d3tales_api package

Subpackages

• d3tales_api.Calculators package
  • Submodules
  • d3tales_api.Calculators.calculators module
    • AvgEHalfCalculator
      • AvgEHalfCalculator.calculate()
    • CAResistanceCalculator
      • CAResistanceCalculator.calculate()
    • CVChargeTransferCalculator
      • CVChargeTransferCalculator.calculate()
    • CVDescriptorCalculator
      • CVDescriptorCalculator.e_half()
      • CVDescriptorCalculator.middle_sweep()
      • CVDescriptorCalculator.peak_splittings()
      • CVDescriptorCalculator.peaks()
      • CVDescriptorCalculator.peaks_for_analysis()
      • CVDescriptorCalculator.prominent_peaks()
      • CVDescriptorCalculator.reversibility()
    • CVDiffusionCalculator
      • CVDiffusionCalculator.calculate()
    • ConcentrationCalculator
      • ConcentrationCalculator.calculate()
    • D3Calculator
      • D3Calculator.__init__()
      • D3Calculator.all_connections
      • D3Calculator.calculate()
      • D3Calculator.description()
      • D3Calculator.make_connections()
    • DeltaGSolvCalc
      • DeltaGSolvCalc.calculate()
    • DirtyElectrodeDetector
      • DirtyElectrodeDetector.calculate()
    • EnergyDiffCalc
      • EnergyDiffCalc.calculate()
    • RMSDCalc
      • RMSDCalc.calculate()
    • RSSCalc
      • RSSCalc.calculate()
    • RadBuriedVolCalc
      • RadBuriedVolCalc.calculate()
    • RadicalSpinCalc
      • RadicalSpinCalc.calculate()
    • RedoxPotentialCalc
      • RedoxPotentialCalc.calculate()
    • RelaxationCalc
      • RelaxationCalc.calculate()
    • ReorganizationCalc
      • ReorganizationCalc.calculate()
  • d3tales_api.Calculators.ocelot_transform module
    • ACParser
      • ACParser.BO_is_OK()
      • ACParser.__init__()
      • ACParser.addBO2mol()
      • ACParser.getUADU()
      • ACParser.get_BO()
      • ACParser.get_UA_pairs()
      • ACParser.get_atomic_charge()
      • ACParser.get_bonds()
      • ACParser.get_valence_info()
      • ACParser.init_rdmol()
      • ACParser.parse()
      • ACParser.parse_bonds()
      • ACParser.set_atomic_charges()
      • ACParser.set_atomic_radicals()
      • ACParser.valences_not_too_large()
    • chiral_stereo_check()
    • clean_charges()
    • pmgmol_to_rdmol()
    • valence_electron()
  • d3tales_api.Calculators.plotters module
    • CVPlotter
      • CVPlotter.live_plot()
      • CVPlotter.live_plot_multi()
      • CVPlotter.plot_data()
    • D3Plotter
      • D3Plotter.plot_data()
    • DFTSpecPlotter
      • DFTSpecPlotter.live_plot()
      • DFTSpecPlotter.plot_data()
  • d3tales_api.Calculators.utils module
    • dict2obj()
    • get_electrode_potential()
    • get_periodic_table()
    • json2obj()
    • rgetattr()
    • rgetkeys()
    • unit_conversion()
  • Module contents
• d3tales_api.D3database package
  • Submodules
  • d3tales_api.D3database.d3database module
    • BackDB
      • BackDB.__init__()
      • BackDB.get_geometry()
    • D3Database
      • D3Database.__init__()
      • D3Database.array_checker()
      • D3Database.dot2dict()
      • D3Database.field_checker()
      • D3Database.insert()
      • D3Database.make_query()
      • D3Database.path_insert()
    • DBconnector
      • DBconnector.__init__()
      • DBconnector.get_collection()
      • DBconnector.get_database()
    • Expflow
      • Expflow.__init__()
    • FrontDB
      • FrontDB.__init__()
      • FrontDB.check_if_in_db()
      • FrontDB.generate_id()
    • ParamsDB
      • ParamsDB.__init__()
      • ParamsDB.check_id()
    • QueryDB
      • QueryDB.__init__()
      • QueryDB.make_query()
    • RobotStatusDB
      • RobotStatusDB.__init__()
      • RobotStatusDB.check_wflow_name()
      • RobotStatusDB.exists
      • RobotStatusDB.get_prop()
      • RobotStatusDB.update_status()
  • d3tales_api.D3database.dft_calculation_list module
    • calc_tuple_list()
    • calculation_list()
