fairmd.idp.quality module

Module quality accumulate functions required for major QualityEvaluation script. TODO: add tests TODO: remove code duplication and commented code

class fairmd.idp.quality.QualSimulation(system: System, op_data, ff_data, idx_path)[source]

Bases: object

get_lipids(molecules=LipidSet[{'BOG', 'TLCL_0H', 'DEPC', 'DHMDMAB', 'DSPC', 'TLCL', 'PAZEPCPROT', 'SAPI', 'SDG', 'DCHOL', 'SLPI', 'POPE', 'DPPG', 'SAPC', 'CHOL', 'DPPE', 'GM1', 'DYPC', 'DOPC', 'DMTAP', 'DLPC', 'TMCL', 'SOPC', 'DMPC', 'DPPGK', 'GB3', 'PAZEPCDEPROT', 'SAPI24', 'DPPC', 'POPS', 'POPG', 'DOPE', 'SDPE', 'DRPC', 'C30', 'DAPC', 'CER180', 'TOCL', 'SLIPC', 'PYPC', 'CER', 'SAPI25', 'SM16', 'SM18', 'DOPS', 'DOG', 'DLIPC', 'POPC', 'POPI', 'DDOPC'}])[source]
molar_fraction(molecule, molecules=LipidSet[{'BOG', 'TLCL_0H', 'DEPC', 'DHMDMAB', 'DSPC', 'TLCL', 'PAZEPCPROT', 'SAPI', 'SDG', 'DCHOL', 'SLPI', 'POPE', 'DPPG', 'SAPC', 'CHOL', 'DPPE', 'GM1', 'DYPC', 'DOPC', 'DMTAP', 'DLPC', 'TMCL', 'SOPC', 'DMPC', 'DPPGK', 'GB3', 'PAZEPCDEPROT', 'SAPI24', 'DPPC', 'POPS', 'POPG', 'DOPE', 'SDPE', 'DRPC', 'C30', 'DAPC', 'CER180', 'TOCL', 'SLIPC', 'PYPC', 'CER', 'SAPI25', 'SM16', 'SM18', 'DOPS', 'DOG', 'DLIPC', 'POPC', 'POPI', 'DDOPC'}]) → float[source]
class fairmd.idp.quality.Experiment[source]

Bases: object

fairmd.idp.quality.prob_S_in_g(OP_exp: float, exp_error: float, OP_sim: float, op_sim_sd: float) → float[source]

Main quality function computing the quality value from experimental and simulation OP data.

Parameters:

  • OP_exp (float) – Experimental OP value

  • exp_error (float) – Experimental error

  • OP_sim (float) – Simulated OP value

  • op_sim_sd (float) – Standard deviation from simulation

Returns:

single-OP quality value or NaN

Return type:

float

fairmd.idp.quality.get_fragments(mapping_dict: dict)[source]
fairmd.idp.quality.filterCH(fragment_key, fragments)[source]
fairmd.idp.quality.checkForCH(fragment_key, fragments)[source]
fairmd.idp.quality.evaluated_percentage(fragments, exp_op_data)[source]
fairmd.idp.quality.fragmentQuality(fragments, exp_op_data, sim_op_data)[source]
fairmd.idp.quality.fragmentQualityAvg(lipid, fragment_qual_dict, fragments)[source]
fairmd.idp.quality.systemQuality(system_fragment_qualities, simulation)[source]
fairmd.idp.quality.calc_k_e(SimExpData)[source]

Scaling factor as defined by Kučerka et al. 2008b, doi:10.1529/biophysj.107.122465

fairmd.idp.quality.FormFactorMinFromData(FormFactor)[source]
fairmd.idp.quality.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

fairmd.idp.quality.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

fairmd.idp.quality.loadSimulations() → List[QualSimulation][source]