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Marco Biasini authoredMarco Biasini authored
entity_io_crd_handler.hh 3.85 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 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
//------------------------------------------------------------------------------
/*
Author: Ansgar Philippsen, Tobias Schmidt
*/
#ifndef OST_IO_ENTITY_IO_PLUGIN_CRD_H
#define OST_IO_ENTITY_IO_PLUGIN_CRD_H
#include <ost/mol/entity_handle.hh>
#include <ost/mol/chain_handle.hh>
#include <ost/mol/residue_handle.hh>
#include <ost/mol/entity_visitor.hh>
#include <ost/io/mol/entity_io_handler.hh>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/filesystem/fstream.hpp>
namespace ost { namespace io {
/// \brief CHARMM coordinate file import
class DLLEXPORT_OST_IO CRDReader {
public:
CRDReader(const boost::filesystem::path& loc);
void Import(mol::EntityHandle& ent);
std::vector<mol::AtomHandle> GetSequentialAtoms() const;
private:
void ParseAndAddAtom(const String& line, mol::EntityHandle& h);
void ParseAndAddAtomExpanded(const String& line, mol::EntityHandle& h);
std::vector<mol::AtomHandle> sequential_atom_list_;
mol::ChainHandle curr_chain_;
mol::ResidueHandle curr_residue_;
int chain_count_;
int residue_count_;
int atom_count_;
boost::filesystem::ifstream infile_;
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
};
/// \brief CHARMM coordinate file export
class DLLEXPORT_OST_IO CRDWriter : public mol::EntityVisitor {
public:
CRDWriter(const String& filename, bool ext=false);
CRDWriter(const boost::filesystem::path& filename, bool ext=false);
CRDWriter(std::ostream& outstream, bool ext=false);
void Write(const mol::EntityView& ent);
void Write(const mol::EntityHandle& ent);
virtual bool VisitAtom(const mol::AtomHandle& atom);
virtual bool VisitResidue(const mol::ResidueHandle& r);
void WriteHeader(const mol::EntityView& ent);
private:
void Init();
std::ofstream outfile_;
std::ostream& outstream_;
bool ext_;
int atom_count_;
int atom_total_;
int res_count_;
};
class DLLEXPORT_OST_IO EntityIOCRDHandler: public EntityIOHandler {
public:
virtual void Import(mol::EntityHandle& ent, const boost::filesystem::path& loc);
virtual void Export(const mol::EntityView& ent,
const boost::filesystem::path& loc) const;
virtual void Import(mol::EntityHandle& ent, std::istream& stream);
virtual void Export(const mol::EntityView& ent, std::ostream& stream) const;
static bool ProvidesImport(const boost::filesystem::path& loc,
const String& format="auto");
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("Crd"); }
static String GetFormatDescription() { return String("CARD format file used by the Charmm software package"); }
};
typedef EntityIOHandlerFactory<EntityIOCRDHandler> EntityIOCRDHandlerFactory;
mol::EntityHandle DLLEXPORT_OST_IO LoadCRD(const String& file_name);
}} // ns
#endif