README

# Copyright (c) 2012 EPFL (Ecole Polytechnique federale de Lausanne)
# Laboratory for Biomolecular Modeling, School of Life Sciences
#
# POW is free software ;
# you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation ;
# either version 2 of the License, or (at your option) any later version.
# POW is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY ;
# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with POW ;
# if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
#
# Author : Matteo Degiacomi, matteothomas.degiacomi@epfl.ch
# Web site : http://lbm.epfl.ch/resources


---------------------------------------------
--- Parallel Optimization Workbench (POW) ---
---------------------------------------------

Requirements
------------

The following python (>=2.5) packages are required:

- numpy
- scipy
- MDAnalysis (for flexible docking modules)
- mpi4py

mpi4py will also require the installation of OpenMPI


How to Launch
-------------

mpiexec -n 4 POW.py module input.dat

where "module" is the type of needed optimization (module), and "input.dat" your setup file


Available modules
-----------------

- DockDimer:       dock two proteins in a heterodimer, given experimental constraints
- DockSymmCircle : rigid/flexible assembly of n monomers according to a circular symmetry
                   and geometric constraints, possibly in the presence of a substrate
- Function:        generic function optimization


Other files
-----------

- Assembly.py :   data structure for heterodimers
- Default.py :    classes common to any POW implementation
- flexibility.py: functions for Principal Components Analysis
- Multimer.py:    data structure for homo multimers 
- parse.py:       performs just the postprocessing, without running PSO. Usage goes as follow:
                  ./parse.py module input_file [logfile]
- POW.py:         main executable
- Protein.py:     data structure for a single monomer (PDB parser)
- PSO.py:         parallel implementation of Particle Swarm Optimization


Known Bugs
----------

- PSO particle repelling function may randomly freeze the optimization process 
  For this reason, at the moment, "repellers" flag should be kept to "off"

- with some versions of MDAnalysis, trajectory alignement may crash.
  For this reason. when performing a flexible assembly with DockSymmCircle,
  the provided trajectory should be already aligned,


Ongoing Improvements
--------------------

- The following modules are being developed
  . Charge: optimize points distribution to match a given electric field
  . DockDimerCG: dock two proteins using a CG potential
  . DockLigand: dock a ligand in a protein active site
  . MatchProtLigand: parameterize protein-ligand interactions for a hybrid AA-CG model

- In DockSymmCircle, flexibility computed after NMA on a single snapshot