/***************************************************************************
                          codegen.h  -  description
                             -------------------
    begin                : Tue Nov 18 01:45:35 2003
    copyright            : (C) 1999-2006 by Cavalli Andrea
    author               : : cavalli $
    date                 : : 2003/12/09 11:10:33 $
    id                   : : coor.h,v 1.1.2.2 2003/12/09 11:10:33 cavalli Exp $
    email                : cavalli@bioc.unizh.ch amc82@cam.ac.uk
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   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 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/
#ifndef __CODEGEN__
#define __CODEGEN__

#include <almost.h>
#include <boost/algorithm/string/replace.hpp>
#include <symboltable.h>
namespace Almost {

  //
  string find_class_doc(string m, string c){
    ZModule * zmod;
    if(SymbolTable::instance().is_modulename(m)){
      zmod = (ZModule *)SymbolTable::current()[m];
      ZExtClass * zclass;
      if(zmod->module_map.find(c)!=zmod->module_map.end()){
	zclass = (ZExtClass*)zmod->module_map[c];
	if(zclass->class_doc.find("__class__")!=zclass->class_doc.end()){
	  string s = zclass->class_doc["__class__"];
	  return s;
	}
      }
    }
    return string();
  }

  string mdbload(string f, string & comment,bool verbose=true){
    stringstream s,c;
    if(verbose){
      c<<"\n\n// <b>Load a Molecular database file MDB.</b><br>\n"
       <<"//<p> Very little can be done in <b><tt>almost</tt></b>, until  a molecular database file MDB has been loaded.\n"
       <<"// Most of the scripts start, therefore, with this command.<br></p>\n";
	//MDB desc
      string d = find_class_doc("mdb","MDB");
      if(d!="")
	c<<d;
      c<<"// <p>In this HOWTO, we assume that "<<f<<" is your the working directory,\n" 
       <<"// that is, the directory from which you will lauch the script. If not use the full path of the file.\n"
       <<"// A copy should be in the <tt>toppar</tt> of your distribution.</p>\n"
	;
      comment = c.str();
    }
    s<<"MDB = mdb.MDB(\""<<f<<"\");\n";
    return s.str();
  }


  string pdbload(string f, string &comment, bool verbose=true){
    stringstream s,c;
    if(verbose){
      c<<"\n\n//<b> Load a Protein data bank file PDB.</b><br>\n";
      string d = find_class_doc("pdb","pdb");
      if(d!="")
	c<<d;
      c<<"// We assume that the file "<<f<<" is in your current-working directory.<br>\n";
      comment = c.str();
    }
    s<<"PDB = pdb.pdb(\""<<f<<"\");\n";
    return s.str();
  }

  string buildmols_and_prot(string p,  string &comment,bool verbose= true){
    stringstream s,c;
    if(verbose){
      c<<"\n\n// <b>Build a Molecules container and add a protein to it.</b><br>\n"
       <<"// <p>This operation is, unfortunately, a little bit more involved than one would expect.\n"
       <<"// The reason is that  <b><tt>almost</tt></b> needs to associate to each atom,\n"
       <<"// bond, etc., the correct force field parameters. In order to do this, atom and fragment names\n"
       <<"// need to follow the naming convetions definend in the MDB file.\n"
       <<"// If this is not the case, it is possible to rename them. See HOWTO make a working PDB for more informations.<br>\n</p>"
       <<"// <p>Here we assume that the PDB you provide is \"correct\".</p>\n"
       <<"// <p>Structures used as starting point in a molecular dynamics simulation (MD)\n"
       <<"// should have a low energy, to avoid problems in the early stages of the \n"
       <<"// simulation.\n"
       <<"//  See the tutorial HOWTO minimize a PDB and  the documentation of the PDB, MDB and Molecules modules for more informations.<br></p>\n";
      string d = find_class_doc("molecules","protein");
      if(d!="")
	c<<d;
     
      comment = c.str();
    }

    s<<"p = molecules.protein(\""+p+"\");\n"
     <<"p.build(PDB[0][0],MDB,\"NTER\",\"CTER\");\n"
     <<"mols = molecules.molecules();\n"
     <<"mols.add_protein(p);\n";
    return s.str();
  }

  string build_missingmols_and_prot(string p, string &comment, bool verbose= true){
    stringstream s,c;
    if(verbose){
      c<<"\n\n// <b>Build a Molecules container and add a protein to it.</b><br>\n"
       <<"// <p>The protein is build using the build_missing() function. This function differs from the standard build() one,\n"
       <<"// in what it does if one or more atoms are missing in the PDB.<br>"
       <<"// In fact, in case of a missing atom, the default build() function will fire an error message and exit.<br>\n"
       <<"// On the contrary, the build_missing() function will try to add all missing atoms\n"
       <<"// using the default amino-acid geometry as defined in the molecular database file.<br></p>\n"
       <<"// <p>Proteins build with build_missing() have usually a very high energy due to steric (van der Waals) clashes.\n"
       <<"// They should, therefore, always be minimized before using them as starting structure in a MD or a Monte Carlo simulation.<br>\n"
       <<"// See the tutorial HOWTO minimize a PDB and the documentation of the PDB, MDB and Molecules modules for more informations.</p>\n";
      comment = c.str();
    }

