manual added figures and links

docs/links.rst

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+.. highlight:: rst
+
+Links
+=====
+
+Download the code and use :file:`setup.py` to install the code using :program:`setuptools`
+python module ::
+
+   $ python setup.py install --user
+
+for python3 ::
+
+   $ python3 setup.py install --user
+
+the code will be installed as a python module. To check that it is properly installed you can
+run the :program:`python` interpret and execute ::
+
+   import symeess
+

docs/tutorials.rst

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+.. highlight:: rst
+
+Tutorials
+=========
+
+Download the code and use :file:`setup.py` to install the code using :program:`setuptools`
+python module ::
+
+   $ python setup.py install --user
+
+for python3 ::
+
+   $ python3 setup.py install --user
+
+the code will be installed as a python module. To check that it is properly installed you can
+run the :program:`python` interpret and execute ::
+
+   import symeess
+

docs/usage.rst

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+.. highlight:: rst
+
+How to use cosymlib
+*******************
+
+**Cosymlib** is a a python library for computing continuous symmetry & shape measures (CSMs & CShMs).
+Besides using the APIs contained in **cosymlib** to build your own custom-made python programs we have
+also written some general scripts to perform standard tasks such as calculating a continuous shape
+measure for a given structure without need of writing a python script. All this general task scripts
+are called using a similar syntax wich inludes the name of the script, the name of the file containing
+the structural data and optional arguments specifying the tasks we want to perform::
+
+   $ script filename -task1 -task2 ... -taskn
+
+For instance, consider a ``struct.xyz`` file containing the following structural information
+for a H\ :sub:`4`\  molecule in an approximately square geometry:
+
+::
+
+    4
+    H4 Quadrangle
+    H    1.1   0.9  0.0
+    H   -1.0   1.1  0.0
+    H   -0.9  -1.2  0.0
+    H    1.1  -1.0  0.0
+
+if we would like to compute the square shape measure S(SP-4) for this 4-vertex
+polygon we simply can call the shape script indicating the name of the .xyz file
+containing the coordinates and use the ``-mesure`` flag with the SP-4 label to indicate
+that we want to use a square (SP-4 stands for square planar structure with 4 vertices)
+as the reference shape::
+
+   $ shape struct.xyz -measure SP-4
+
+and the shape script wil call the APIs in cosymlib to read first your input file, generate a
+molecule object, calculate the S(SP-4) continuous shape measure for it, and print
+the result of the calculation on the screen.
+
+If, for instance, we also want the coordinates for the square with the best overlap
+with our problem structure, we just need to include the ``-structure`` option in our call::
+
+   $ shape struct.xyz -measure SP-4 -structure
+
+The general task scripts include also ``symmg`` and ``cchir`` for
+calculating continuous symmetry and chirality measures for polyhedral structures, as well as
+the ``wfsymm`` script for the continuous symmetry analysis wavefunctions and electron densities.
+
+Besides these four basic scripts we have also included ``cosym``, a general script that allows to perform
+any of the basic calculations above. We could, for instance, use directly ``cosym`` to calculate the previous
+shape measure using the following command::
+
+$ cosym struct.xyz -shape_measure SP-4 -structure
+
+Notice that when using ``cosym`` some of the optional arguments in ``shape`` change to indicate which type
+of calculation we would like to perform. For instance, ``-measure`` becomes ``-shape_measure``.
+On the other hand, other arguments such as ``-structure``, which have also the same meaning when
+calculating shape, symmetry or chirality measures, remain the same when used in combination with the
+general ``cosym`` script.
+
+Taking into account users of our previous programs, we have also written a stand-alone script
+``shape_classic`` which is able to read an ``old_shape.dat`` input file containing both
+the structural information and the necessary keywords to run a full CShM calculation as it was done
+in our previous ``SHAPE`` program.
+
+In the sections below you can find a detailed description of all stand-alone scripts as well as all APIs
+included in the present distribution of **cosymlib**.
+
+--------
+
+General task scripts
+--------------------
+qqqqq
+
+--------
+
+cosym
+^^^^^
+qqqqq
+
+--------
+
+shape
+^^^^^
+qqqqq
+
+--------
+
+shape_classic
+^^^^^^^^^^^^^
+To run ``shape_classic`` you only need an ``old_shape.dat`` input file containing both
+the structural information and the necessary keywords to run a full CShM calculation as in
+the old ``SHAPE`` program::
+
+   $ shape_classic old_shape.dat
+
+The script will perform all tasks indicated in the input file, creating the necessary output
+files, normally ``old_shape.out`` and ``old_shape.tab`` with the same information as when using
+our previous ``SHAPE`` program.  Follow the link below  for a pdf version of the user guide for
+SHAPE ver. 2.1 where you will find all information to perform a continuous shape analysis using
+this option.
+
+:download: `SHAPE ver. 2.1 User's guide.  <User_Manual_SHAPE_v2.1.pdf>`
+
+
+
+--------
+
+symmg
+^^^^^
+qqqqq
+
+--------
+
+cchir
+^^^^^
+qqqqq
+
+--------
+
+wfsymm
+^^^^^^
+qqqqq
+
+--------
+
+Specific task scripts
+---------------------
+
+qqqqq
+
+--------
+
+shape_map
+^^^^^^^^^
+qqqqq
+
+--------
+
+Using cosymlib's APIs
+---------------------
+
+qqqqq
+
+--------
+
+
+