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src/b/i/biskit-2.4/Biskit/AmberEntropist.py   biskit(Download)
        @rtype: [ int ]
        """
        remaining = MU.difference( range( n_members ), excluded )
        tripple = self.tripples( remaining, trippleIndex+1 )[-1]
        return MU.union( excluded, list(tripple) )
        @rtype: [ int ]
        """
        remaining = MU.difference( range( n_members ), excluded )
        new_i = remaining[index]
        return excluded + [ new_i ]
            self.log.add("excluding members: " + str(exclude))
 
        return traj.takeMembers( MU.difference( members, exclude ) )
 
 

src/b/i/biskit-2.4/Biskit/AmberEntropyMaster.py   biskit(Download)
        n_com_members = t.n_members
 
        self.cl = self.cl or MU.difference( range(t.ref.lenChains()), self.cr)
        rec = t.ref.takeChains( self.cr, breaks=0 )
        lig = t.ref.takeChains( self.cl, breaks=0 )

src/b/i/biskit-2.4/Biskit/atomCharger.py   biskit(Download)
                             (len(refres)-len(iref), self.__resinfo(res,j)) )
 
                    missing = MA.difference( range(len(refres)), iref )
                    self.log.add('\t'+str(N.take( refres['name'], missing )) )
                    self.log.add(
                             (len(res)-len(i), self.__resinfo(res,j)) )
 
                    missing = MA.difference( range(len(res)), i )
                    self.log.add('\t'+str(N.take( res['name'], missing )) )
                    self.log.add('\tGiving up. Whole residue will be set to charge 0.')

src/b/i/biskit-2.4/scripts/Biskit/killpp.py   biskit(Download)
force= 'f' in o
if 'e' in o:
    hosts = MU.difference( hosts, toList( o['e'] ) )
 
msg = "KILL All jobs matching '%s' on all hosts?? Y/N " % phrase