fairmd.lipids.databankLibrary module

Library contains all API functions and many functions used in building and analyzing the FAIRMD Lipids

fairmd.lipids.databankLibrary.CalcAreaPerMolecule(system) → None | float[source]

Calculate average area per lipid for a system.

It is using the apl.json file where area per lipid as a function of time calculated by the calcAPL.py is stored.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

Returns:

area per lipid (Å^2)

fairmd.lipids.databankLibrary.GetThickness(system)[source]

Gets thickness for a simulation defined with system from the thickness.json file where thickness calculated by the calc_thickness.py is stored.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

Returns:

membrane thickess (nm) or None

fairmd.lipids.databankLibrary.ShowEquilibrationTimes(system: System)[source]

Prints relative equilibration time for each lipid within a simulation defined by system. Relative equilibration times are calculated with NMRPCA_timerelax.py and stored in eq_times.json files.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

fairmd.lipids.databankLibrary.GetEquilibrationTimes(system: System)[source]

Returns relative equilibration time for each lipid within a simulation defined by system. Relative equilibration times are calculated with NMRPCA_timerelax.py and stored in eq_times.json files.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

Returns:

dictionary of relative equilibration times for each lipid

fairmd.lipids.databankLibrary.GetOP(system)[source]

Returns a dictionary containing the order parameter data time for each lipid in the system, stored in LipidNameOrderParameters.json files.

Parameters:

system – NMRlipids databank dictionary defining a simulation.

Returns:

dictionary contaning, for each lipid, the order parameter data: average OP, standard deviation, and standard error of mean. Contains None if LipidNameOrderParameters.json missing.

fairmd.lipids.databankLibrary.GetNlipids(system: System)[source]

Returns the total number of lipids in a simulation defined by system.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

Returns:

the total number of lipids in the system.

fairmd.lipids.databankLibrary.getLipids(system: System, molecules=LipidSet[{'TOCL', 'DPPC', 'POPE', 'POPC', 'CHOL'}])[source]

Returns a string using MDAnalysis notation that can used to select all lipids from the system.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation.

Returns:

a string using MDAnalysis notation that can used to select all lipids from the system.

fairmd.lipids.databankLibrary.getAtoms(system: System, lipid: str)[source]

Return system specific atom names of a lipid

Parameters:

  • system – System simulation object

  • lipid – universal lipid name

Returns:

string of system specific atom names

fairmd.lipids.databankLibrary.system2MDanalysisUniverse(system)[source]

Takes the system dictionary as an input, downloads the required files to the FAIRMD Lipids directory and retuns MDAnalysis universe corressponding the system.

Parameters:

system – FAIRMD Lipids dictionary describing the simulation.

Returns:

MDAnalysis universe

fairmd.lipids.databankLibrary.read_trj_PN_angles(molname: str, atom1: str, atom2: str, mda_universe: Universe)[source]

Calculate the P-N vector angles with respect to membrane normal from the simulation defined by the MDAnalysis universe.

Parameters:

  • molname – residue name of the molecule for which the P-N vector angle will be calculated

  • atom1 – name of the P atom in the simulation

  • atom2 – name of the N atom in the simulation

  • MDAuniverse – MDAnalysis universe of the simulation to be analyzed

Returns:

tuple (angles of all molecules as a function of time, time averages for each molecule, the average angle over time and molecules, the error of the mean calculated over molecules)

fairmd.lipids.databankLibrary.calcArea(system) → float[source]

Return area of the calculated based on the area per lipid stored in the databank.

Parameters:

system – a system dictionary

Returns:

area of the system (Å^2)

fairmd.lipids.databankLibrary.GetFormFactorMin(system)[source]

Return list of minima of form factor of system.

Parameters:

system – a system dictionary

Returns:

list of form factor minima

fairmd.lipids.databankLibrary.averageOrderParameters(system)[source]

Returns average order paramaters of sn-1 and sn-2 acyl chains based on universal atom names. The names starting with M_G1C will be assigned to sn-1 and names starting M_G2C to sn-2.

Parameters system:

a system dictionary

Returns:

average of sn-1 and sn-2 order parameters

fairmd.lipids.databankLibrary.calcLipidFraction(system, lipid)[source]

Return the number fraction of lipid with respect to total number of lipids.

Parameters:

  • system – a system dictionary

  • lipid – universal molecule name of lipid

Returns:

number fraction of lipid with respect total number of lipids

fairmd.lipids.databankLibrary.getHydrationLevel(system) → float[source]

Return hydration level of the system.

Hydration level is defined as the number of water molecules divided by number of lipid molecules.

Parameters:

system – a system dictionary

Returns:

number of water molecules divided by number of lipid molecules