<commit_before>Introduction
============
Ramaplot is a Python program used to generate `Ramachandran plot
<https://en.wikipedia.org/wiki/Ramachandran_plot>`_ figures using matplotlib.
Ramachandran plots are a powerful method of visualizing the distribution of
backbone Φ and Ψ dihedral angles in peptides and proteins, or of other
properites as a function of Φ and Ψ. Ramaplot configuration is powered by
`myplotspec <http://karltdebiec.github.io/myplotspec>`_, enabling powerful
configuration options from `YAML
<http://www.yaml.org/spec/1.2/spec.html>`_-format text files. Several types of
experimental and simulated datasets are currently supported.

.. image:: examples/example.png

Supported Datasets
------------------

Experiment
~~~~~~~~~~

Neighbor-Dependent Ramachandran Distributions
_____________________________________________
The Neighbor-Dependent Ramachandran Distribution (NDRD) dataset is a collection
of Φ/Ψ probability distributions measured from the loop (non-α/β) regions of
solved structures. In addition to distributions for all 20 amino acids, left-
and right-neighbor distributions are available for each pair of amino acids,
which may be used to calculate distributions of each amino-acid triplet. The
complete dataset includes residues identified as turn, coil, bridge, π helix,
and 310 helix; versions including only turn, coil, and bridge, only turn, and
only coil are available as well. This dataset may be obtained from
`<http://dunbrack.fccc.edu/ndrd>`_.

`<NAME>, Wang, Guoli, Shapovalov, Maxim, Mitra, Rajib, Jordan, <NAME>,
Dunbrack Jr. <NAME>. Neighbor-Dependent Ramachandran Probability
Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process
Model. PLoS Computational Biology. 2010. 6. e1000763.
<http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000763>`_

Conformation-Dependent Library
______________________________
The Conformation-Dependent Library (CDL) dataset is a collection of averages
and standard deviations of backbone bond lengths, angles, and ω as a function
of Φ and Ψ, measured from solved structures. The dataset is divided into 8
classes: isoleucine/valine, glycine, proline, and all other residues, each
leading into proline or residues other than proline. This dataset may be
obtained from `<http://dunbrack.fccc.edu/nmhrcm>`_ and
`<http://dunbrack.fccc.edu/omega>`_.

`<NAME>., <NAME>., <NAME>. <NAME>., <NAME>.
Andrew. Conformation Dependence of Backbone Geometry in Proteins. Structure.
2009. 17. 1316-1325.
<http://www.sciencedirect.com/science/article/pii/S0969212609003359>`_

`<NAME>., Driggers, <NAME>., <NAME>., <NAME>.,
<NAME>., <NAME>. Andrew. Nonplanar Peptide Bonds in Proteins are Common
and Conserved but not Biased Toward Active Sites. Proceedings of the National
Acadedemy of the Sciences of the United States of America. 2012. 109. 449-453.
<http://www.pnas.org/content/109/2/449>`_

Simulation
~~~~~~~~~~

Molecular Dynamics Simulation
_____________________________
The distribution of observed Φ and Ψ dihedral angles from a molecular dynamics
simulation may be calculated from a text file containing a timeseries,
typically calculated from the trajectory using `cpptraj
<https://github.com/Amber-MD/cpptraj>`_. Alternatively, the average value of
another property as a function of Φ and Ψ may be calculated. (Work in
progress)

`Roe, <NAME>., <NAME>, <NAME>. PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of
Chemical Theory and Computation. 2013. 93084–3095.
<http://pubs.acs.org/doi/abs/10.1021/ct400341p>`_<commit_msg>Removed 'wip' status of MD simulation analysis<commit_after>Introduction
============
Ramaplot is a Python program used to generate `Ramachandran plot
<https://en.wikipedia.org/wiki/Ramachandran_plot>`_ figures using matplotlib.
Ramachandran plots are a powerful method of visualizing the distribution of
backbone Φ and Ψ dihedral angles in peptides and proteins, or of other
properites as a function of Φ and Ψ. Ramaplot configuration is powered by
`myplotspec <http://karltdebiec.github.io/myplotspec>`_, enabling powerful
configuration options from `YAML
<http://www.yaml.org/spec/1.2/spec.html>`_-format text files. Several types of
experimental and simulated datasets are currently supported.

.. image:: examples/example.png

Supported Datasets
------------------

Experiment
~~~~~~~~~~

Neighbor-Dependent Ramachandran Distributions
_____________________________________________
The Neighbor-Dependent Ramachandran Distribution (NDRD) dataset is a collection
of Φ/Ψ probability distributions measured from the loop (non-α/β) regions of
solved structures. In addition to distributions for all 20 amino acids, left-
and right-neighbor distributions are available for each pair of amino acids,
which may be used to calculate distributions of each amino-acid triplet. The
complete dataset includes residues identified as turn, coil, bridge, π helix,
and 310 helix; versions including only turn, coil, and bridge, only turn, and
only coil are available as well. This dataset may be obtained from
`<http://dunbrack.fccc.edu/ndrd>`_.

`<NAME>, Shapovalov, <NAME>,
<NAME>r. Roland L. Neighbor-Dependent Ramachandran Probability
Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process
Model. PLoS Computational Biology. 2010. 6. e1000763.
<http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000763>`_

Conformation-Dependent Library
______________________________
The Conformation-Dependent Library (CDL) dataset is a collection of averages
and standard deviations of backbone bond lengths, angles, and ω as a function
of Φ and Ψ, measured from solved structures. The dataset is divided into 8
classes: isoleucine/valine, glycine, proline, and all other residues, each
leading into proline or residues other than proline. This dataset may be
obtained from `<http://dunbrack.fccc.edu/nmhrcm>`_ and
`<http://dunbrack.fccc.edu/omega>`_.

`Berkholz, <NAME>., <NAME>., <NAME>. <NAME>., <NAME>.
Andrew. Conformation Dependence of Backbone Geometry in Proteins. Structure.
2009. 17. 1316-1325.
<http://www.sciencedirect.com/science/article/pii/S0969212609003359>`_

`<NAME>., <NAME>., <NAME>., <NAME>.,
<NAME>., <NAME>. Nonplanar Peptide Bonds in Proteins are Common
and Conserved but not Biased Toward Active Sites. Proceedings of the National
Acadedemy of the Sciences of the United States of America. 2012. 109. 449-453.
<http://www.pnas.org/content/109/2/449>`_

Simulation
~~~~~~~~~~

Molecular Dynamics Simulation
_____________________________
The distribution of observed Φ and Ψ dihedral angles from a molecular dynamics
simulation may be calculated from a text file containing a timeseries,
typically calculated from the trajectory using `cpptraj
<https://github.com/Amber-MD/cpptraj>`_. Alternatively, the average value of
another property as a function of Φ and Ψ may be calculated.

`Roe, <NAME>., <NAME>, <NAME>. PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of
Chemical Theory and Computation. 2013. 93084–3095.
<http://pubs.acs.org/doi/abs/10.1021/ct400341p>`_
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