dnaMD Module
============

**dnaMD** is written in Python and it is also available as Python module. It
can be used in Python scripting for fast and flexible analysis
of `do_x3dna <do_x3dna_usage.html>`_ data.

**dnaMD** module contain a :class:`dnaMD.DNA` class and other functions.

.. currentmodule:: dnaMD

Summary
-------

dnaMD.DNA class
~~~~~~~~~~~~~~~

.. autosummary::
    DNA.get_parameters
    DNA.set_base_pair_parameters
    DNA.set_helical_radius
    DNA.set_base_step_parameters
    DNA.get_mean_error
    DNA.set_helical_axis
    DNA.time_vs_parameter
    DNA.parameter_distribution
    DNA.set_major_minor_groove
    DNA.set_backbone_dihedrals
    DNA.generate_smooth_axis
    DNA.calculate_curvature_tangent
    DNA.calculate_angle_bw_tangents
    DNA.write_haxis_pdb


dnaMD module
~~~~~~~~~~~~
.. currentmodule:: dnaMD
.. autosummary::
    setParametersFromFile
    read_param_file
    get_error
    dev_parameters_vs_axis
    localDeformationVsBPS
    vector_angle


dnaMD.dnaEY class
~~~~~~~~~~~~~~~~~

.. currentmodule:: dnaMD.dnaEY

.. autosummary::
    dnaEY.getStretchTwistBendModulus
    dnaEY.getStretchTwistModulus
    dnaEY.getModulusByTime
    dnaEY.getGlobalDeformationEnergy
    dnaEY.calculateLocalElasticity
    dnaEY.getLocalElasticityByTime
    dnaEY.getLocalDeformationEnergy

Detailed Documentation
----------------------

.. toctree::
   :maxdepth: 1

   dnaMD.DNA class <dna_class_api>
   Other functions in dnaMD <dnaMD_api>
   dnaMD.dnaEY class  <dnaEY_api>