Source code for mdtraj.nmr.scalar_couplings

#!/usr/bin/env python
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, TJ Lane, Osama El-Gabalawy
#
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# GNU Lesser General Public License for more details.
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"""
This file contains scripts for calculating scalar (J) Couplings from backbone dihedrals.
"""

import numpy as np

from mdtraj.geometry import compute_phi

J3_HN_CB_coefficients = {  # See full citations below in docstring references.
    "Bax2007": dict(
        phi0=+60 * np.pi / 180.0,
        A=3.71,
        B=-0.59,
        C=0.08,
    ),  # From Table 1. in paper
}

J3_HN_CB_uncertainties = {
    # Values in [Hz]
    "Bax2007": 0.22,
}

J3_HN_C_coefficients = {  # See full citations below in docstring references.
    "Bax2007": dict(
        phi0=+180 * np.pi / 180.0,
        A=4.36,
        B=-1.08,
        C=-0.01,
    ),  # From Table 1. in paper
}

J3_HN_C_uncertainties = {
    # Values in [Hz]
    "Bax2007": 0.30,
}

J3_HN_HA_coefficients = {  # See full citations below in docstring references.
    "Ruterjans1999": dict(
        phi0=-60 * np.pi / 180.0,
        A=7.90,
        B=-1.05,
        C=0.65,
    ),  # From Table 1. in paper.
    "Bax2007": dict(
        phi0=-60 * np.pi / 180.0,
        A=8.4,
        B=-1.36,
        C=0.33,
    ),  # From Table 1. in paper
    "Bax1997": dict(
        phi0=-60 * np.pi / 180.0,
        A=7.09,
        B=-1.42,
        C=1.55,
    ),  # From Table 2. in paper
}

J3_HN_HA_uncertainties = {
    # Values in [Hz]
    "Ruterjans1999": 0.25,
    "Bax2007": 0.36,
    "Bax1997": 0.39,
}


def _J3_function(phi, A, B, C, phi0):
    """Return a scalar couplings with a given choice of karplus coefficients.  USES RADIANS!"""
    return A * np.cos(phi + phi0) ** 2.0 + B * np.cos(phi + phi0) + C


[docs] def compute_J3_HN_HA(traj, model="Bax2007"): """Calculate the scalar coupling between HN and H_alpha. This function does not take into account periodic boundary conditions (it will give spurious results if the three atoms which make up any angle jump across a PBC (are not "wholed")) Parameters ---------- traj : mdtraj.Trajectory Trajectory to compute J3_HN_HA for model : string, optional, default="Bax2007" Which scalar coupling model to use. Must be one of Bax2007, Bax1999, or Ruterjans1999 Returns ------- indices : np.ndarray, shape=(n_phi, 4), dtype=int Atom indices (zero-based) of the phi dihedrals J : np.ndarray, shape=(n_frames, n_phi) Scalar couplings (J3_HN_HA, in [Hz]) of this trajectory. `J[k]` corresponds to the phi dihedral associated with atoms `indices[k]` Notes ----- The coefficients are taken from the references below--please cite them. References ---------- .. [1] Schmidt, J. M., Blümel, M., Löhr, F., & Rüterjans, H. "Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles." J. Biomol. NMR, 14, 1 1-12 (1999) .. [2] Vögeli, B., Ying, J., Grishaev, A., & Bax, A. "Limits on variations in protein backbone dynamics from precise measurements of scalar couplings." J. Am. Chem. Soc., 129(30), 9377-9385 (2007) .. [3] Hu, J. S., & Bax, A. "Determination of ϕ and ξ1 Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?." J. Am. Chem. Soc., 119(27), 6360-6368 (1997) """ indices, phi = compute_phi(traj) if model not in J3_HN_HA_coefficients: raise (KeyError("model must be one of %s" % J3_HN_HA_coefficients.keys())) J = _J3_function(phi, **J3_HN_HA_coefficients[model]) return indices, J
[docs] def compute_J3_HN_C(traj, model="Bax2007"): """Calculate the scalar coupling between HN and C_prime. This function does not take into account periodic boundary conditions (it will give spurious results if the three atoms which make up any angle jump across a PBC (are not "wholed")) Parameters ---------- traj : mdtraj.Trajectory Trajectory to compute J3_HN_C for model : string, optional, default="Bax2007" Which scalar coupling model to use. Must be one of Bax2007 Returns ------- indices : np.ndarray, shape=(n_phi, 4), dtype=int Atom indices (zero-based) of the phi dihedrals J : np.ndarray, shape=(n_frames, n_phi) Scalar couplings (J3_HN_C, in [Hz]) of this trajectory. `J[k]` corresponds to the phi dihedral associated with atoms `indices[k]` Notes ----- The coefficients are taken from the references below--please cite them. References ---------- .. [1] Hu, J. S., & Bax, A. "Determination of ϕ and ξ1 Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?." J. Am. Chem. Soc., 119(27), 6360-6368 (1997) """ indices, phi = compute_phi(traj) if model not in J3_HN_C_coefficients: raise (KeyError("model must be one of %s" % J3_HN_C_coefficients.keys())) J = _J3_function(phi, **J3_HN_C_coefficients[model]) return indices, J
[docs] def compute_J3_HN_CB(traj, model="Bax2007"): """Calculate the scalar coupling between HN and C_beta. This function does not take into account periodic boundary conditions (it will give spurious results if the three atoms which make up any angle jump across a PBC (are not "wholed")) Parameters ---------- traj : mdtraj.Trajectory Trajectory to compute J3_HN_CB for model : string, optional, default="Bax2007" Which scalar coupling model to use. Must be one of Bax2007 Returns ------- indices : np.ndarray, shape=(n_phi, 4), dtype=int Atom indices (zero-based) of the phi dihedrals J : np.ndarray, shape=(n_frames, n_phi) Scalar couplings (J3_HN_CB, in [Hz]) of this trajectory. `J[k]` corresponds to the phi dihedral associated with atoms `indices[k]` Notes ----- The coefficients are taken from the references below--please cite them. References ---------- .. [1] Hu, J. S., & Bax, A. "Determination of ϕ and ξ1 Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?." J. Am. Chem. Soc., 119(27), 6360-6368 (1997) """ indices, phi = compute_phi(traj) if model not in J3_HN_CB_coefficients: raise (KeyError("model must be one of %s" % J3_HN_CB_coefficients.keys())) J = _J3_function(phi, **J3_HN_CB_coefficients[model]) return indices, J