Index

A

add() (fairmd.lipids.molecules.MoleculeSet method) add_simulation() (in module fairmd.lipids.bin.add_simulation) align_traj() (fairmd.lipids.analib.analyze_nmrpca.Concatenator method)

assign_resnames() (fairmd.lipids.analib.analyze_nmrpca.Topology method) atom_names() (fairmd.lipids.analib.analyze_nmrpca.Topology method) averageOrderParameters() (in module fairmd.lipids.databankLibrary)

C

calc_file_sha1_hash() (in module fairmd.lipids.databankio) calc_k_e() (in module fairmd.lipids.quality) calcArea() (in module fairmd.lipids.databankLibrary) CalcAreaPerMolecule() (in module fairmd.lipids.databankLibrary) calcLipidFraction() (in module fairmd.lipids.databankLibrary) calculate_time() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method) check_api() (in module developer.AutocompleteMetadata) check_integrity() (in module developer.ValidateData) check_mapping() (fairmd.lipids.molecules.Molecule method) checkForCH() (in module fairmd.lipids.quality) clone_repo() (in module fairmd.lipids.bin.initialize_data) CompactJSONEncoder (class in fairmd.lipids.auxiliary.jsonEncoders) compare_neutralized() (in module developer.align_mapping)

compute_databank() (in module fairmd.lipids.bin.compute_databank) computeAPL() (in module fairmd.lipids.analyze) computeMAICOS() (in module fairmd.lipids.analyze) computeNMRPCA() (in module fairmd.lipids.analyze) computeOP() (in module fairmd.lipids.analyze) computeTH() (in module fairmd.lipids.analyze) concatenate() (fairmd.lipids.analib.analyze_nmrpca.Concatenator method) concatenate_traj() (fairmd.lipids.analib.analyze_nmrpca.Concatenator method) (fairmd.lipids.analib.analyze_nmrpca.Parser method) concatenate_traj_with_merging() (fairmd.lipids.analib.analyze_nmrpca.Concatenator method) Concatenator (class in fairmd.lipids.analib.analyze_nmrpca) CONTAINER_TYPES (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) content (fairmd.lipids.core.System property) create_databank_directories() (in module fairmd.lipids.databankio)

D

Databank (class in fairmd.lipids.core) delete_info_file() (in module developer.ProcessInfoFile) DensityPlanar (class in fairmd.lipids.analib.maicos) developer module developer.align_mapping module developer.AutocompleteMetadata module developer.ProcessInfoFile module developer.RunAnalysis module

developer.ValidateData module DielectricPlanar (class in fairmd.lipids.analib.maicos) DiporderPlanar (class in fairmd.lipids.analib.maicos) discard() (fairmd.lipids.molecules.MoleculeSet method) download_and_extract_zip() (in module fairmd.lipids.bin.initialize_data) download_resource_from_uri() (in module fairmd.lipids.databankio) download_toy_folder() (in module fairmd.lipids.bin.initialize_data) download_traj() (fairmd.lipids.analib.analyze_nmrpca.Parser method) download_with_progress_with_retry() (in module fairmd.lipids.databankio) dump_data() (fairmd.lipids.analib.analyze_nmrpca.Parser method)

E

encode() (fairmd.lipids.analib.maicos.NumpyArrayEncoder method) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder method) evaluate_quality() (in module fairmd.lipids.bin.evaluate_quality)

evaluated_percentage() (in module fairmd.lipids.quality) Experiment (class in fairmd.lipids.bin.match_experiments) (class in fairmd.lipids.quality) extract_sameas() (in module developer.AutocompleteMetadata)

