NMRlipids databank API functions

The functions that help analyzing data in the NMRlipids databank are described here. These functions locate in databanklibrary.py. To get started using these functions, first create the folder where you want to work

mkdir NMRlipids/
cd NMRlipids

then clone the NMRlipids databank git into this folder

git clone https://github.com/NMRLipids/Databank.git

You can then start to work with the template or write a code from the scratch. The minimum python code to intialize NMRlipids databank is

import sys
databankPath =  './Databank/'   # this is the local path for the cloned Databank git
sys.path.insert(1, databankPath + '/Scripts/BuildDatabank/')
from databankLibrary import *
systems = initialize_databank(databankPath)

After running this, systems is the list of dictionaries where each dictionary is a simulation in the NMRlipids databank. A simulation dictionary contains the content of the README.yaml for that simulation. The content of README.yaml files is described in User input and content of README.yaml files. systems can be then used to loop over all simulations:

for system in systems:
    print(system)

Examples on analyses over NMRlipids databank can be found from the template and codes used to analyze the results for the NMRlipids databank manuscript.

The functions available to analyze the simulations are listed in here:

databankLibrary.initialize_databank(databankPath)[source]

Intializes the NMRlipids databank.

Parameters:: databankPath – path for the local location of the NMRlipids databank, for example ../../Databank
Returns:: list of dictionaries that contain the content of README.yaml files for each system.

databankLibrary.print_README(system)[source]

Prints the content of system dictionary in human readable format.

Parameters:: system – NMRlipids databank dictionary defining a simulation.

databankLibrary.CalcAreaPerMolecule(system)[source]

Calculates average area per lipid for a simulation defined with 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 – NMRlipids databank dictionary defining a simulation.
Returns:: area per lipid (Å^2)

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 – NMRlipids databank dictionary defining a simulation.
Returns:: membrane thickess (nm)

databankLibrary.ShowEquilibrationTimes(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 – NMRlipids databank dictionary defining a simulation.

databankLibrary.GetNlipids(system)[source]

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

Parameters:: system – NMRlipids databank dictionary defining a simulation.
Returns:: the total number of lipids in the system.

databankLibrary.getLipids(system, 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', 'GM1', 'DPPGK', 'GB3']))[source]

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

Parameters:: system – NMRlipids databank dictionary defining a simulation.
Returns:: a string using MDAnalysis notation that can used to select all lipids from the system.

databankLibrary.plotSimulation(ID, lipid)[source]

Creates plots of form factor and C-H bond order parameters for the selected lipid from a simulation with the given ID number.

Parameters:

ID – NMRlipids databank ID number of the simulation
lipid – universal molecul name of the lipid

databankLibrary.simulation2universal_atomnames(system, molecule, atom)[source]

Get force field specific atom name corresponding to universal atom name from the system.

Parameters:

mapping_file – path for the mapping file
atom1 – universal atom name

Returns:

force field specific atom name

databankLibrary.read_mapping_file(mapping_file, atom1)[source]

Get force field specific atom name corresponding to universal atom name from the mapping file.

Parameters:

mapping_file – path for the mapping file
atom1 – universal atom name

Returns:

force field specific atom name

databankLibrary.loadMappingFile(mapping_file)[source]

Load mapping file into a dictionary

Param:: name of the mapping file
Returns:: mapping dictionary

databankLibrary.getAtoms(system, lipid)[source]

Return system specific atom names of a lipid

Parameters:

system – system dictionary
lipid – universal lipid name

Returns:

string of system specific atom names

databankLibrary.getUniversalAtomName(system, atomName, lipid)[source]

Returns the universal atom name corresponding the simulation specific atomName of a lipid in a simulation defined by the system.

Parameters:

system – system dictionary
atomName – simulation specific atomname
lipid – universal lipid name

Returns:

universal atomname (string)

databankLibrary.ShowTable(SortedQualities, quality)[source]

Shows a table of simulation qualities against experimental data.

Parameters:

SortedQualities – list of dictionaries to be shown, available in folder Data/Ranking/
quality – should be either TotalQuality or universal lipid name. First one shows the system total quality. Latter shows the individual lipid quality.

databankLibrary.system2MDanalysisUniverse(system)[source]

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

Parameters:: system – NMRlipids databank dictionary describing the simulation.
Returns:: MDAnalysis universe

databankLibrary.read_trj_PN_angles(molname, atom1, atom2, MDAuniverse)[source]

Calculates 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:

list where the first element are the angles of all molecules as a function of time, second element contains time averages for each molecule, third element contains the average angle over time and molecules, and fourth element is the error of the mean calculated over molecules.

databankLibrary.calcArea(system)[source]

Returns 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)

databankLibrary.GetFormFactorMin(system)[source]

Return list of minima of form factor of system.

Parameters:: system – a system dictionary
Returns:: list of form factor minima

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

databankLibrary.calcLipidFraction(system, lipid)[source]

Returns 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

databankLibrary.getHydrationLevel(system)[source]

Returns hydration level of the system, i.e., 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