  • d3tales_api.D3database.info_from_smiles module
    • GenerateMolInfo
      • GenerateMolInfo.__init__()
      • GenerateMolInfo.get_mol_info()
    • base64_to_image()
    • find_lowest_e_conf()
    • image_to_base64()
  • d3tales_api.D3database.restapi module
    • D3talesData
      • D3talesData.__init__()
      • D3talesData.get_master_df()
      • D3talesData.get_prop_data()
      • D3talesData.hist_1d()
      • D3talesData.hist_2d()
      • D3talesData.rgetkeys()
    • RESTAPI
      • RESTAPI.__init__()
      • RESTAPI.cookies
      • RESTAPI.csrftoken
      • RESTAPI.get_client()
      • RESTAPI.get_process()
      • RESTAPI.post_process()
  • d3tales_api.D3database.schema2class module
    • Schema2Class
      • Schema2Class.__init__()
      • Schema2Class.md_table()
  • d3tales_api.D3database.schema2model module
    • determine_model_name()
    • get_required_string()
    • parse_model()
  • Module contents
• d3tales_api.Processors package
  • Submodules
  • d3tales_api.Processors.back2front module
    • CV2Front
      • CV2Front.__init__()
      • CV2Front.cv_meta_calcs()
      • CV2Front.e_halfs
      • CV2Front.from_json()
      • CV2Front.generate_hash()
      • CV2Front.get_conditions()
      • CV2Front.process()
      • CV2Front.prop_dict()
    • DOI2Front
      • DOI2Front.__init__()
      • DOI2Front.check_extr_props()
      • DOI2Front.cir_convert()
      • DOI2Front.from_json()
      • DOI2Front.get_literature_data()
      • DOI2Front.get_mol_id()
    • Gaus2FrontCharacterization
      • Gaus2FrontCharacterization.__init__()
      • Gaus2FrontCharacterization.adiabatic_electron_affinity()
      • Gaus2FrontCharacterization.adiabatic_electron_affinity_2()
      • Gaus2FrontCharacterization.adiabatic_ionization_energy()
      • Gaus2FrontCharacterization.adiabatic_ionization_energy_2()
      • Gaus2FrontCharacterization.electron_reorganization_energy()
      • Gaus2FrontCharacterization.find_data()
      • Gaus2FrontCharacterization.from_data()
      • Gaus2FrontCharacterization.get_all_data()
      • Gaus2FrontCharacterization.get_data()
      • Gaus2FrontCharacterization.hash_id()
      • Gaus2FrontCharacterization.hole_reorganization_energy()
      • Gaus2FrontCharacterization.oxidation_potential()
      • Gaus2FrontCharacterization.reduction_potential()
      • Gaus2FrontCharacterization.relaxation_anion1_groundState()
      • Gaus2FrontCharacterization.relaxation_cation1_groundState()
      • Gaus2FrontCharacterization.relaxation_groundState_anion1()
      • Gaus2FrontCharacterization.relaxation_groundState_cation1()
      • Gaus2FrontCharacterization.return_descriptor_dict()
      • Gaus2FrontCharacterization.rmsd_anion1_anion2()
      • Gaus2FrontCharacterization.rmsd_cation1_cation2()
      • Gaus2FrontCharacterization.rmsd_groundState_anion1()
      • Gaus2FrontCharacterization.rmsd_groundState_cation1()
      • Gaus2FrontCharacterization.solvation_energy()
      • Gaus2FrontCharacterization.species_descriptors
      • Gaus2FrontCharacterization.vertical_electron_affinity()
      • Gaus2FrontCharacterization.vertical_electron_affinity_2()
      • Gaus2FrontCharacterization.vertical_ionization_energy()
      • Gaus2FrontCharacterization.vertical_ionization_energy_2()
  • d3tales_api.Processors.d3tales_parser module
    • ProcessCA
      • ProcessCA.__init__()
      • ProcessCA.data_dict
    • ProcessCV
      • ProcessCV.__init__()
      • ProcessCV.data_dict
    • ProcessDFT
      • ProcessDFT.__init__()
      • ProcessDFT.conditions
      • ProcessDFT.data_dict
      • ProcessDFT.hash_id
      • ProcessDFT.is_groundState
      • ProcessDFT.mol_info
    • ProcessNlp
      • ProcessNlp.__init__()
      • ProcessNlp.data_dict
      • ProcessNlp.download_article()
      • ProcessNlp.from_dataframe()
      • ProcessNlp.from_html()
      • ProcessNlp.from_parsed_json()
