @@ def generate_phasetransfer_binding_args( """ jar_args = make_java_arguments(jar_path, memory_req=kwargs.pop("memory_req", None)) - binding_args = ["--energies", "solvationbinding"] + binding_args = ["--energies", "solvationbinding", + "-f", frac_occ_filename ] solvent_args = generate_solvent_calc_args( output_filename, solvent_filename, **kwargs ) diff --git a/phasecalculator/test/analysistest/fgipanalysistest.py b/phasecalculator/test/analysistest/fgipanalysistest.py index c70315eba02c73ff2f43744664a10a3fa53229da..b9fd26cc00c92a21e59b5321e4c8685da40b9ef8 100755 --- a/phasecalculator/test/analysistest/fgipanalysistest.py +++ b/phasecalculator/test/analysistest/fgipanalysistest.py @@ -48,6 +48,11 @@ class FGIPAnalysisTestCase(unittest.TestCase): .absolute() .as_posix() ) + self.frac_occ_filename = ( + (self.parent_directory / "resources/expected_solvent_fracocc.xml") + .absolute() + .as_posix() + ) self.poly_file = ( ( self.parent_directory @@ -69,7 +74,7 @@ class FGIPAnalysisTestCase(unittest.TestCase): \label{fig:1-butanol0_165water0_835solvationmap} \end{figure} """ - + self.frac_occ_inf_dict = fgipanalysis.solvmapgen.fractionaloccupancycalculator.read_fractional_occupancy_information(self.frac_occ_filename) def tearDown(self): """Clean up after tests. @@ -94,7 +99,7 @@ class FGIPAnalysisTestCase(unittest.TestCase): """ results, latex_blocks = fgipanalysis.create_solv_map_and_fgips_from_files( - self.solvent_filename, [self.poly_file], "" + self.frac_occ_filename, [self.poly_file], "" ) self.assertListEqual([(0, 0)], results) self.assertMultiLineEqual(self.expected_latex, latex_blocks) @@ -113,7 +118,7 @@ class FGIPAnalysisTestCase(unittest.TestCase): plot_outputs, filenames = fgipanalysis.create_solvation_plots_from_poly_files( fgipanalysis.EPSILON_I_LIST, fgipanalysis.EPSILON_J_LIST, - self.solvent_filename, + self.frac_occ_filename, [self.poly_file], 8, ) @@ -132,7 +137,7 @@ class FGIPAnalysisTestCase(unittest.TestCase): plot_outputs, filenames = fgipanalysis.create_solvation_plots_from_poly_files( fgipanalysis.EPSILON_I_LIST, fgipanalysis.EPSILON_J_LIST, - self.solvent_filename, + self.frac_occ_filename, [self.poly_file], 8, ) @@ -165,7 +170,7 @@ class FGIPAnalysisTestCase(unittest.TestCase): solv_plot, matrix_res = fgipanalysis.create_solvation_plot( fgipanalysis.EPSILON_I_LIST, fgipanalysis.EPSILON_J_LIST, - self.solvent_filename, + self.frac_occ_inf_dict, "1-butanol0.165water0.835", self.poly_file, 8, diff --git a/phasecalculator/test/resources/expected_solvent_fracocc.xml b/phasecalculator/test/resources/expected_solvent_fracocc.xml new file mode 100644 index 0000000000000000000000000000000000000000..4d7992af4247a08658aff28367e723fee99bea5a --- /dev/null +++ b/phasecalculator/test/resources/expected_solvent_fracocc.xml @@ -0,0 +1,307 @@ +<?xml version="1.0" encoding="UTF-8"?> +<?xml-stylesheet type="text/xsl" href="http://www-hunter.ch.cam.ac.uk/xlst/phase.xsl"?> +<phase:FractionalOccupancyCollection xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xml-cml.org/schema http://www-hunter.ch.cam.ac.uk/schema/cmlschema.xsd http://www-hunter.ch.cam.ac.uk/SSIP http://www-hunter.ch.cam.ac.uk/schema/SSIP.xsd http://www-hunter.ch.cam.ac.uk/PhaseSchema http://www-hunter.ch.cam.ac.uk/schema/PhaseSchema.xsd"> + <phase:FractionalOccupancies> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-0.900solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.000solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-1.900solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.000solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-10.900solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.000solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-11.900solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.000solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="-12.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy 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phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="7.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy 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phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="8.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="8.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="8.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="8.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="8.900solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.000solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.100solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.200solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.300solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.400solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.500solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.600solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.700solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.800solute" phase:temperature="298.0"/> + <phase:FractionalOccupancy phase:value="1.2090405933333335" phase:solventID="1-butanol0.165water0.835" phase:soluteID="9.900solute" phase:temperature="298.0"/> + </phase:FractionalOccupancies> +</phase:FractionalOccupancyCollection> diff --git a/phasecalculator/test/runnerstest/fgipanalysisrunnertest.py