F

fairmd module fairmd.lipids module fairmd.lipids.analib module fairmd.lipids.analib.analyze_nmrpca module fairmd.lipids.analib.databankop module fairmd.lipids.analib.maicos module fairmd.lipids.analyze module fairmd.lipids.auxiliary module fairmd.lipids.auxiliary.elements module fairmd.lipids.auxiliary.jsonEncoders module fairmd.lipids.bin module fairmd.lipids.bin.add_simulation module, [1] fairmd.lipids.bin.compute_databank module, [1] fairmd.lipids.bin.evaluate_quality module, [1] fairmd.lipids.bin.initialize_data module, [1] fairmd.lipids.bin.make_ranking module, [1] fairmd.lipids.bin.match_experiments module, [1] fairmd.lipids.core module

fairmd.lipids.databankio module fairmd.lipids.databankLibrary module fairmd.lipids.ipylib module fairmd.lipids.ipylib.jpyroutines module fairmd.lipids.ipylib.plottings module fairmd.lipids.molecules module fairmd.lipids.quality module fairmd.lipids.SchemaValidation module fairmd.lipids.SchemaValidation.engines module fairmd.lipids.SchemaValidation.ValidateYAML module fairmd.lipids.utils module filterCH() (in module fairmd.lipids.quality) find_OP() (in module fairmd.lipids.analib.databankop) find_pairs() (in module fairmd.lipids.bin.match_experiments) find_uname() (in module developer.align_mapping) first_last_carbon() (in module fairmd.lipids.analib.maicos) FMDL_DATA_PATH (in module fairmd.lipids) FMDL_EXP_PATH (in module fairmd.lipids) FMDL_MOL_PATH (in module fairmd.lipids) FMDL_SIMU_PATH (in module fairmd.lipids) FormFactorMinFromData() (in module fairmd.lipids.quality) FormFactorPlanar (class in fairmd.lipids.analib.maicos) formfactorQuality() (in module fairmd.lipids.quality) formfactorQualitySIMtoEXP() (in module fairmd.lipids.quality) fragmentQuality() (in module fairmd.lipids.quality) fragmentQualityAvg() (in module fairmd.lipids.quality)

G

get() (fairmd.lipids.molecules.MoleculeSet method) get_1mol_selstr() (in module developer.align_mapping) get_args() (in module developer.ProcessInfoFile) get_autocorrelations() (fairmd.lipids.analib.analyze_nmrpca.PCA method) get_brutto_formula() (in module developer.align_mapping) get_chebi() (in module developer.AutocompleteMetadata) get_chembl() (in module developer.AutocompleteMetadata) get_chembl_id_from_unichem() (in module developer.AutocompleteMetadata) get_file_size_with_retry() (in module fairmd.lipids.databankio) get_fragments() (in module fairmd.lipids.quality) get_ions() (fairmd.lipids.bin.match_experiments.Experiment method) (fairmd.lipids.bin.match_experiments.SearchSystem method) get_latest_release_tag() (in module fairmd.lipids.bin.initialize_data) get_lipid_autocorrelation() (fairmd.lipids.analib.analyze_nmrpca.PCA method) get_lipid_resnames() (fairmd.lipids.analib.analyze_nmrpca.Topology method) get_lipids() (fairmd.lipids.bin.match_experiments.Experiment method) (fairmd.lipids.bin.match_experiments.SearchSystem method) (fairmd.lipids.quality.QualSimulation method)

get_nearest_value() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method) get_proj() (fairmd.lipids.analib.analyze_nmrpca.PCA method) get_pubchem() (in module developer.AutocompleteMetadata) get_pubchem_synonyms() (in module developer.AutocompleteMetadata) get_struc_top_traj_fnames() (in module fairmd.lipids.SchemaValidation.engines) get_systems() (fairmd.lipids.core.Databank method) get_unichem() (in module developer.AutocompleteMetadata) getAtoms() (in module fairmd.lipids.databankLibrary) GetEquilibrationTimes() (in module fairmd.lipids.databankLibrary) GetFormFactorMin() (in module fairmd.lipids.databankLibrary) getHydrationLevel() (in module fairmd.lipids.databankLibrary) getLipids() (in module fairmd.lipids.databankLibrary) GetNlipids() (in module fairmd.lipids.databankLibrary) GetOP() (in module fairmd.lipids.databankLibrary) GetThickness() (in module fairmd.lipids.databankLibrary) git_exists() (in module fairmd.lipids.bin.initialize_data) guess_elements() (in module fairmd.lipids.auxiliary.elements)

