pdb_reader.h

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// -*- mode: c++; -*-
//
//The Biomolecule Toolkit (BTK) is a C++ library for use in the
//modeling, analysis, and design of biological macromolecules.
//Copyright (C) 2001, Eric Alm <ealm3141@users.sourceforge.net>
//
//This program is free software; you can redistribute it and/or modify
//it under the terms of the GNU Lesser General Public License as published
//by the Free Software Foundation; either version 2.1 of the License, or (at
//your option) 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
//Lesser General Public License for more details. 
//
//You should have received a copy of the GNU Lesser General Public License 
//along with this program; if not, write to the Free Software Foundation, 
//Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.

//pdb_reader.h

/*** PDBReader:

  This class is designed to read in PDB files. 

  Its scope is limited to the folowing tasks:
  - read and parse every ATOM and HETATOM line into a record
  - return one polymer chain at a time
  - filter out all but the requested chain
  - provide the list of chains, the pdb header, and the remarks

  TODO: add this functionallity
  - fix non-standard names for standard atoms??
  - handle multiple models in a pdb (NMR structures)

  If you want more specific behaviour, write a wrapper.

  Many protein-specific fixes are relegated to later processing
  in pdb_reader customers, including renumbering residues,
  checking for continuity, and rebuilding missing atoms.

***/

#ifndef PDB_READER_H
#define PDB_READER_H

#include "pdb_atom.h"

#include <iosfwd>
#include <string>
#include <vector>


namespace BTK {

class PDBReader {

 public:
  PDBReader(std::string const & filename) : 
    _filename(filename), _stream(NULL), _buffer(),
    _model_loaded(false), _stream_loaded(false){}
  PDBReader(std::istream & stream) : 
    _filename(), _stream(&stream), _buffer(),
    _model_loaded(false), _stream_loaded(false){}
  ~PDBReader();

  std::string get_header();
  std::vector<PDBAtom> get_chain(const unsigned chain_index);
  std::vector<PDBAtom> get_chain(const char chain_id);
  //  std::vector<PDBAtom> get_next_chain();
  //  std::vector<PDBAtom> get_chains(int chain_id=' ');
  //  std::vector<string> get_remarks();
  std::vector<char> get_chain_labels();

  //  void SearchPDBPath(char *filename); // find the pdb file in 

 private:

  void load_stream(); 
  void load_model(); 

  std::string _filename;
  std::istream *_stream;
  std::vector<std::string> _buffer;
  bool _model_loaded; //keep track of whether data was read
  bool _stream_loaded; //keep track of whether stream is open
};

}

#endif // PDB_READER_H

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