Index

A

add() (Scripts.DatabankLib.settings.molecules.MoleculeSet method) align_traj() (Scripts.DatabankLib.analyze_nmrpca.Concatenator method) apply_rotation() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test)

assign_electrons() (Scripts.DatabankLib.form_factor.FormFactor method) assign_resnames() (Scripts.DatabankLib.analyze_nmrpca.Topology method) atom_names() (Scripts.DatabankLib.analyze_nmrpca.Topology method) averageOrderParameters() (in module Scripts.DatabankLib.databankLibrary)

B

build_all_Hs_calc_OP() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) BuildDatabank.AddData module BuildDatabank.buildH_calcOP_test module BuildDatabank.check_mappings module

BuildDatabank.makeRanking module BuildDatabank.QualityEvaluation module BuildDatabank.searchDATABANK module buildHs_on_1C() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test)

C

calc_angle() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) calc_k_e() (in module Scripts.DatabankLib.quality) calc_OP() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) calc_rotation_matrix() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) calcArea() (in module Scripts.DatabankLib.databankLibrary) CalcAreaPerMolecule() (in module Scripts.DatabankLib.databankLibrary) calcLipidFraction() (in module Scripts.DatabankLib.databankLibrary) calculate_density() (Scripts.DatabankLib.form_factor.FormFactor method) calculate_time() (Scripts.DatabankLib.analyze_nmrpca.TimeEstimator method) calculate_weight() (Scripts.DatabankLib.form_factor.FormFactor method) checkForCH() (in module Scripts.DatabankLib.quality)

CompactJSONEncoder (class in Scripts.DatabankLib.jsonEncoders) computeAPL() (in module Scripts.DatabankLib.analyze) computeFF() (in module Scripts.DatabankLib.analyze) computeNMRPCA() (in module Scripts.DatabankLib.analyze) computeOP() (in module Scripts.DatabankLib.analyze) computeTH() (in module Scripts.DatabankLib.analyze) concatenate() (Scripts.DatabankLib.analyze_nmrpca.Concatenator method) concatenate_traj() (Scripts.DatabankLib.analyze_nmrpca.Concatenator method) (Scripts.DatabankLib.analyze_nmrpca.Parser method) concatenate_traj_with_merging() (Scripts.DatabankLib.analyze_nmrpca.Concatenator method) Concatenator (class in Scripts.DatabankLib.analyze_nmrpca) CONTAINER_TYPES (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder attribute) content (Scripts.DatabankLib.core.System property) cross_product() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test)

D

DatabankLib.databankop module delete_info_file() (in module Scripts.WorkflowScripts.Workflow_utils)

discard() (Scripts.DatabankLib.settings.molecules.MoleculeSet method) download_traj() (Scripts.DatabankLib.analyze_nmrpca.Parser method) dump_data() (Scripts.DatabankLib.analyze_nmrpca.Parser method)

E

encode() (Scripts.DatabankLib.form_factor.NumpyArrayEncoder method) (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder method) evaluated_percentage() (in module Scripts.DatabankLib.quality)

Experiment (class in BuildDatabank.searchDATABANK) (class in Scripts.BuildDatabank.searchDATABANK) (class in Scripts.DatabankLib.quality)

F

fast_build_all_Hs_calc_OP() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) fast_buildHs_on_1C() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) filterCH() (in module Scripts.DatabankLib.quality) find_OP() (in module DatabankLib.databankop) (in module Scripts.DatabankLib.databankop) find_pairs() (in module BuildDatabank.searchDATABANK) (in module Scripts.BuildDatabank.searchDATABANK)

FormFactor (class in Scripts.DatabankLib.form_factor) FormFactorMinFromData() (in module Scripts.DatabankLib.quality) formfactorQuality() (in module Scripts.DatabankLib.quality) formfactorQualitySIMtoEXP() (in module Scripts.DatabankLib.quality) fourier() (Scripts.DatabankLib.form_factor.FormFactor method) fragmentQuality() (in module Scripts.DatabankLib.quality) fragmentQualityAvg() (in module Scripts.DatabankLib.quality)

