update docs

README.rst

@@ -43,10 +43,42 @@ The following example shows how to use **WaterNetworkAnalysis** to prepare a MD
 
 .. code:: python
 
-   import WaterNetworkAnalysis as WNA
-   # load some example
-   # Run classification
-   # Create visualisations
-   # plot results
+   from WaterNetworkAnalysis import WaterNetworkAnalysis as WNA
+   import os
+   # MD trajectory filename
+   trajectory="md_pl.xtc"
+   # topology filename
+   topology="md_pl.gro"
+   # ligand name
+   ligand = 'SLB'
+   # distance to select water molecules around
+   distance = 15.0
+   # define active site by aminoacid residue numbers
+   active_site_aminoacids = [10,11,124,127,147,149,150,151,153,154,168,169,17,170,173,187,188,191,197,212,214,49,65,66,67,69,70,72]
+   analysis=WNA(aminoacids_in_activesite=active_site_aminoacids)
+   # if trajectory is not aligned align it and extract water molecules inside 15 A around active site
+   if not os.isfile('aligned_trajectory.xtc'):
+       analysis.align_trajectory(trajectory, topology,every=10)
+       analysis.extract_waters_from_trajectory(topologyology=topology, dist=distance)
+   elif not os.isfile('water_coordinates.dat'):
+       analysis.extract_waters_from_trajectory(traj='aligned_trajectory.xtc',topologyology=topology, dist=distance)
+   else:
+       analysis.load_H2O(fname='water_coordinates.dat')
+   # If the procedure hasn't started start it, else restart it or if finished load results
+   if not os.isfile('Clustering_results.dat'):
+        if not os.isfile('Clustering_results_temp.dat'):
+            analysis.cluster()
+        else:
+            analysis.restart_cluster()
+   else:
+       analysis.read_results()
+   # Make results in pdb file
+   analysis.make_results_pdb("aligned.pdb",ligand,mode="cathegorise")
+   analysis.make_results_pdb("aligned.pdb",ligand)
+   # create a PyMol visualisation session
+   analysis.visualise_pymol()
 
 
+
+.. image:: figs/Results.png
+  :width: 600