schrodinger.trajectory.jcoupling module

A module of classes to analyze NMR Jcouplings in Desmond trajectories.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.trajectory.jcoupling.Jcoupling(atomsel, jtype='JHn_Ha', from_phi=True, *args, **kargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

A class to calculate NMR J-coupling, using Karplus’ relation. This gives an empirical relationship between NMR J-coupling constants and the torsion dihedrals.

3J(phi) = A cos^2(phi+theta) + B cos(phi+theta) + C

A, B and C are the constants parameterized by:

Hu & Bax; JACS (1997)

More recent parameters are by:

Schmidt, et al.; Biomol NMR (199)

theta is an offset. if phi is measured from the backbone (C’-N-CA-C’), then offset needs to be provided, otherwise if offset is zero.

DIHED_ATOMS = {'JHa_C': ['C', 'N', 'CA', 'HA'], 'JHa_N': ['HA', 'CA', 'C', 'N'], 'JHn_Ha': ['H', 'N', 'CA', 'HA'], 'JHn_Cb': ['H', 'N', 'CA', 'CB'], 'JHn_C': ['H', 'N', 'CA', 'C'], 'Jc_c': ['C', 'N', 'CA', 'C']}

PARAMS = {'JHa_C': {'A': 3.76, 'theta': 120.0, 'C': 0.89, 'B': -1.63}, 'JHa_N': {'A': -0.88, 'theta': 60.0, 'C': -0.27, 'B': -0.61}, 'JHn_Ha': {'A': 7.9, 'theta': -60.0, 'C': 0.65, 'B': -1.05}, 'JHn_Cb': {'A': 2.9, 'theta': 60.0, 'C': 0.18, 'B': -0.56}, 'JHn_C': {'A': 4.41, 'theta': 180.0, 'C': 0.24, 'B': -1.36}, 'Jc_c': {'A': 1.51, 'theta': 0.0, 'C': 0.52, 'B': -1.09}}

backbone_asl = ' and (backbone or (sidechain and atom.ptype CB))'

convert_phi_to_j(params)

doFrameInit(frame)

find_dihedrals(st)

getFrameResults()

get_quartets(st, pdb_atom_names)

processFrame(frame)