pdb_reader.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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 3.0 of the License, or (at your option)
// any later version.
// This library 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 library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_IO_PDB_READER_HH
#define OST_IO_PDB_READER_HH
/*
  Author: Marco Biasini
 */

#include <boost/iostreams/filtering_stream.hpp>
#include <boost/filesystem/fstream.hpp>
#include <ost/string_ref.hh>
#include <ost/seq/sequence_list.hh>
#include <ost/mol/residue_handle.hh>
#include <ost/mol/entity_handle.hh>
#include <ost/mol/chain_handle.hh>
#include <ost/mol/atom_handle.hh>
#include <ost/mol/xcs_editor.hh>

#include <ost/io/module_config.hh>
#include <ost/io/mol/io_profile.hh>
namespace ost { namespace io {

class DLLEXPORT_OST_IO PDBReader {
  struct HSEntry {
    mol::ResNum start;
    mol::ResNum end;
    String chain;
  };
  struct HetEntry {
    HetEntry(char c, mol::ResNum n): chain(c), num(n) {}
    char        chain;
    mol::ResNum num;
  };
  struct CompndEntry {
    CompndEntry(std::vector<String>  c, int n): chains(c), mol_id(n) {}
    std::vector<String> chains;
    int mol_id;
  };
  typedef std::vector<HSEntry> HSList;
  typedef std::vector<HetEntry>  HetList;
  typedef std::vector<CompndEntry> CompndList;
public:
  PDBReader(const String& filename, const IOProfile& profile);
  PDBReader(const boost::filesystem::path& loc, const IOProfile& profile);
  PDBReader(std::istream& instream, const IOProfile& profile);

  bool HasNext();

  void Import(mol::EntityHandle& ent,
        const String& restrict_chains="");
  void SetReadSeqRes(bool flag) { read_seqres_=flag; }
  bool GetReadSeqRes() const { return read_seqres_; }
  
  seq::SequenceList GetSeqRes() const { return seqres_; }
private:
  void ParseSeqRes(const StringRef& line, int line_num);
  void ParseCompndEntry(const StringRef& line, int line_num);
  void ClearState();
  void AssignSecStructure(mol::EntityHandle ent);
  void AssignMolIds(mol::EntityHandle ent);
  void ParseAndAddAtom(const StringRef& line, int line_num,
                       mol::EntityHandle& h, const StringRef& record_type);
  void ThrowFaultTolerant(const String& msg);
  bool ParseAtomIdent(const StringRef& line, int line_num, 
                      String& chain_name, StringRef& res, 
                      mol::ResNum& resnum, StringRef& atom_name, char& alt_loc,
                      const StringRef& record_type, int& serial);
  void ParseAnisou(const StringRef& line, int line_num,
                   mol::EntityHandle& h);
  void ParseHelixEntry(const StringRef& line);
  void ParseStrandEntry(const StringRef& line);
  void Init(const boost::filesystem::path& loc);
  bool EnsureLineLength(const StringRef& line, size_t size);
  void ParseConectEntry(const StringRef& line, int line_num, mol::EntityHandle& ent);
  std::map<int, mol::AtomHandle> amap_; // <serial_number, AtomHandle>
  mol::ChainHandle curr_chain_;
  mol::ResidueHandle curr_residue_;
  int chain_count_;
  int residue_count_;
  int atom_count_;
  int line_num_;
  bool hard_end_;
  int num_model_records_;
  String restrict_chains_;
  HSList helix_list_;
  HSList strand_list_;
  boost::filesystem::ifstream infile_;
  std::istream& instream_;
  boost::iostreams::filtering_stream<boost::iostreams::input>  in_;
  String curr_line_;
  HetList  hets_;
  CompndList compnds_;
  std::pair <bool, int> mol_id_;
  bool skip_next_;
  bool data_continues_;
  String old_key_;
  // this needs to be set to true for reading pqr
  // file (i.e. pdb formatted file with charges in occupacy
  // column, and radii in b-factor column)
  bool is_pqr_;
  IOProfile profile_;
  bool charmm_style_;
  bool warned_name_mismatch_;
  bool read_seqres_;
  bool warned_rule_based_;
  seq::SequenceList seqres_;
};

}}

#endif