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|
.. _analysis:
.. currentmodule:: mdtraj
Analysis Reference
==================
Trajectory analysis is the heart of MDTraj. These functions can be used to run
a variety of analyses on :class:`mdtraj.Trajectory` objects.
It's usually as simple as ::
>>> import mdtraj as md
>>> t = md.load('trajectory.pdb')
>>> print(md.compute_phi(t))
Root-mean-square deviation (RMSD)
---------------------------------
.. autosummary::
:toctree: api/generated/
rmsd
rmsf
lprmsd
Trajectory.superpose
Hydrogen Bonding
----------------
.. autosummary::
:toctree: api/generated/
baker_hubbard
kabsch_sander
wernet_nilsson
Pi-Stacking
-----------
.. autosummary::
:toctree: api/generated/
pi_stacking
Secondary Structure
-------------------
.. autosummary::
:toctree: api/generated/
compute_dssp
Shape Metrics
-------------------
.. autosummary::
:toctree: api/generated/
compute_gyration_tensor
principal_moments
asphericity
acylindricity
relative_shape_antisotropy
Surface Area, Radius of Gyration and Inertia
--------------------------------------------
.. autosummary::
:toctree: api/generated/
shrake_rupley
compute_rg
compute_inertia_tensor
Distances
---------
.. autosummary::
:toctree: api/generated/
compute_distances
compute_displacements
compute_neighbors
compute_contacts
compute_drid
compute_center_of_mass
geometry.squareform
compute_rdf
Bond Angles and Dihedrals
-------------------------
.. autosummary::
:toctree: api/generated/
compute_angles
compute_dihedrals
compute_phi
compute_psi
compute_chi1
compute_chi2
compute_chi3
compute_chi4
compute_omega
NMR Observables
---------------
.. autosummary::
:toctree: api/generated/
compute_J3_HN_C
compute_J3_HN_CB
compute_J3_HN_HA
chemical_shifts_shiftx2
chemical_shifts_ppm
chemical_shifts_spartaplus
reindex_dataframe_by_atoms
Thermodynamic Quantities
------------------------
.. autosummary::
:toctree: api/generated/
dipole_moments
static_dielectric
isothermal_compressability_kappa_T
thermal_expansion_alpha_P
density
Order Parameters
----------------
.. autosummary::
:toctree: api/generated/
compute_nematic_order
compute_directors
|