G

get_args() (in module Scripts.WorkflowScripts.ProcessInfoFile) get_autocorrelations() (Scripts.DatabankLib.analyze_nmrpca.PCA method) get_CH() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) get_CH2() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) get_CH3() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) get_CH_double_bond() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) get_databank_paths() (in module Scripts.WorkflowScripts.Workflow_utils) get_electrons() (Scripts.DatabankLib.form_factor.FormFactor static method) get_fragments() (in module Scripts.DatabankLib.quality) get_indexes() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) get_ions() (BuildDatabank.searchDATABANK.Experiment method) (BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.BuildDatabank.searchDATABANK.Experiment method) (Scripts.BuildDatabank.searchDATABANK.SearchSystem method)

get_lipid_autocorrelation() (Scripts.DatabankLib.analyze_nmrpca.PCA method) get_lipid_resnames() (Scripts.DatabankLib.analyze_nmrpca.Topology method) get_lipids() (BuildDatabank.searchDATABANK.Experiment method) (BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.BuildDatabank.searchDATABANK.Experiment method) (Scripts.BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.DatabankLib.quality.QualSimulation method) get_nearest_value() (Scripts.DatabankLib.analyze_nmrpca.TimeEstimator method) get_proj() (Scripts.DatabankLib.analyze_nmrpca.PCA method) get_struc_top_traj_fnames() (in module Scripts.DatabankLib.settings.engines) getAtoms() (in module Scripts.DatabankLib.databankLibrary) GetFormFactorMin() (in module Scripts.DatabankLib.databankLibrary) getHydrationLevel() (in module Scripts.DatabankLib.databankLibrary) getLipids() (in module Scripts.DatabankLib.databankLibrary) GetNlipids() (in module Scripts.DatabankLib.databankLibrary) GetThickness() (in module Scripts.DatabankLib.databankLibrary) getUniversalAtomName() (in module Scripts.DatabankLib.databankLibrary)

I

idx_path (BuildDatabank.searchDATABANK.SearchSystem attribute) (Scripts.BuildDatabank.searchDATABANK.SearchSystem attribute) indent_str (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder property) init_dic_OP() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test)

initialize_databank() (in module Scripts.DatabankLib.core) ion_conc() (BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.BuildDatabank.searchDATABANK.SearchSystem method) is_merge_needed() (Scripts.DatabankLib.analyze_nmrpca.Topology method) iterencode() (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder method)

L

Lipid (class in Scripts.DatabankLib.settings.molecules) lipids_dict (in module Scripts.DatabankLib.settings.molecules) lipids_set (in module Scripts.DatabankLib.settings.molecules) LipidSet (class in Scripts.DatabankLib.settings.molecules) load_experiments() (in module BuildDatabank.searchDATABANK) (in module Scripts.BuildDatabank.searchDATABANK) load_from_data() (Scripts.DatabankLib.settings.molecules.LipidSet static method) (Scripts.DatabankLib.settings.molecules.NonLipidSet static method)

load_simulations() (in module BuildDatabank.searchDATABANK) (in module Scripts.BuildDatabank.searchDATABANK) loadMappingFile() (in module Scripts.DatabankLib.databankLibrary) loadSimulations() (in module Scripts.DatabankLib.quality) loc() (Scripts.DatabankLib.core.SystemsCollection method) log_pairs() (in module BuildDatabank.searchDATABANK) (in module Scripts.BuildDatabank.searchDATABANK)