I

idx_path (fairmd.lipids.bin.match_experiments.SearchSystem attribute) indent_str (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder property) initialize_data() (in module fairmd.lipids.bin.initialize_data) initialize_databank() (in module fairmd.lipids.core)

ion_conc() (fairmd.lipids.bin.match_experiments.SearchSystem method) is_merge_needed() (fairmd.lipids.analib.analyze_nmrpca.Topology method) is_system_suitable_4_maicos() (in module fairmd.lipids.analib.maicos) iterencode() (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder method)

L

Lipid (class in fairmd.lipids.molecules) lipids_dict (in module fairmd.lipids.molecules) lipids_set (in module fairmd.lipids.molecules) LipidSet (class in fairmd.lipids.molecules) load_existing_metadata() (in module developer.AutocompleteMetadata) load_experiments() (in module fairmd.lipids.bin.match_experiments)

load_from_data() (fairmd.lipids.molecules.LipidSet static method) (fairmd.lipids.molecules.NonLipidSet static method) load_simulations() (in module fairmd.lipids.bin.match_experiments) loadSimulations() (in module fairmd.lipids.quality) loc() (fairmd.lipids.core.SystemsCollection method) log_pairs() (in module fairmd.lipids.bin.match_experiments)

M

main() (in module developer.align_mapping) (in module developer.AutocompleteMetadata) (in module developer.RunAnalysis) make_ranking() (in module fairmd.lipids.bin.make_ranking) mapping_dict (fairmd.lipids.molecules.Molecule property) mapping_file (fairmd.lipids.molecules.Molecule property) match_experiments() (in module fairmd.lipids.bin.match_experiments) MAX_ITEMS (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) MAX_WIDTH (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) md2uan() (fairmd.lipids.molecules.Molecule method) metadata (fairmd.lipids.molecules.Lipid property) (fairmd.lipids.molecules.Molecule property) (fairmd.lipids.molecules.NonLipid property) mk_universe_compact() (in module developer.align_mapping) module developer developer.align_mapping developer.AutocompleteMetadata developer.ProcessInfoFile developer.RunAnalysis developer.ValidateData fairmd fairmd.lipids fairmd.lipids.analib fairmd.lipids.analib.analyze_nmrpca fairmd.lipids.analib.databankop fairmd.lipids.analib.maicos fairmd.lipids.analyze fairmd.lipids.auxiliary fairmd.lipids.auxiliary.elements fairmd.lipids.auxiliary.jsonEncoders fairmd.lipids.bin fairmd.lipids.bin.add_simulation, [1] fairmd.lipids.bin.compute_databank, [1] fairmd.lipids.bin.evaluate_quality, [1] fairmd.lipids.bin.initialize_data, [1] fairmd.lipids.bin.make_ranking, [1] fairmd.lipids.bin.match_experiments, [1] fairmd.lipids.core fairmd.lipids.databankio fairmd.lipids.databankLibrary fairmd.lipids.ipylib fairmd.lipids.ipylib.jpyroutines fairmd.lipids.ipylib.plottings fairmd.lipids.molecules fairmd.lipids.quality fairmd.lipids.SchemaValidation fairmd.lipids.SchemaValidation.engines fairmd.lipids.SchemaValidation.ValidateYAML fairmd.lipids.utils

molar_fraction() (fairmd.lipids.bin.match_experiments.SearchSystem method) (fairmd.lipids.quality.QualSimulation method) Molecule (class in fairmd.lipids.molecules) molecule_ff_set (in module fairmd.lipids.molecules) MoleculeError MoleculeMappingError molecules_dict (in module fairmd.lipids.molecules) molecules_set (in module fairmd.lipids.molecules) MoleculeSet (class in fairmd.lipids.molecules)

