Index

A

apply_rotation() (in module buildH_calcOP_test)

averageOrderParameters() (in module databankLibrary)

B

build_all_Hs_calc_OP() (in module buildH_calcOP_test) buildH_calcOP_test module

buildHs_on_1C() (in module buildH_calcOP_test)

C

calc_angle() (in module buildH_calcOP_test) (in module OrderParameter) calc_k_e() (in module QualityEvaluation) calc_OP() (in module buildH_calcOP_test) (OrderParameter.OrderParameter method) calc_rotation_matrix() (in module buildH_calcOP_test) calc_z_dim() (in module OrderParameter) calcArea() (in module databankLibrary) CalcAreaPerMolecule() (in module databankLibrary)

calcLipidFraction() (in module databankLibrary) check_densities module check_mappings module checkForCH() (in module QualityEvaluation) createPDBs module cross_product() (in module buildH_calcOP_test)

D

Data (class in searchDATABANK) databankLibrary module

dic_lipids module Dihedrals (class in OrderParameter)

E

evaluated_percentage() (in module QualityEvaluation)

Experiment (class in QualityEvaluation) (class in searchDATABANK)

F

fast_build_all_Hs_calc_OP() (in module buildH_calcOP_test) fast_buildHs_on_1C() (in module buildH_calcOP_test) filterCH() (in module QualityEvaluation) find_OP() (in module OrderParameter) findPairs() (in module searchDATABANK)

FormFactorMinFromData() (in module QualityEvaluation) formfactorQuality() (in module QualityEvaluation) formfactorQualitySIMtoEXP() (in module QualityEvaluation) fragmentQuality() (in module QualityEvaluation) fragmentQualityAvg() (in module QualityEvaluation)

G

get_avg_std_OP (OrderParameter.OrderParameter property) get_avg_std_stem_OP (OrderParameter.OrderParameter property) get_CH() (in module buildH_calcOP_test) get_CH2() (in module buildH_calcOP_test) get_CH3() (in module buildH_calcOP_test) get_CH_double_bond() (in module buildH_calcOP_test) get_indexes() (in module buildH_calcOP_test) get_op_res (OrderParameter.OrderParameter property) getAtoms() (in module databankLibrary) GetFormFactorMin() (in module databankLibrary)

getFragments() (in module QualityEvaluation) getHydrationLevel() (in module databankLibrary) getIons() (searchDATABANK.Experiment method) (searchDATABANK.Simulation method) getLipids() (in module databankLibrary) (QualityEvaluation.Simulation method) (searchDATABANK.Experiment method) (searchDATABANK.Simulation method) GetNlipids() (in module databankLibrary) GetThickness() (in module databankLibrary) getUniversalAtomName() (in module databankLibrary)

I

init_dic_OP() (in module buildH_calcOP_test)

initialize_databank() (in module databankLibrary) ionConcentration() (searchDATABANK.Simulation method)

L

loadExperiments() (in module searchDATABANK) loadMappingFile() (in module databankLibrary) (in module QualityEvaluation)

loadSimulations() (in module QualityEvaluation) (in module searchDATABANK) logPairs() (in module searchDATABANK)

M

main() (in module buildH_calcOP_test) (in module searchDATABANK) make_dic_atname2genericname() (in module buildH_calcOP_test) make_dic_Cname2Hnames() (in module buildH_calcOP_test) make_dic_lipids_with_indexes() (in module buildH_calcOP_test) module buildH_calcOP_test check_densities check_mappings createPDBs databankLibrary dic_lipids openmm_parser OrderParameter QualityEvaluation searchDATABANK

molarFraction() (QualityEvaluation.Simulation method) (searchDATABANK.Simulation method)

N

norm() (in module buildH_calcOP_test)

normalize() (in module buildH_calcOP_test)

O

openmm_input() (in module openmm_parser) openmm_parser module

openmmParser (class in openmm_parser) OrderParameter module OrderParameter (class in OrderParameter)

P

pandasdf2pdb() (in module buildH_calcOP_test) parse_op_input() (in module OrderParameter) parseCommandLineArgs() (in module buildH_calcOP_test)

parseDihedralInput() (in module OrderParameter) plotSimulation() (in module databankLibrary) print_README() (in module databankLibrary) prob_S_in_g() (in module QualityEvaluation)

Q

QualityEvaluation module

R

read_inp_input() (in module openmm_parser) read_mapping_file() (in module databankLibrary) read_trajs_calc_OPs() (in module OrderParameter)

read_trj_PN_angles() (in module databankLibrary) (in module OrderParameter) read_xml_input() (in module openmm_parser)

S

searchDATABANK module setDt() (openmm_parser.openmmParser method) setPressure() (openmm_parser.openmmParser method) setPType() (openmm_parser.openmmParser method) setTempurature() (openmm_parser.openmmParser method)

ShowEquilibrationTimes() (in module databankLibrary) ShowTable() (in module databankLibrary) Simulation (class in QualityEvaluation) (class in searchDATABANK) simulation2universal_atomnames() (in module databankLibrary) system2MDanalysisUniverse() (in module databankLibrary) systemQuality() (in module QualityEvaluation)

T

totalLipidConcentration() (searchDATABANK.Simulation method)

V

vec2quaternion() (in module buildH_calcOP_test)