fairmd.lipids.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:

fmdl_match_experiments

No arguments are needed.

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

Bases: object

system: dict

idx_path: str

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

get_ions(ions)[source]

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

ion_conc(molecule, exp_counter_ions)[source]

total_lipid_conc()[source]

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

Bases: object

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

get_ions(ions) → list[str][source]

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

fairmd.lipids.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.

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

fairmd.lipids.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

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