      • ProcessNlp.from_prop_list()
      • ProcessNlp.get_affiliations()
      • ProcessNlp.get_basic_info()
      • ProcessNlp.get_main_text()
      • ProcessNlp.make_author_entry()
    • ProcessPotBase
      • ProcessPotBase.__init__()
      • ProcessPotBase.data_dict
      • ProcessPotBase.data_format()
      • ProcessPotBase.mol_info
      • ProcessPotBase.pot_conditions
      • ProcessPotBase.reagent_format()
    • ProcessUvVis
      • ProcessUvVis.__init__()
      • ProcessUvVis.no_sql_data
      • ProcessUvVis.sql_absorbance_data
      • ProcessUvVis.sql_data
    • float_from_str()
  • d3tales_api.Processors.expflow_parser module
    • ProcessExpFlowObj
      • ProcessExpFlowObj.__init__()
      • ProcessExpFlowObj.apparatus_by_id
      • ProcessExpFlowObj.get_apparatus()
      • ProcessExpFlowObj.get_concentration()
      • ProcessExpFlowObj.get_param_quantity()
      • ProcessExpFlowObj.get_reagents()
      • ProcessExpFlowObj.instrument_name
      • ProcessExpFlowObj.molecule_id
      • ProcessExpFlowObj.property_by_action()
      • ProcessExpFlowObj.reagents_by_id
      • ProcessExpFlowObj.redox_mol
      • ProcessExpFlowObj.redox_mol_concentration
      • ProcessExpFlowObj.solvent
    • ProcessExperimentRun
      • ProcessExperimentRun.cv_metadata
      • ProcessExperimentRun.get_electrode()
    • get_id()
  • d3tales_api.Processors.parser_cv module
    • ParseChiBase
      • ParseChiBase.__init__()
      • ParseChiBase.extract_value_unit()
    • ParseChiCA
      • ParseChiCA.__init__()
      • ParseChiCA.get_data_calcs()
      • ParseChiCA.resistance
    • ParseChiCV
      • ParseChiCV.__init__()
      • ParseChiCV.calculate_plotting()
      • ParseChiCV.calculate_prop()
    • ParseChiESI
      • ParseChiESI.__init__()
    • break_list()
    • break_scan_data()
  • d3tales_api.Processors.parser_dft module
    • ProcessCCLIB
      • ProcessCCLIB.__init__()
      • ProcessCCLIB.cclib_parse()
      • ProcessCCLIB.get_freq_dicts()
      • ProcessCCLIB.get_radical_stability_score()
      • ProcessCCLIB.get_sites_dict()
    • ProcessGausLog
      • ProcessGausLog.__init__()
      • ProcessGausLog.dipole_moments
      • ProcessGausLog.get_pmgmol()
      • ProcessGausLog.get_solvent_info()
      • ProcessGausLog.get_tddft_excitations()
      • ProcessGausLog.homo_lumo
      • ProcessGausLog.omega
      • ProcessGausLog.parse_tddft()
      • ProcessGausLog.pcm_info
      • ProcessGausLog.runtime
      • ProcessGausLog.tuning_parameter
    • ProcessPsi4Log
      • ProcessPsi4Log.__init__()
  • d3tales_api.Processors.parser_ir module
  • d3tales_api.Processors.parser_uvvis module
    • ParseExcel
      • ParseExcel.__init__()
      • ParseExcel.absorbance_data
      • ParseExcel.date_recorded
      • ParseExcel.integration_time
      • ParseExcel.parse_file()
  • d3tales_api.Processors.processing_firetasks module
    • ApproveJobs
      • ApproveJobs.run_task()
    • FileTransferTask
      • FileTransferTask.run_task()
    • ProcessFile
      • ProcessFile.run_task()
    • SendToStorage
      • SendToStorage.run_task()
    • UpdateApprovalStatus
      • UpdateApprovalStatus.run_task()
    • UpdateBackendDB
      • UpdateBackendDB.run_task()
    • UpdateFrontendDB
      • UpdateFrontendDB.run_task()
    • UpdateUserDB
      • UpdateUserDB.run_task()
    • mkdir_p()
    • test_path()
  • Module contents
• d3tales_api.Workflows package
  • Submodules
  • d3tales_api.Workflows.D3TaLES_FW module
    • DihedRot
      • DihedRot.__init__()
    • EmailEnd
      • EmailEnd.__init__()
    • EmailStart
      • EmailStart.__init__()
    • Energy
      • Energy.__init__()
    • InitializeMolecule
      • InitializeMolecule.__init__()
    • MolOpt
      • MolOpt.__init__()
    • Optimization
      • Optimization.__init__()
    • TDDFT
      • TDDFT.__init__()
    • WTuning
      • WTuning.__init__()
  • d3tales_api.Workflows.Gaussian module
