Minimal code snippet to compute OP values using NMRlipids kernels

[comcon1]

This is what @tfmFerreira asked to have during the last meeting. Selection of pairs is up to user, but this is the minimal example demonstrating how the engine designed by @batukav can be called.

#!/usr/bin/env python3

import MDAnalysis as mda
import fairmd.lipids.analib.databankop as dbop
import sys

topf = sys.argv[1]
trjf = sys.argv[2]
resn = sys.argv[3]

print("Finding pairs..")
u = mda.Universe(topf, trjf)

opkernels = []
for atom in u.select_atoms(f"resname {resn}").residues[0].atoms:
    if atom.element in ['C', 'N']:
        for bond in atom.bonds:
            neib = bond[1] if atom == bond[0] else bond[0]
            if neib.element != 'H':
                continue
            print(atom.name, neib.name)
            op = dbop._OrderParameter(
                atom.resname, 
                atom.name, 
                neib.name,
                atom.resname+":"+atom.name, 
                atom.resname+":"+atom.name
            )
            opkernels.append(op)
del(u)

print("Calculating OPs..")
dbop._read_trajs_calc_OPs(opkernels, topf, [trjf])

print("Printing OPs..")
for _i, op in enumerate(opkernels):
    op.avg, op.std, op.stem = op.get_avg_std_stem_OP
    print(f"{op.name} {op.avg!s} {op.stem!s}")