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_phi, n_frames)
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
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_phi, n_frames)
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
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_phi, n_frames)
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
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
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
----------
"""
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
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"))
:param mdtraj.Trajectory traj: Trajectory to compute J3_HN_HA for
:param string, optional, default="Bax2007" model :
Which scalar coupling model to use. Must be one of Bax2007, Bax1999, or Ruterjans1999
:return np.ndarray, shape=(n_phi, 4), dtype=int indices :
Atom indices (zero-based) of the phi dihedrals
:return np.ndarray, shape=(n_frames, n_phi) J:
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)
.. [4] Habeck, M.; Rieping, W.; Nilges, M. Bayesian Estimation of Karplus
Parameters and Torsion Angles from Three-Bond Scalar Couplings Constants.
J. Magn. Reson. 2005, 177 (1), 160–165.
.. [5] Vuister, G. W.; Bax, A. Quantitative J Correlation: A New Approach for
Measuring Homonuclear Three-Bond JHN,Hα Coupling Constants in 15N-Enriched
Proteins. J. Am. Chem. Soc. 1993, 115 (17), 7772–7777.
.. [6] Pardi, A.; Billeter, M.; Wüthrich, K. Calibration of the Angular
Dependence of the Amide Proton-C Alpha Proton Coupling Constants,
3JHN Alpha, in a Globular Protein. Use of 3JHN Alpha for Identification
of Helical Secondary Structure. J. Mol. Biol. 1984, 180 (3), 741–751.
"""
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