    • GaussianBase
      • GaussianBase.post_job()
      • GaussianBase.run_check()
      • GaussianBase.setup_calc()
      • GaussianBase.setup_files()
    • RunGaussianDihedRot
      • RunGaussianDihedRot.run_task()
    • RunGaussianEnergy
      • RunGaussianEnergy.run_task()
    • RunGaussianOpt
      • RunGaussianOpt.run_task()
    • RunGaussianTDDFT
      • RunGaussianTDDFT.run_task()
    • RunWtuning
      • RunWtuning.run_task()
  • d3tales_api.Workflows.Gromacs module
  • d3tales_api.Workflows.Initialize module
    • EmailFinished
      • EmailFinished.run_task()
    • EmailStarting
      • EmailStarting.run_task()
    • Mail
      • Mail.__init__()
      • Mail.send()
    • MoleculeInit
      • MoleculeInit.run_task()
  • d3tales_api.Workflows.ParamSet module
    • GausParamSet
      • GausParamSet.__init__()
      • GausParamSet.from_json()
    • GaussianParameters
      • GaussianParameters.__init__()
    • VaspParamSet
      • VaspParamSet.__init__()
      • VaspParamSet.from_json()
    • VaspParameters
      • VaspParameters.__init__()
    • sett()
  • d3tales_api.Workflows.utils module
    • generate_gaussian_input()
    • get_central_dihed()
    • get_db_geom()
    • get_groundState()
    • get_hash_id()
    • get_scfs()
    • get_tddft_excitations()
    • orig_conditions()
    • orig_hash_id()
    • parse_tddft()
    • runtime_from_log()
    • start_from_smiles()
    • write_nto()
    • zip_files()
  • d3tales_api.Workflows.wf_writer module
    • d3tales_wf()
    • hf_wf()
    • huckaba_wf()
    • just_anion()
    • just_initialize()
    • just_nmr()
    • just_tddft()
    • solv_wf()
    • specialized_job()
  • d3tales_api.Workflows.wtuning module
    • WtuningJob
      • WtuningJob.__init__()
      • WtuningJob.alpha_atune()
      • WtuningJob.alpha_format()
      • WtuningJob.alpha_iopstr
      • WtuningJob.alpha_tune()
      • WtuningJob.atuning_cycle()
      • WtuningJob.beta_iopstr
      • WtuningJob.extract_abs()
      • WtuningJob.extract_energy()
      • WtuningJob.gauss_run()
      • WtuningJob.geo_opt()
      • WtuningJob.iop_route_params
      • WtuningJob.log_add()
      • WtuningJob.omega_FindC()
      • WtuningJob.omega_extract()
      • WtuningJob.omega_format()
      • WtuningJob.omega_gauss_do()
      • WtuningJob.omega_iopstr
      • WtuningJob.omega_tune()
      • WtuningJob.omega_wtune()
      • WtuningJob.to_dict()
      • WtuningJob.to_file()
      • WtuningJob.wtuning_cycle()
    • gauss_in_gen()
  • Module contents

Submodules

d3tales_api.database_info module

d3tales_api.database_info.db_info_generator(db_file=None)

Get information about database connections. This function requires either a db_file argument or a DB_INFO_FILE environment variable. This argument or environment variable should be a path to a JSON file containing connection information for the databases. The keys should be the database names such as frontend, backend, expflow, and fireworks.

Parameters

db_file – str, path to database info JSON file

Returns

JSON object containing information about database connections

d3tales_api.database_info.source_groups_generator(group_file=None)

Get information about database connections. This function requires either a group_file argument or a GROUP_FILE environment variable. This argument or environment variable should be a path to a JSON file containing source group information. The keys should be source group names and the values should be strings with two digit numbers, e.g., {“Risko”: “06”}.

Parameters

group_file – str, path to database info JSON file

Returns

JSON object containing information about source group codes

Module contents

d3tales_api.

API designed for the D3TaLES project. Includes data processing, database access functions, and property calculators. Pip install may require –use-deprecated=legacy-resolver