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)

apply() (fairmd.lipids.auxiliary.opconvertor.NamingRegistry class method) assign_resnames() (fairmd.lipids.analib.analyze_nmrpca.Topology method) atom_names() (fairmd.lipids.analib.analyze_nmrpca.Topology method) atoms_by() (fairmd.lipids.molecules.Lipid method)

B

block_average_time_series() (in module fairmd.lipids.auxiliary) (in module fairmd.lipids.auxiliary.routines)

build_nice_OPdict() (in module fairmd.lipids.auxiliary.opconvertor) build_universe() (fairmd.lipids.api.UniverseConstructor method)

C

calc_file_sha1_hash() (in module fairmd.lipids.databankio) calc_k_e() (in module fairmd.lipids.quality) calculate_time() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method) check_api() (in module developer.autocomplete_metadata) check_integrity() (in module developer.validate_data) check_mapping() (fairmd.lipids.molecules.Molecule method) checkForCH() (in module fairmd.lipids.quality) clear_mddata() (fairmd.lipids.api.UniverseConstructor method) clone_repo() (in module fairmd.lipids.bin.initialize_data) CompactJSONEncoder (class in fairmd.lipids.auxiliary) (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.CompactJSONEncoder attribute) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) create_simulation_directories() (in module fairmd.lipids.databankio)

D

data (fairmd.lipids.experiment.Experiment property) (fairmd.lipids.experiment.FFExperiment property) (fairmd.lipids.experiment.OPExperiment property) delete_info_file() (in module developer.process_info_file) DensityPlanar (class in fairmd.lipids.analib.maicos) developer module developer.align_mapping module developer.autocomplete_metadata module developer.process_info_file module

developer.run_global_analysis module developer.validate_data 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_mddata() (fairmd.lipids.api.UniverseConstructor method) download_resource_from_uri() (in module fairmd.lipids.databankio) download_toy_folder() (in module fairmd.lipids.bin.initialize_data) 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.CompactJSONEncoder method) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder method) evaluate_quality() (in module fairmd.lipids.bin.evaluate_quality) evaluated_percentage() (in module fairmd.lipids.quality) exp_id (fairmd.lipids.experiment.Experiment property) Experiment (class in fairmd.lipids.experiment) (class in fairmd.lipids.quality)

ExperimentCollection (class in fairmd.lipids.experiment) ExperimentError exptype (fairmd.lipids.experiment.Experiment property) (fairmd.lipids.experiment.FFExperiment property) (fairmd.lipids.experiment.OPExperiment property) extract_sameas() (in module developer.autocomplete_metadata)

