## 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
## 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 $
## last $Date: 2012-02-23 19:10:59 -0500 (Thu, 23 Feb 2012) $
## $Revision: 1086 $
Run ptraj entropy analysis on existing amber trajectory (.crd) and
topology (.parm7) file.
import os.path as osp
import re
import tempfile
import Biskit.tools as T
## import Biskit.settings as settings
from Biskit.Errors import BiskitError
from Biskit.Executor import Executor
class EntropistError( BiskitError ):
class AmberCrdEntropist( Executor ):
    Run ptraj entropy analysis on existing amber trajectory (.crd) and
    topology (.parm7) file.
    ## template for ptraj input script
    ptraj_script = """
    trajin %(f_crd)s %(start)i %(stop)i %(step)i
    matrix mwcovar name mwc
    analyze matrix mwc vecs 0 thermo
    def __init__( self, f_parm, f_crd, f_template=None,
                  s=0, e=None, step=1, **kw ):
        @param f_parm: path to amber topology file
        @type  f_parm: str
        @param f_crd: path to amber trajectory file
        @type  f_crd: str
        @param f_template: alternative ptraj input template (default: None)
        @type  f_template: str 
        @param s: start frame (default: 0, first)
        @type  s: int
        @param e: end frame (default: None, last)
        @type  e: int
        @param step: frame offset (default: 1, no offset )
        @type  step: int
        @param kw: additional key=value parameters for Executor:
        @type  kw: key=value pairs
          debug    - 0|1, keep all temporary files (default: 0)
          verbose  - 0|1, print progress messages to log (log != STDOUT)
          node     - str, host for calculation (None->local) NOT TESTED
                          (default: None)
          nice     - int, nice level (default: 0)
          log      - Biskit.LogFile, program log (None->STOUT) (default: None)
        template = f_template or self.ptraj_script
        Executor.__init__( self, 'ptraj', template=template, push_inp=0, **kw )
        self.f_parm = T.absfile( f_parm )
        self.f_crd  = T.absfile( f_crd )
        self.start = s
        self.stop  = e or 10000000
        self.step  = step
        ## default result
        self.result = { 'T':None, 'mass':None, 'vibes':None,
                        'S_total':None, 'S_trans':None, 'S_rot':None,
                        'contributions':None, 'nframes':None,
                        'version':self.version(), 'node':self.node }
    def version( self ):
        Version of class.
        @return: version
        @rtype: str
        return 'AmberCrdEntropist $Revision: 1086 $'
    def command( self ):
        Build the command string.
        @return: command
        @rtype: str
        return "%s %s %s" % (self.exe.bin, self.f_parm, self.f_in)
    def __tryMatch( self, regex, str, integer=0 ):
        m = regex.search( str )
        if m:
            return round( float( m.groups()[0] ), 3 )
        return None
    def finish( self ):
        Overrides Executor method
        self.result = self.parsePtrajResult( self.f_out )
    def isFailed( self ):
        Detect whether external program failed, override!
        if not osp.exists( self.f_out ):
            return 1
        return 0
    def parsePtrajResult( self, f_out ):
        Extract results from ptraj.
        @param f_out: result of ptraj run
        @type  f_out: str
        @return: extracted prtaj result
        @rtype: dict
        @raise EntropistError: if unexpected end of ptraj output file
        ## regular expressions for parsing of ptraj output
        re_thermo= re.compile('- Thermochemistry -')
        re_T     = re.compile('^\s*temperature\s*(\d+\.\d+)\s*kelvin')
        re_mass  = re.compile('^\s*molecular mass\D*(\d+\.\d+)\s*amu')
        re_vibes = re.compile('^\s*Warning--\s*(\d+)\s*vibrations have low')
        re_table = re.compile('^-{80}$')
        re_value = re.compile('(-*\d+\.\d+)$')
        re_nsets = re.compile('Successfully read in (\d+) sets')
        r = self.result
            lines = open( f_out, 'r' ).readlines()
            l = lines.pop()
            while not r['nframes']:
                r['nframes'] = r['nframes'] or self.__tryMatch( re_nsets, l )
                l = lines.pop()
            while not re_thermo.search(l):
                l = lines.pop()
            while not re_table.search(l):
                r['T']    = r['T']     or self.__tryMatch( re_T, l )
                r['mass'] = r['mass']  or self.__tryMatch( re_mass, l )
                r['vibes']= r['vibes'] or self.__tryMatch( re_vibes,l )
                l = lines.pop()
            l = lines.pop()
            v = []
            while lines:
                v += [ self.__tryMatch( re_value, l ) ]
                l = lines.pop()
            r['S_total'], r['S_trans'], r['S_rot'], r['S_vibes'] = tuple(v[:4])
            r['contributions'] = v[4:]
        except IndexError:
            raise EntropistError, 'unexpected end of ptraj output file.'
        return r
if __name__ == '__main__':
    print "Setting up"
    f = T.testRoot() + '/Amber/AmberCrdEntropist/' 
    e = AmberCrdEntropist( f + 'lig_traj.parm',
                           f + 'lig_traj.crd', debug=0, verbose=1)
    print "Running"