    s<<"p = molecules.protein(\""+p+"\");\n"
     <<"p.build_missing(PDB[0][0],MDB,\"NTER\",\"CTER\");\n"
     <<"mols = molecules.molecules();\n"
     <<"mols.add_protein(p);\n";
    return s.str();
  }

  
  string setupmdoptions( string &comment,bool verbose=true){
    stringstream s,c;
    if(verbose){
      c<<"\n\n// <b>Setup the molecular dynamics simulation</b><br>\n"
       <<"//<p>In <b><tt>almost</tt></b>, a molecular dynamics simulation (MD) is controlled by a structure, mdoptions, that stores all\n"
       <<"// user setup.<br>\n"
       <<"// Molecular dynamics options are of two types: (1) force field options and (2) run options.\n"
       <<"// With the first category of options one can select the kind of force field to use in the simulation,\n"
       <<"// with the second group the details of the simulation such as number of steps, temperature, etc.\n"
       <<"// To make life easier, a convenience function initializes all force field options to their default values.\n"
       <<"// See the documentation of the md module for additional informations.</p>\n";
      comment = c.str();
    }


    s<<"opts = md.c19_defaults(md.SASA,md.BERE);\n"
     <<"opts.temp =330;\n"
     <<"opts.time_step =0.002;\n"
     <<"opts.nprint =1000;\n"
     <<"opts.steps = 10000;\n"
     <<"opts.gamma_water = 5;\n"
     <<"opts.rst = \"run_sasa.rst\";\n"
     <<"opts.trj = \"run_sasa.dcd\";\n"
     <<"opts.dat=\"run_sasa.dat\";\n"
     <<"print opts;\n";
    return s.str();
  }

  string setupenergyoptions(string & comment, bool verbose = true){
    stringstream s,c;
    //coment here
    if(verbose){
      c<<"\n\n// Create a energy_options() object to select the force field\n"
       <<"// to be used.<br>"
       <<"// An energy_options object can be created either using the class \n"
       <<"// constructor energy.energy_options() or the convenience functions:<br>\n"
       <<"// energy.c19_defaults(int) and energy.c22_defaults().<br>\n"
       <<"// See the documentation of the energy module for details.\n"
	;
      comment = c.str();
    }
    s<<"opts = energy.c19_defauts();\n";
    return s.str();
  }

  string runmd(string &comment, bool verbose = true){
    stringstream s,c;

    if(verbose){

      c<<"\n\n// <b>And now run...</b><br>\n"
       <<"// <p>Now, create a molecular dynamics object and run the simulation.\n"
       <<"// That's it!</p>\n"
       <<"// <p>The last coordinates are stored in the res Molecules object and saved to\n"
       <<"// a file with the molecules.molecules2pdb() function.</p>\n"
	;  
      comment = c.str();    
    }

    s<<"MD = md.md();\n"
     <<"res = MD.run(mols,opts,MDB);\n"
     <<"molecules.molecules2pdb(res,\"res.pdb\");\n"
      ;
    return s.str();
  }
  
  string runmini(string & comment, bool verbose = true){
    stringstream s,c;
    if(verbose){
      c<<"Now start the minimization. That's it.\n";
      comment = c.str();
    }
    s<<"minimize.sd(mols,opts,MDB,1000,0.001);\n";
    
    return s.str();
  }


  string calcene(string & comment, bool verbose = true){
    stringstream s,c;
    if(verbose){
      c<<"// <p>Now compute the enrgy and print the result.\n"
       <<"// The energy function return an object of type energy.data.</p>\n"
	;
      string d =find_class_doc("energy","data");
      if(d.size()!=0)
	c << d;
      comment = c.str();
    }
    s<<"e = energy.energy(mols,opts,MDB);\n"
     <<"print e;\n"
     <<"//print e[\"vdw\"]; // To print a component.\n"
      ;
    return s.str();
  }

  string mkhowtostr(string comment, string code){
    boost::replace_all(comment,"//","");
//     string res = "<div class=\"note\">"+comment +"</div>\n"+
//       +"\n<p><pre>"+code+"</pre></p>\n";
    string res = "<div class=\"comment\"><p>"+comment +"</p></div>\n"+
      +"\n<div class=\"note\"><p><pre>"+code+"</pre></p></div>\n";
    return res;
  }
}

#endif
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