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searchindex.js
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Search.setIndex({"alltitles": {"AUTHORS_CONTACT": [[3, "authors-contact"]], "AddData module": [[0, "adddata-module"]], "Adding experimental data into the NMRlipids databank": [[5, "adding-experimental-data-into-the-nmrlipids-databank"], [14, "adding-experimental-data-into-the-nmrlipids-databank"]], "Adding simulations into the NMRlipids databank": [[4, "adding-simulations-into-the-nmrlipids-databank"], [14, "adding-simulations-into-the-nmrlipids-databank"]], "BATCHID": [[3, "batchid"]], "BuildDatabank": [[16, "builddatabank"]], "COMPOSITION (compulsory)": [[3, "composition-compulsory"]], "COMPOSITION (output)": [[3, "composition-output"]], "COUNTER_IONS": [[5, "counter-ions"]], "CPT (Gromacs)": [[3, "cpt-gromacs"]], "Contents:": [[14, null]], "DATEOFRUNNIG": [[3, "dateofrunnig"]], "DIR_WRK (compulsory)": [[3, "dir-wrk-compulsory"]], "DOI (compulsory)": [[3, "doi-compulsory"]], "DOI:": [[5, "doi"]], "EDR (Gromacs)": [[3, "edr-gromacs"]], "EXPERIMENT": [[3, "experiment"]], "Examples and tutorials": [[13, "examples-and-tutorials"]], "FF": [[3, "ff"]], "FF_DATE": [[3, "ff-date"]], "FF_SOURCE": [[3, "ff-source"]], "FormFactor.json": [[15, "formfactor-json"]], "FormFactorQuality.json": [[15, "formfactorquality-json"]], "ID": [[3, "id"]], "ION_CONCENTRATIONS": [[5, "ion-concentrations"]], "Indices and tables": [[14, "indices-and-tables"]], "Individual force field names for molecules": [[3, "individual-force-field-names-for-molecules"]], "LOG (Gromacs)": [[3, "log-gromacs"]], "List and descriptions of NMRlipids databank files": [[15, "list-and-descriptions-of-nmrlipids-databank-files"]], "MOLAR_FRACTIONS": [[5, "molar-fractions"]], "Molecule names": [[17, "id1"]], "NMRlipids Databank-API": [[14, "nmrlipids-databank-api"]], "NMRlipids Databank-GUI": [[14, "nmrlipids-databank-gui"]], "NMRlipids databank API functions": [[11, "nmrlipids-databank-api-functions"]], "NMRlipids databank is an overlay databank.": [[14, "nmrlipids-databank-is-an-overlay-databank"]], "NUMBER_OF_ATOMS": [[3, "number-of-atoms"]], "OrderParameter module": [[1, "module-OrderParameter"]], "PREEQTIME (compulsory)": [[3, "preeqtime-compulsory"]], "PUBLICATION": [[3, "publication"]], "Plotting basic simulation properties": [[13, "id1"]], "QualityEvaluation module": [[2, "module-QualityEvaluation"]], "README.yaml": [[15, "readme-yaml"]], "SOFTWARE (compulsory)": [[3, "software-compulsory"]], "SOFTWARE_VERSION": [[3, "software-version"]], "SYSTEM (compulsory)": [[3, "system-compulsory"]], "SYSTEM_quality.json": [[15, "system-quality-json"]], "Show ranking tables of simulations based in their quality against experimental data": [[13, "id2"]], "Showing statistics from the NMRlipids databank": [[13, "id9"]], "Steps to add experimental data": [[5, "steps-to-add-experimental-data"]], "System requirements": [[14, "system-requirements"]], "TEMPERATURE": [[3, "temperature"], [5, "temperature"]], "TIMELEFTOUT (compulsory)": [[3, "timeleftout-compulsory"]], "TOP (Gromacs)": [[3, "top-gromacs"]], "TOTAL_LIPID_CONCENTRATION": [[5, "total-lipid-concentration"]], "TPR (compulsory)": [[3, "tpr-compulsory"]], "TRAJECTORY_SIZE": [[3, "trajectory-size"]], "TRJ (compulsory)": [[3, "trj-compulsory"]], "TRJLENGTH": [[3, "trjlength"]], "TYPEOFSYSTEM (compulsory)": [[3, "typeofsystem-compulsory"]], "Template for more advance API usage": [[13, "id6"]], "TotalDensity.json": [[15, "totaldensity-json"]], "UNITEDATOM_DICT (compulsory for united atom trajectories)": [[3, "unitedatom-dict-compulsory-for-united-atom-trajectories"]], "Universal atom names in mapping files": [[17, "universal-atom-names-in-mapping-files"]], "Universal molecule and atom names": [[17, "universal-molecule-and-atom-names"]], "User input and content of README.yaml files": [[3, "user-input-and-content-of-readme-yaml-files"]], "Welcome to NMRlipids databank\u2019s documentation!": [[14, "welcome-to-nmrlipids-databank-s-documentation"]], "apl.json": [[15, "apl-json"]], "buildH_calcOP_test module": [[6, "module-buildH_calcOP_test"]], "check_bonds module": [[7, "check-bonds-module"]], "check_densities module": [[8, "module-check_densities"]], "check_mappings module": [[9, "module-check_mappings"]], "createPDBs module": [[10, "module-createPDBs"]], "dic_lipids module": [[12, "module-dic_lipids"]], "eq_times.json": [[15, "eq-times-json"]], "info.yaml": [[15, "info-yaml"]], "mapping files": [[15, "mapping-files"]], "openmm_parser module": [[18, "module-openmm_parser"]], "searchDATABANK module": [[19, "module-searchDATABANK"]], "thickness.json": [[15, "thickness-json"]], "{lipid name}_FragmentQuality.json": [[15, "lipid-name-fragmentquality-json"]], "{lipid name}_OrderParameters.json": [[15, "lipid-name-orderparameters-json"]], "{lipid name}_OrderParameters_quality.json": [[15, "lipid-name-orderparameters-quality-json"]]}, "docnames": ["AddData", "OrderParameter", "QualityEvaluation", "READMEcontent", "addingData", "addingExpData", "buildH_calcOP_test", "check_bonds", "check_densities", 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"buildH_calcOP_test.calc_rotation_matrix", false]], "calc_z_dim() (in module orderparameter)": [[1, "OrderParameter.calc_z_dim", false]], "calcarea() (in module databanklibrary)": [[11, "databankLibrary.calcArea", false]], "calcareapermolecule() (in module databanklibrary)": [[11, "databankLibrary.CalcAreaPerMolecule", false]], "calclipidfraction() (in module databanklibrary)": [[11, "databankLibrary.calcLipidFraction", false]], "check_densities": [[8, "module-check_densities", false]], "check_mappings": [[9, "module-check_mappings", false]], "checkforch() (in module qualityevaluation)": [[2, "QualityEvaluation.checkForCH", false]], "createpdbs": [[10, "module-createPDBs", false]], "cross_product() (in module buildh_calcop_test)": [[6, "buildH_calcOP_test.cross_product", false]], "data (class in searchdatabank)": [[19, "searchDATABANK.Data", false]], "databanklibrary": [[11, "module-databankLibrary", false]], "dic_lipids": [[12, "module-dic_lipids", false]], "dihedrals (class in 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