[DOC] add readme files

Author: hroest

src/README.md

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+source
+=============
+
+This contains the source code. It contains the following folders:
+
+- [Examples](examples/)
+

src/examples/README.md

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+Examples
+=============
+
+This folder contains example scripts using pyOpenMS:
+
+* `convertToMGF.py`
+    * A simple script to convert any spectra file readable by OpenMS (for
+      example `mzXML` or `mzML`)  to the `MGF` format. Python is only used to
+      read in the spectra while writing of MGF is done natively in Python. MGF
+      is used an example of any file format that is not currenly available
+      through the OpenMS C++ library, showing how such a sample implementation
+      could look like.
+- `peakpicker_scipyFFT.py`
+    * A peakpicker using fast fourier transform (FFT) provided in `scipy` to
+      smooth the provided spectrum and then applies the OpenMS
+      `PeakPickerHiRes` on the result. The input spectrum and the picked peaks
+      are then plotted using `matplotlib`, completing the integration of Python
+      and OpenMS on multiple levels.
+- `pymol_example.py`
+    * An example of mapping identified peptide sequences from an MS/MS
+      experiment onto a 3D crystal strucutre of a protein using Python with
+      `pymol`. 
+- `runPhosphoScoring.py`
+    * An implementation of a phospho-site scoring algorithm completely in
+      Python using the available OpenMS data structures. It compares its result
+      with the search-engine provided result and the one of the AScore
+      algorithm as implemented in OpenMS.