integrated the part for Density Map docking
added New module for density creation from pdb file and CCC calculation
between reference and simulated density mpa
new function to create pdb files by each processor. These pdb files are
created to later be converted in simulated density maps
-CCC_SimulMap : integrated laplacian filter to > 10 A density maps
-ClusterAndDraw: modifications made so that it can be launched directly
in the postprocess function run of DockSymmCirlce and HeteroMultimer
instead inside of POW.py
-DockSymmCircle: replaced the previous postprocess run function with
function to create distance matrix and clustering
-Heteromultimer: same as above
-POW: Removed the distance matrix creation method and replaced it by
standard post.run() (which is now running in parallel!)
- POW now manages modules having a path
- DockSymmCircle postprocessing deals also with flexible cases
generalised the write_pdb function by taking the one from the parent
module (DockSymmCircle for example)
added a write_pdb function called by the ClusterAndDraw module
Created a write_pdb function that is called by the ClusterAndDraw module
to write the pdbs
Function to compute distance matrix has been standardised and moved to
cluster and draw
put the creation of coords and indexes for the postprocessing in the
run() instead of in the computDistance function as it was slowing down
the creation of the distance matrix
parse.py now runs with parallel postprocessing (to be launched with
mpirun)
Merge remote-tracking branch 'origin/master'
DockSymmCircle postprocessing deals with trajectories as well (write_pdb
function). Removed module-specific call in Cluster and Draw. Parse looks
neater.
Cleaned ClusterAndDraw (using more generic names for functions, instead
of references to proteins). Added default functions for distance and
output making (user can supersede them at will in specific module).
Fixed a bug in DockSymmCircle related to flexible protein assembly. PSO
search space was not centred on protein's conformational space.
fixed boundary reflexive boundary conditions and removed few prints from
DockSymmCircle
Added the possibility to extract also non clustered solution from
dendrogram tree selection
added files
Merge branch 'master' of git@github.com:degiacom/POW

Conflicts:
	.settings/org.eclipse.core.resources.prefs
	DockSymmCircle.py
	parse.py
added the clustered indexes to the make output function