#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program 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 3 of the
## License, or any later version.
##
## This program 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 find a copy of the GNU General Public License in the file
## license.txt along with this program; if not, write to the Free
## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
##
##
## last $Author: graik $
## $Date: 2012-02-23 19:10:59 -0500 (Thu, 23 Feb 2012) $
## $Revision: 1086 $
 
import Biskit.Mod.modUtils as modUtils
 
from Biskit.Mod import *
from Biskit.Mod import Modeller as M
from Biskit.Mod import TemplateCleaner as TS
from Biskit.Mod import TemplateFilter as TF
import Biskit.tools as tools
from Biskit import EHandler
from Biskit import LogFile
 
from Biskit.Pymoler import Pymoler
from Biskit.Trajectory import Trajectory
 
import sys, os.path
import string
import glob
 
def _use( o ):
    print """
Build model using Modeller.
 
Syntax: model.py [ -o |outFolder| -log |logFile| -h |host_computer|
                   -top |input_script_template|
                   -v |verbosity|
                   -zfilter |x.x| -idfilter |percent|
                   ...and more, see below...]
 
Options:
    -o         output folder for results      (default: .)
    -log       log file                       (default: STDOUT)
    -node      host computer for calculation  (default: local computer)
               -> must be accessible w/o password via ssh, check!
    -s         show structures on Pymol superimposed on average
    -dry       do not run Modeller; just set up and try post-processing
               existing results
    -v         verbosity level (0 - 3)
 
    -? or -help .. this help screen
 
    The remaining options are simply passed on to Modeller but are usually
    left at their default:
 
    -fasta_target |file with target sequence|
    -template_folder |folder containing template PDBs for modeller|
    -f_pir |file containing alignment|
    -starting_model |first homology model to report [1]|
    -ending_model |last model to report [10]|
    -zfilter |float|
               ignore templates that are more than z standard deviations below
               the average sequence identity to the target (0..switch off)
               (default: see Biskit.Mod.TemplateFilter.py)
    -idfilter |float|
               ignore templates that have less than idfilter fraction sequence
               identity to target sequence (the best template is always kept)
               (0..switch filtering off)
 
    -mod_template |file|
               Provide a different input script template (see Modeller.py).
               You can use either old style modeller.top files or new-style
               python scripts -- see biskit/Biskit/data/modeller for an example.
 
    Further options are passed on to the Executor parent class, for
    example:
 
    -debug |1| to not delete any temporary files
    -nice |int| to adjust a non-0 nice level
 
 
 
input: ./templates/modeller/*.pdb
       ./t_coffee/final.pir_aln
 
output: ./modeller/modeller.log
                  /*.B9999000??   <- models
        /model_??.pdb   <- processed PDBs ordered by modeller score
 
Default options:
"""
    for key, value in o.items():
        print "\t-",key, "\t",value
    sys.exit(0)
 
 
def defaultOptions():
    return {'o':'.',
            'log': None,
            'node':None,
            'v':1,
            'zfilter':TF.Z_CUTOFF,
            'idfilter':TF.ID_CUTOFF,
            }
 
def convertOptions( o ):
    """
    Translate commandline options where needed.
    You may need to add some entries here if you want to override exotic
    Executor parameters from the commandline.
    """
    o['verbose'] = int( o.get('v',1) )
    del o['v']
 
    o['outFolder'] = tools.absfile( o.get('o','.') )
    del o['o']
 
    o['zfilter'] = float( o.get('zfilter',0) )
    o['idfilter']= float( o.get('idfilter',0))
 
    o['log'] = o.get('log', None)
    if o['log']:
        o['log'] = LogFile( o['o'] + '/' + options['log'], 'a' )
 
    o['debug'] = int( o.get('debug', 0) )
    o['nice']  = int( o.get('nice', 0) )
 
    if 'ending_model' in o:
        o['ending_model'] = int( o['ending_model'] )
 
    if 'starting_model' in o:
        o['starting_model'] = int( o['starting_model'] )
 
    return o
 
def __printMatrix( matrix ):
    """
    Print the part right of the diagonal in a matrix
    """
    nr = len( matrix )
    for i in range(nr): print '%5i'%(i+1),
    for i in range(nr):
        print '\n%2i'%(i+1),
        for k in range(i):
            print ' '*5,
        for j in range(i, nr):
            print '%5.2f'%matrix[i,j],
 
### MAIN ###
 
options   = tools.cmdDict( defaultOptions() )
 
if '?' in options or 'help' in options:
    _use( defaultOptions() )
 
options = convertOptions( options )
 
## Test, comment in for testing
# outFolder = tools.testRoot() + '/Mod/project'
 
###################
## Modeller
##
## Build model using Modeller.
 
## input: templates/modeller/*.pdb
##        t_coffee/final.pir_aln
##
## output: modeller/modeller.log
##                 /*.B9999000??   <- models
try:
 
    if options['verbose'] > 0:
        print "\n"+\
              "Type model.py -? or model.py -help for a full list of options!"
 
    m8 = M( **options )
 
    if not 'dry' in options:
        r = m8.run()  ## comment out for testing
 
except:
    EHandler.error( 'Error while modelling.')
 
 
#####################
## Show output
 
## show result in PyMol
if options.has_key('s'):
    names = []
 
    ## fit backbone of all models to average until convergence
    models =  glob.glob( '%s/target.B*'%(m8.outFolder + m8.F_RESULT_FOLDER) )
    traj = Trajectory( models )
    traj.blockFit2ref( mask=traj[0].maskBB() )
 
    ## calculate and print rmsd matrix
    rmsHeavy = traj.pairwiseRmsd()
    print '\nHEAVY ATOM RMSD BETWEEN MODELS::'
    __printMatrix( rmsHeavy )
 
    ## same thing for backbone atoms
    BBMask = traj[0].maskBB()
    traj.blockFit2ref( mask = BBMask )
    rmsBB = traj.pairwiseRmsd( aMask = BBMask  )
    print '\nBACKBONE RMSD BETWEEN MODELS:'
    __printMatrix( rmsBB )
 
    ## get all templates
    templates =  glob.glob( '%s*'%( m8.outFolder + TS. F_MODELLER ))
 
    p=Pymoler()
    ## add models
    for i in range( len(traj) ):
        print 'Pymol.add model', i
        p.addPdb( traj[i], 'model_%i'%i ) 
        names  += [ 'model_%i'%i ]
 
    ## load all templates and align to first model
    for t in templates:
        name = string.split( string.split(t, '/')[-1], '.')[0]
        names  += [ name ]
        p.addPdb( t, name )
        p.add( 'align %s, model_0'%name )
 
    ## color things in different colors
    colors = p.addColors( len(names),
                          firstColor=[1.0, 0.0, 0.0],
                          lastColor=[0.0, 0.0, 1.0] )
 
    for i in range( len(names) ):
        p.add('color %s, %s'%(colors[i], names[i]) )
 
    p.add('hide all')
    p.add('show line')
 
    ## don't show sidechains and carboxyl oxygen - too messy
    p.add('select bb, not name c+ca+n')
    p.add('hide line, bb')
 
    p.add('select none')
    p.add('zoom all')
 
    print 'writing pymol script and models...'
 
    p.show()