N

name (fairmd.lipids.molecules.Molecule property) names (fairmd.lipids.molecules.MoleculeSet property)

NonLipid (class in fairmd.lipids.molecules) NonLipidSet (class in fairmd.lipids.molecules) NumpyArrayEncoder (class in fairmd.lipids.analib.maicos)

P

Parser (class in fairmd.lipids.analib.analyze_nmrpca) PCA (class in fairmd.lipids.analib.analyze_nmrpca) PCA() (fairmd.lipids.analib.analyze_nmrpca.PCA method) plotSimulation() (in module fairmd.lipids.ipylib) (in module fairmd.lipids.ipylib.plottings)

prepare_gmx_traj() (fairmd.lipids.analib.analyze_nmrpca.Parser method) prepare_OpenMM_traj() (fairmd.lipids.analib.analyze_nmrpca.Parser method) prepare_traj() (fairmd.lipids.analib.analyze_nmrpca.Parser method) print_README() (in module fairmd.lipids.core) prob_S_in_g() (in module fairmd.lipids.quality)

Q

QualSimulation (class in fairmd.lipids.quality)

R

RCODE_COMPUTED (in module fairmd.lipids) RCODE_ERROR (in module fairmd.lipids) RCODE_SKIPPED (in module fairmd.lipids) read_trj_PN_angles() (in module fairmd.lipids.databankLibrary) readme (fairmd.lipids.core.System property) register_mapping() (fairmd.lipids.molecules.Molecule method)

resolve_doi_url() (in module fairmd.lipids.databankio) resolve_download_file_url() (in module fairmd.lipids.databankio) retry_with_exponential_backoff() (in module fairmd.lipids.databankio) run_analysis() (in module developer.ProcessInfoFile) (in module fairmd.lipids.utils) run_dry_run() (in module developer.ProcessInfoFile) run_merger() (fairmd.lipids.analib.analyze_nmrpca.Topology method)

S

save() (fairmd.lipids.analib.maicos.DensityPlanar method) (fairmd.lipids.analib.maicos.DielectricPlanar method) (fairmd.lipids.analib.maicos.DiporderPlanar method) (fairmd.lipids.analib.maicos.FormFactorPlanar method) SearchSystem (class in fairmd.lipids.bin.match_experiments) setup_folders() (in module developer.ProcessInfoFile) ShowEquilibrationTimes() (in module fairmd.lipids.databankLibrary)

showTable() (in module fairmd.lipids.ipylib) (in module fairmd.lipids.ipylib.jpyroutines) System (class in fairmd.lipids.core) system (fairmd.lipids.bin.match_experiments.SearchSystem attribute) system2MDanalysisUniverse() (in module fairmd.lipids.databankLibrary) systemQuality() (in module fairmd.lipids.quality) SystemsCollection (class in fairmd.lipids.core)

T

TimeEstimator (class in fairmd.lipids.analib.analyze_nmrpca) timerelax() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method)

Topology (class in fairmd.lipids.analib.analyze_nmrpca) total_lipid_conc() (fairmd.lipids.bin.match_experiments.SearchSystem method) traj_centering_for_maicos() (in module fairmd.lipids.analib.maicos)

U

uan2selection() (fairmd.lipids.molecules.Molecule method)

uname2element() (in module fairmd.lipids.auxiliary.elements) update_metadata() (in module developer.AutocompleteMetadata)

V

validate_info_dict() (in module fairmd.lipids.SchemaValidation.ValidateYAML)

validate_info_file() (in module fairmd.lipids.SchemaValidation.ValidateYAML) validate_path() (fairmd.lipids.analib.analyze_nmrpca.Parser method)