searchDATABANK script

class BuildDatabank.searchDATABANK.Simulation(readme)[source]

Bases: object

readme: dict
indexingPath: str
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', 'TMCL', 'GM1', 'DPPGK', 'GB3', 'BOG']))[source]
getIons(ions)[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', 'TMCL', 'GM1', 'DPPGK', 'GB3', 'BOG'])) → float[source]
ionConcentration(molecule, exp_counter_ions)[source]
totalLipidConcentration()[source]
class BuildDatabank.searchDATABANK.Experiment(readme: dict, molname: str, dataPath: str, exptype: str)[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', 'TMCL', 'GM1', 'DPPGK', 'GB3', 'BOG'])) → List[str][source]
getIons(ions) → List[str][source]
BuildDatabank.searchDATABANK.loadSimulations() → List[Simulation][source]

Generates the list of Simulation objects. Go through all README.yaml files.

BuildDatabank.searchDATABANK.loadExperiments(experimentType: str) → List[Experiment][source]

Loops over the experiment entries in the experiment databank and read experiment readme and order parameter files into objects.

BuildDatabank.searchDATABANK.findPairs(experiments: List[Experiment], simulations: List[Simulation])[source]
BuildDatabank.searchDATABANK.logPairs(pairs, fd: IO[str]) → None[source]

Write found correspondences into log file.

pairs: [(Simulation, Experiment), …] fd: file descriptor for writting into

BuildDatabank.searchDATABANK.main()[source]

Main program function. Not for exporting.