DatabankLib.bin.match_experiments module

Match simulations with experiments in the databank.

Script goes through all simulations and experiments in the databank and finds pairs of simulations and experiments that match in composition, temperature and other conditions. The found pairs are written into the simulation README.yaml files and into a log file.

Usage:

nml_match_experiments

No arguments are needed.

class DatabankLib.bin.match_experiments.SearchSystem(readme)[source]

Bases: object

system: dict

idx_path: str

get_lipids(molecules=LipidSet[{'POPC', 'DPPC', 'CHOL', 'TOCL', 'POPE'}])[source]

get_ions(ions)[source]

molar_fraction(molecule, molecules=LipidSet[{'POPC', 'DPPC', 'CHOL', 'TOCL', 'POPE'}]) → float[source]

ion_conc(molecule, exp_counter_ions)[source]

total_lipid_conc()[source]

class DatabankLib.bin.match_experiments.Experiment(readme: dict, molname: str, data_path: str, exptype: str)[source]

Bases: object

get_lipids(molecules=LipidSet[{'POPC', 'DPPC', 'CHOL', 'TOCL', 'POPE'}]) → list[str][source]

get_ions(ions) → list[str][source]

DatabankLib.bin.match_experiments.load_simulations() → list[SearchSystem][source]: Generates the list of Simulation objects. Go through all README.yaml files.

DatabankLib.bin.match_experiments.load_experiments(exp_type: str) → list[Experiment][source]: Loops over the experiment entries in the experiment databank and read experiment readme and order parameter files into objects.

DatabankLib.bin.match_experiments.find_pairs(experiments: list[Experiment], simulations: list[SearchSystem])[source]

DatabankLib.bin.match_experiments.log_pairs(pairs, fd: IO[str]) → None[source]

Write found correspondences into log file.

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

DatabankLib.bin.match_experiments.match_experiments()[source]: Main program function. Not for exporting.