M

main() (in module BuildDatabank.buildH_calcOP_test) (in module BuildDatabank.searchDATABANK) (in module Scripts.BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.searchDATABANK) (in module Scripts.BuildDocs.source.run_apidoc) (in module Scripts.WorkflowScripts.ProcessInfoFile) (in module Scripts.WorkflowScripts.RunAnalysis) make_dic_atname2genericname() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) make_dic_Cname2Hnames() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) make_dic_lipids_with_indexes() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) mapping_dict (Scripts.DatabankLib.settings.molecules.Molecule property) MAX_ITEMS (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder attribute) MAX_WIDTH (Scripts.DatabankLib.jsonEncoders.CompactJSONEncoder attribute) module BuildDatabank.AddData BuildDatabank.buildH_calcOP_test BuildDatabank.check_mappings BuildDatabank.makeRanking BuildDatabank.QualityEvaluation BuildDatabank.searchDATABANK DatabankLib.databankop Scripts Scripts.AnalyzeDatabank Scripts.AnalyzeDatabank.calc_FormFactors Scripts.AnalyzeDatabank.calc_thickness Scripts.AnalyzeDatabank.calcAPL Scripts.AnalyzeDatabank.calcOrderParameters Scripts.AnalyzeDatabank.NMRPCA_timerelax Scripts.BuildDatabank Scripts.BuildDatabank.AddData Scripts.BuildDatabank.buildH_calcOP_test Scripts.BuildDatabank.check_bonds Scripts.BuildDatabank.check_densities Scripts.BuildDatabank.check_mappings Scripts.BuildDatabank.makeRanking Scripts.BuildDatabank.QualityEvaluation Scripts.BuildDatabank.searchDATABANK Scripts.BuildDocs Scripts.BuildDocs.source Scripts.BuildDocs.source.conf Scripts.BuildDocs.source.run_apidoc Scripts.DatabankLib Scripts.DatabankLib.analyze Scripts.DatabankLib.analyze_nmrpca Scripts.DatabankLib.core Scripts.DatabankLib.databankio Scripts.DatabankLib.databankLibrary Scripts.DatabankLib.databankop Scripts.DatabankLib.form_factor Scripts.DatabankLib.jsonEncoders Scripts.DatabankLib.openmm_parser Scripts.DatabankLib.plottings Scripts.DatabankLib.quality Scripts.DatabankLib.settings Scripts.DatabankLib.settings.dic_lipids_UA Scripts.DatabankLib.settings.engines Scripts.DatabankLib.settings.molecules Scripts.DatabankLib.utils Scripts.updateGUI Scripts.updateGUI.createPDBs Scripts.WorkflowScripts Scripts.WorkflowScripts.ProcessInfoFile Scripts.WorkflowScripts.RunAnalysis Scripts.WorkflowScripts.Workflow_utils updateGUI.createPDBs

molar_fraction() (BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.DatabankLib.quality.QualSimulation method) Molecule (class in Scripts.DatabankLib.settings.molecules) molecule_ff_set (in module Scripts.DatabankLib.settings.molecules) molecules_dict (in module Scripts.DatabankLib.settings.molecules) molecules_set (in module Scripts.DatabankLib.settings.molecules) MoleculeSet (class in Scripts.DatabankLib.settings.molecules)

N

name (Scripts.DatabankLib.settings.molecules.Molecule property) names (Scripts.DatabankLib.settings.molecules.MoleculeSet property) NMLDB_DATA_PATH (in module Scripts.DatabankLib) NMLDB_EXP_PATH (in module Scripts.DatabankLib) NMLDB_MOL_PATH (in module Scripts.DatabankLib) NMLDB_ROOT_PATH (in module Scripts.DatabankLib) NMLDB_SIMU_PATH (in module Scripts.DatabankLib)

NonLipid (class in Scripts.DatabankLib.settings.molecules) NonLipidSet (class in Scripts.DatabankLib.settings.molecules) norm() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) normalize() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) NumpyArrayEncoder (class in Scripts.DatabankLib.form_factor)

O

openmm_input() (in module Scripts.DatabankLib.openmm_parser)

OpenMMParser (class in Scripts.DatabankLib.openmm_parser)

P

pandasdf2pdb() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) parse_op_input() (in module DatabankLib.databankop) (in module Scripts.DatabankLib.databankop) parseCommandLineArgs() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test) Parser (class in Scripts.DatabankLib.analyze_nmrpca)

PCA (class in Scripts.DatabankLib.analyze_nmrpca) PCA() (Scripts.DatabankLib.analyze_nmrpca.PCA method) plotSimulation() (in module Scripts.DatabankLib.plottings) prepare_gmx_traj() (Scripts.DatabankLib.analyze_nmrpca.Parser method) prepare_OpenMM_traj() (Scripts.DatabankLib.analyze_nmrpca.Parser method) prepare_traj() (Scripts.DatabankLib.analyze_nmrpca.Parser method) print_README() (in module Scripts.DatabankLib.core) prob_S_in_g() (in module Scripts.DatabankLib.quality)

Q

QualSimulation (class in Scripts.DatabankLib.quality)