b/phasecalculator/test/runnerstest/fgipanalysisrunnertest.py index 6b00b1d8dca8a16784e155fa2112c2aa629a3431..9d1bb8e4f60133bca3c2c2e3f7a5dbdb87947570 100755 --- a/phasecalculator/test/runnerstest/fgipanalysisrunnertest.py +++ b/phasecalculator/test/runnerstest/fgipanalysisrunnertest.py @@ -59,6 +59,11 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase): .absolute() .as_posix() ) + self.frac_occ_filename = ( + (self.parent_directory / "resources/expected_solvent_fracocc.xml") + .absolute() + .as_posix() + ) self.example_jar = ( (self.parent_directory / "resources" / "example.jar").absolute().as_posix() ) @@ -121,6 +126,7 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase): results, latex_blocks = fgiprunner.calc_energies_and_fgips( self.example_jar, self.binding_output_filename, + self.frac_occ_filename, self.solvent_filename, self.directory_base, ) @@ -149,7 +155,7 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase): """ results, latex_blocks = fgiprunner.run_fgip_analysis( - self.solvent_filename, self.filename_list, self.directory + self.frac_occ_filename, self.filename_list, self.directory ) self.assertListEqual([(0, 0)], results) self.assertMultiLineEqual(self.expected_latex, latex_blocks) @@ -182,6 +188,8 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase): self.example_jar, "--energies", "solvationbinding", + "-f", + self.frac_occ_filename, "--calc", "--conccalc", "-o", @@ -196,6 +204,7 @@ class FGIPAnalysisRunnerTestCase(unittest.TestCase): "298.0", ] process = fgiprunner.run_binding_energy_calculation( - self.example_jar, self.binding_output_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/phasecalculatorrunnertest.py b/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py index 7ccd815ca8369fc407b280ac746e3bd9475e255d..a8338b1c8ff3b51e2aa40cf2ea88cadd4baec901 100755 --- a/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py +++ b/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py @@ -94,6 +94,11 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase): .absolute() .as_posix() ) + self.frac_occ_filename = ( + (parent_directory / "resources/expected_solvent_fracocc.xml") + .absolute() + .as_posix() + ) self.expected_binding_file = ( (parent_directory / "resources" / "expected_solventbinding.xml") .absolute() @@ -160,6 +165,7 @@ 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") def test_run_all_analysis(self): """Test @@ -230,7 +236,7 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase): self.assertListEqual(expected_args, process.args) def test_create_output_dir(self): - """Test + """Test expected output directory created. Returns ------- @@ -242,7 +248,7 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase): ) def test_create_free_energy_output_filename(self): - """Test + """Test expected filename produced. Returns ------- @@ -256,7 +262,7 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase): self.assertEqual(expected_filename, actual_filename) def test_create_binding_energy_output_filename(self): - """Test + """Test expected filename produced. Returns ------- @@ -269,8 +275,19 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase): ) self.assertEqual(expected_filename, actual_filename) + def test_create_fractional_occupancy_filename(self): + """Test expected filename produced. + + Returns + ------- + None. + + """ + expected_filename = "solvent_filename_fracocc.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 + """Test expected filename produced. Returns ------- diff --git a/phasecalculator/test/runnerstest/phasetransferrunnertest.py b/phasecalculator/test/runnerstest/phasetransferrunnertest.py index 8bbfb5591e48de74d76051f8001a23dbb7732a53..a0b3eadd2d2965b02c26a6459023db76b2f5c194 100755 --- a/phasecalculator/test/runnerstest/phasetransferrunnertest.py +++ b/phasecalculator/test/runnerstest/phasetransferrunnertest.py @@ -78,6 +78,16 @@ class PhasetransferRunnerTestCase(unittest.TestCase): .absolute() .as_posix() ) + self.phase_output_filename = ( + (parent_directory / "resources" / "expected_phaseout.xml") + .absolute() + .as_posix() + ) + self.frac_occ_filename = ( + (parent_directory / "resources" / "expected_fracocc.xml") + .absolute() + .as_posix() + ) def tearDown(self): """Clean up after tests. @@ -130,6 +140,8 @@ class PhasetransferRunnerTestCase(unittest.TestCase): self.example_jar, "--energies", "solvationbinding", + "-f", + self.frac_occ_filename, "--calc", "--conccalc", "-o", @@ -144,7 +156,8 @@ class PhasetransferRunnerTestCase(unittest.TestCase): "298.0", ] process = phaserun.run_phasetransfer_binding_energy( - self.example_jar, self.binding_output_filename, self.solvent_filename + self.example_jar, self.binding_output_filename, + self.frac_occ_filename, self.solvent_filename ) self.assertListEqual(expected_args, process.args) @@ -268,6 +281,8 @@ class PhasetransferRunnerTestCase(unittest.TestCase): self.example_jar, "--energies", "solvationbinding", + "-f", + self.frac_occ_filename, "--calc", "--conccalc", "-o", @@ -282,7 +297,8 @@ class PhasetransferRunnerTestCase(unittest.TestCase): "298.0", ] actual_args = phaserun.generate_phasetransfer_binding_args( - self.example_jar, self.binding_output_filename, self.solvent_filename + self.example_jar, self.binding_output_filename, + self.frac_occ_filename, self.solvent_filename ) self.assertListEqual(expected_args, actual_args)