F

fairmd module fairmd.lipids module fairmd.lipids.analib module fairmd.lipids.analib.analyze_nmrpca module fairmd.lipids.analib.databankop module, [1] fairmd.lipids.analib.formfactor module fairmd.lipids.analib.maicos module fairmd.lipids.analyze module fairmd.lipids.api module fairmd.lipids.auxiliary module fairmd.lipids.auxiliary.jsonEncoders module fairmd.lipids.auxiliary.mollib module fairmd.lipids.auxiliary.opconvertor module fairmd.lipids.auxiliary.routines 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.experiment module fairmd.lipids.ipylib module fairmd.lipids.ipylib.plottings module fairmd.lipids.molecules module fairmd.lipids.quality module fairmd.lipids.schema_validation module fairmd.lipids.schema_validation.engines module fairmd.lipids.schema_validation.validate_info_dict module fairmd.lipids.schema_validation.validate_yaml module fairmd.lipids.utils module FFExperiment (class in fairmd.lipids.experiment) filterCH() (in module fairmd.lipids.quality) find_OP() (in module fairmd.lipids.analib.databankop), [1] find_pairs_and_change_sims() (in module fairmd.lipids.bin.match_experiments) first_last_carbon() (in module fairmd.lipids.analib.maicos) FMDL_DATA_PATH (in module fairmd.lipids) FMDL_EXP_PATH (in module fairmd.lipids) FMDL_MAICOS_NCORES (in module fairmd.lipids) FMDL_MOL_PATH (in module fairmd.lipids) FMDL_SIMU_PATH (in module fairmd.lipids) FormFactorPlanar (class in fairmd.lipids.analib.maicos) 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_ApL_data() (in module fairmd.lipids.api) get_args() (in module developer.process_info_file) get_autocorrelations() (fairmd.lipids.analib.analyze_nmrpca.PCA method) get_brutto_formula() (in module developer.align_mapping) get_chebi() (in module developer.autocomplete_metadata) get_chembl() (in module developer.autocomplete_metadata) get_chembl_id_from_unichem() (in module developer.autocomplete_metadata) get_eqtimes() (in module fairmd.lipids.api) get_FF() (in module fairmd.lipids.api) get_ffq_scaling() (in module fairmd.lipids.quality) get_fragments() (in module fairmd.lipids.quality) get_hydration() (fairmd.lipids.core.System method) (fairmd.lipids.experiment.Experiment 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.quality.QualSimulation method) get_mean_ApL() (in module fairmd.lipids.api) get_mins_from_ffdata() (in module fairmd.lipids.analib.formfactor) get_nearest_value() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method) get_OP() (in module fairmd.lipids.api) get_proj() (fairmd.lipids.analib.analyze_nmrpca.PCA method) get_pubchem() (in module developer.autocomplete_metadata) get_pubchem_synonyms() (in module developer.autocomplete_metadata) get_quality() (in module fairmd.lipids.api) get_struc_top_traj_fnames() (in module fairmd.lipids.schema_validation.engines) get_tails_of_lipid() (in module fairmd.lipids.auxiliary.mollib) get_thickness() (in module fairmd.lipids.api) get_total_area() (in module fairmd.lipids.api) get_unichem() (in module developer.autocomplete_metadata) git_exists() (in module fairmd.lipids.bin.initialize_data) guess_elements() (in module fairmd.lipids.auxiliary.mollib)

H

HEADGRP (fairmd.lipids.analib.analyze_nmrpca.Topology attribute)

I

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

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.CompactJSONEncoder method) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder method)

L

Lipid (class in fairmd.lipids.molecules) lipids_set (in module fairmd.lipids.molecules) LipidSet (class in fairmd.lipids.molecules) load_existing_metadata() (in module developer.autocomplete_metadata) load_from_data() (fairmd.lipids.core.SystemsCollection static method) (fairmd.lipids.experiment.ExperimentCollection static method) (fairmd.lipids.molecules.LipidSet static method) (fairmd.lipids.molecules.NonLipidSet static method)

load_simulation_qe() (in module fairmd.lipids.quality) log_pairs() (in module fairmd.lipids.bin.match_experiments)

M

main() (in module developer.align_mapping) (in module developer.autocomplete_metadata) (in module developer.run_global_analysis) (in module fairmd.lipids.schema_validation.validate_yaml) 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.CompactJSONEncoder attribute) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) MAX_WIDTH (fairmd.lipids.auxiliary.CompactJSONEncoder attribute) (fairmd.lipids.auxiliary.jsonEncoders.CompactJSONEncoder attribute) md2uan() (fairmd.lipids.molecules.Molecule method) mda_gen_selection_mols() (in module fairmd.lipids.api) mda_read_trj_tilt_angles() (in module fairmd.lipids.api) membrane_composition() (fairmd.lipids.core.System method) (fairmd.lipids.experiment.Experiment method) metadata (fairmd.lipids.experiment.Experiment property) (fairmd.lipids.molecules.Lipid property) (fairmd.lipids.molecules.Molecule property) (fairmd.lipids.molecules.NonLipid property) module developer developer.align_mapping developer.autocomplete_metadata developer.process_info_file developer.run_global_analysis developer.validate_data fairmd fairmd.lipids fairmd.lipids.analib fairmd.lipids.analib.analyze_nmrpca fairmd.lipids.analib.databankop, [1] fairmd.lipids.analib.formfactor fairmd.lipids.analib.maicos fairmd.lipids.analyze fairmd.lipids.api fairmd.lipids.auxiliary fairmd.lipids.auxiliary.jsonEncoders fairmd.lipids.auxiliary.mollib fairmd.lipids.auxiliary.opconvertor fairmd.lipids.auxiliary.routines 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.experiment fairmd.lipids.ipylib fairmd.lipids.ipylib.plottings fairmd.lipids.molecules fairmd.lipids.quality fairmd.lipids.schema_validation fairmd.lipids.schema_validation.engines fairmd.lipids.schema_validation.validate_info_dict fairmd.lipids.schema_validation.validate_yaml fairmd.lipids.utils