R

RCODE_COMPUTED (in module Scripts.DatabankLib) RCODE_ERROR (in module Scripts.DatabankLib) RCODE_SKIPPED (in module Scripts.DatabankLib) read_inp_input() (in module Scripts.DatabankLib.openmm_parser) read_trj_PN_angles() (in module Scripts.DatabankLib.databankLibrary) read_xml_input() (in module Scripts.DatabankLib.openmm_parser)

readme (Scripts.DatabankLib.core.System property) register_mapping() (Scripts.DatabankLib.settings.molecules.Molecule method) residue_electrons_all() (Scripts.DatabankLib.form_factor.FormFactor method) run_analysis() (in module Scripts.DatabankLib.utils) run_command() (in module Scripts.WorkflowScripts.Workflow_utils) run_merger() (Scripts.DatabankLib.analyze_nmrpca.Topology method) run_python_script() (in module Scripts.WorkflowScripts.Workflow_utils)

S

Scripts module Scripts.AnalyzeDatabank module Scripts.AnalyzeDatabank.calc_FormFactors module Scripts.AnalyzeDatabank.calc_thickness module Scripts.AnalyzeDatabank.calcAPL module Scripts.AnalyzeDatabank.calcOrderParameters module Scripts.AnalyzeDatabank.NMRPCA_timerelax module Scripts.BuildDatabank module Scripts.BuildDatabank.AddData module Scripts.BuildDatabank.buildH_calcOP_test module Scripts.BuildDatabank.check_bonds module Scripts.BuildDatabank.check_densities module Scripts.BuildDatabank.check_mappings module Scripts.BuildDatabank.makeRanking module Scripts.BuildDatabank.QualityEvaluation module Scripts.BuildDatabank.searchDATABANK module Scripts.BuildDocs module Scripts.BuildDocs.source module Scripts.BuildDocs.source.conf module Scripts.BuildDocs.source.run_apidoc module Scripts.DatabankLib module Scripts.DatabankLib.analyze module Scripts.DatabankLib.analyze_nmrpca module Scripts.DatabankLib.core module Scripts.DatabankLib.databankio module

Scripts.DatabankLib.databankLibrary module Scripts.DatabankLib.databankop module Scripts.DatabankLib.form_factor module Scripts.DatabankLib.jsonEncoders module Scripts.DatabankLib.openmm_parser module Scripts.DatabankLib.plottings module Scripts.DatabankLib.quality module Scripts.DatabankLib.settings module Scripts.DatabankLib.settings.dic_lipids_UA module Scripts.DatabankLib.settings.engines module Scripts.DatabankLib.settings.molecules module Scripts.DatabankLib.utils module Scripts.updateGUI module Scripts.updateGUI.createPDBs module Scripts.WorkflowScripts module Scripts.WorkflowScripts.ProcessInfoFile module Scripts.WorkflowScripts.RunAnalysis module Scripts.WorkflowScripts.Workflow_utils module SearchSystem (class in BuildDatabank.searchDATABANK) (class in Scripts.BuildDatabank.searchDATABANK) set_dt() (Scripts.DatabankLib.openmm_parser.OpenMMParser method) set_pressure() (Scripts.DatabankLib.openmm_parser.OpenMMParser method) set_ptype() (Scripts.DatabankLib.openmm_parser.OpenMMParser method) set_tempurature() (Scripts.DatabankLib.openmm_parser.OpenMMParser method) ShowEquilibrationTimes() (in module Scripts.DatabankLib.databankLibrary) simulation2universal_atomnames() (in module Scripts.DatabankLib.databankLibrary) system (BuildDatabank.searchDATABANK.SearchSystem attribute) System (class in Scripts.DatabankLib.core) system (Scripts.BuildDatabank.searchDATABANK.SearchSystem attribute) system2MDanalysisUniverse() (in module Scripts.DatabankLib.databankLibrary) systemQuality() (in module Scripts.DatabankLib.quality) SystemsCollection (class in Scripts.DatabankLib.core)

T

TimeEstimator (class in Scripts.DatabankLib.analyze_nmrpca) timerelax() (Scripts.DatabankLib.analyze_nmrpca.TimeEstimator method)

Topology (class in Scripts.DatabankLib.analyze_nmrpca) total_lipid_conc() (BuildDatabank.searchDATABANK.SearchSystem method) (Scripts.BuildDatabank.searchDATABANK.SearchSystem method)

U

updateGUI.createPDBs module

V

validate_path() (Scripts.DatabankLib.analyze_nmrpca.Parser method)

vec2quaternion() (in module BuildDatabank.buildH_calcOP_test) (in module Scripts.BuildDatabank.buildH_calcOP_test)