QualityEvaluation module

class QualityEvaluation.Simulation(readme, OPdata, FFdata, indexingPath)[source]

Bases: object

getLipids(molecules=dict_keys(['POPC', 'POPG', 'POPS', 'POPE', 'PYPC', 'PAzePCprot', 'PAzePCdeprot', 'DMPC', 'DPPC', 'DPPE', 'DPPG', 'DEPC', 'DRPC', 'DYPC', 'DLPC', 'DLIPC', 'DOG', 'DOPC', 'DOPE', 'DDOPC', 'DOPS', 'DSPC', 'DAPC', 'DMTAP', 'SDG', 'SDPE', 'SOPC', 'POPI', 'SAPI', 'SAPI24', 'SAPI25', 'SLPI', 'CER', 'CER180', 'CHOL', 'DCHOL', 'DHMDMAB', 'SLiPC', 'SM16', 'SM18', 'TOCL', 'TLCL_0H', 'GM1', 'DPPGK', 'GB3']))[source]

molarFraction(molecule, molecules=dict_keys(['POPC', 'POPG', 'POPS', 'POPE', 'PYPC', 'PAzePCprot', 'PAzePCdeprot', 'DMPC', 'DPPC', 'DPPE', 'DPPG', 'DEPC', 'DRPC', 'DYPC', 'DLPC', 'DLIPC', 'DOG', 'DOPC', 'DOPE', 'DDOPC', 'DOPS', 'DSPC', 'DAPC', 'DMTAP', 'SDG', 'SDPE', 'SOPC', 'POPI', 'SAPI', 'SAPI24', 'SAPI25', 'SLPI', 'CER', 'CER180', 'CHOL', 'DCHOL', 'DHMDMAB', 'SLiPC', 'SM16', 'SM18', 'TOCL', 'TLCL_0H', 'GM1', 'DPPGK', 'GB3']))[source]

class QualityEvaluation.Experiment[source]: Bases: object

QualityEvaluation.loadMappingFile(path_to_mapping_file)[source]

QualityEvaluation.prob_S_in_g(OP_exp, exp_error, OP_sim, op_sim_sd)[source]

QualityEvaluation.getFragments(mapping_file)[source]

QualityEvaluation.filterCH(fragment_key, fragments)[source]

QualityEvaluation.checkForCH(fragment_key, fragments)[source]

QualityEvaluation.evaluated_percentage(fragments, exp_op_data)[source]

QualityEvaluation.fragmentQuality(fragments, exp_op_data, sim_op_data)[source]

QualityEvaluation.fragmentQualityAvg(lipid, fragment_qual_dict, fragments)[source]

QualityEvaluation.systemQuality(system_fragment_qualities)[source]

QualityEvaluation.calc_k_e(SimExpData)[source]: Scaling factor as defined by Kučerka et al. 2008b, doi:10.1529/biophysj.107.122465

QualityEvaluation.FormFactorMinFromData(FormFactor)[source]

QualityEvaluation.formfactorQuality(simFFdata, expFFdata)[source]: Calculate form factor quality for a simulation as defined by Kučerka et al. 2010, doi:10.1007/s00232-010-9254-5

QualityEvaluation.formfactorQualitySIMtoEXP(simFFdata, expFFdata)[source]: Calculate form factor quality for a simulation as defined by Kučerka et al. 2010, doi:10.1007/s00232-010-9254-5

QualityEvaluation.loadSimulations()[source]