molar_fraction() (fairmd.lipids.quality.QualSimulation method) Molecule (class in fairmd.lipids.molecules) molecule_ff_set (in module fairmd.lipids.molecules) MoleculeError MoleculeMappingError MoleculeSet (class in fairmd.lipids.molecules)

N

n_lipids (fairmd.lipids.core.System property) name (fairmd.lipids.molecules.Molecule property) names (fairmd.lipids.molecules.MoleculeSet property)

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

O

OPExperiment (class in fairmd.lipids.experiment)

P

parse_valid_config_settings() (in module fairmd.lipids.schema_validation.validate_info_dict) Parser (class in fairmd.lipids.analib.analyze_nmrpca) path (fairmd.lipids.experiment.Experiment property) paths (fairmd.lipids.api.UniverseConstructor property) 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_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) rdkit_object (fairmd.lipids.molecules.Lipid property) readme (fairmd.lipids.core.System property) (fairmd.lipids.experiment.Experiment property)

register_mapping() (fairmd.lipids.molecules.Molecule method) resolve_file_url() (in module fairmd.lipids.databankio) run_analysis() (in module developer.process_info_file) (in module fairmd.lipids.utils) run_dry_run() (in module developer.process_info_file) run_file() (in module fairmd.lipids.schema_validation.validate_yaml) 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) setup_folders() (in module developer.process_info_file) smi2uan() (fairmd.lipids.molecules.Lipid method)

solubles_set (in module fairmd.lipids.molecules) solution_composition() (fairmd.lipids.core.System method) (fairmd.lipids.experiment.Experiment method) System (class in fairmd.lipids.core) system (fairmd.lipids.api.UniverseConstructor property) systemQuality() (in module fairmd.lipids.quality) SystemsCollection (class in fairmd.lipids.core)

T

TAILSN1 (fairmd.lipids.analib.analyze_nmrpca.Topology attribute) TAILSN2 (fairmd.lipids.analib.analyze_nmrpca.Topology attribute) target_folder() (fairmd.lipids.experiment.Experiment class method) (fairmd.lipids.experiment.FFExperiment class method) (fairmd.lipids.experiment.OPExperiment class method)

TimeEstimator (class in fairmd.lipids.analib.analyze_nmrpca) timerelax() (fairmd.lipids.analib.analyze_nmrpca.TimeEstimator method) Topology (class in fairmd.lipids.analib.analyze_nmrpca) traj_centering_for_maicos_gromacs() (in module fairmd.lipids.analib.maicos) traj_centering_for_maicos_mda() (in module fairmd.lipids.analib.maicos) traj_centering_for_maicos_mda_parallel() (in module fairmd.lipids.analib.maicos)

U

uan2selection() (fairmd.lipids.molecules.Molecule method) uname2element() (in module fairmd.lipids.auxiliary.mollib)

UniverseConstructError UniverseConstructor (class in fairmd.lipids.api) update_metadata() (in module developer.autocomplete_metadata)

V

validate_info_dict() (in module fairmd.lipids.schema_validation.validate_yaml) validate_info_file() (in module fairmd.lipids.schema_validation.validate_yaml) validate_readme_dict() (in module fairmd.lipids.schema_validation.validate_yaml) validate_readme_file() (in module fairmd.lipids.schema_validation.validate_yaml)

verify_data() (fairmd.lipids.experiment.Experiment method) (fairmd.lipids.experiment.FFExperiment method) (fairmd.lipids.experiment.OPExperiment method) verify_lipid() (fairmd.lipids.analib.analyze_nmrpca.Parser static method)

Y

YamlBadConfigError