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stage
include
ost
io
mol
sdf_reader.hh
Go to the documentation of this file.
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//------------------------------------------------------------------------------
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// This file is part of the OpenStructure project <www.openstructure.org>
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//
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// Copyright (C) 2008-2011 by the OpenStructure authors
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//
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// This library is free software; you can redistribute it and/or modify it under
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// the terms of the GNU Lesser General Public License as published by the Free
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// Software Foundation; either version 3.0 of the License, or (at your option)
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// any later version.
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// This library is distributed in the hope that it will be useful, but WITHOUT
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// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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// details.
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//
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// You should have received a copy of the GNU Lesser General Public License
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// along with this library; if not, write to the Free Software Foundation, Inc.,
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// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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//------------------------------------------------------------------------------
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/*
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Author: Tobias Schmidt
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*/
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#ifndef OST_IO_SDF_READER_HH
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#define OST_IO_SDF_READER_HH
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#include <boost/filesystem/fstream.hpp>
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#include <
ost/mol/chain_handle.hh
>
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#include <
ost/mol/residue_handle.hh
>
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#include <
ost/io/module_config.hh
>
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namespace
ost {
namespace
io {
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class
DLLEXPORT_OST_IO
SDFReader
{
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public
:
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SDFReader
(
const
String
& filename);
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SDFReader
(
const
boost::filesystem::path& loc);
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SDFReader
(std::istream& instream);
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bool
HasNext();
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void
Import(
mol::EntityHandle
& ent);
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private
:
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void
ClearState(
const
boost::filesystem::path& loc);
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void
NextMolecule();
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void
ParseAndAddHeader(
const
String
& line,
int
line_num,
mol::EntityHandle
& ent,
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mol::XCSEditor
& editor);
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void
ParseAndAddAtom(
const
String
& line,
int
line_num,
mol::EntityHandle
& ent,
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bool
hetatm,
mol::XCSEditor
& editor);
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void
ParseAndAddBond(
const
String
& line,
int
line_num,
mol::EntityHandle
& ent,
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mol::XCSEditor
& editor);
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mol::ChainHandle
curr_chain_;
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mol::ResidueHandle
curr_residue_;
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int
chain_count_;
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int
residue_count_;
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int
atom_count_;
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int
bond_count_;
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int
line_num;
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boost::filesystem::ifstream infile_;
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std::istream& instream_;
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};
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}}
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#endif
String
std::string String
Definition:
base.hh:54
ost::mol::EntityHandle
Protein or molecule.
Definition:
entity_handle.hh:54
ost::io::SDFReader
Definition:
sdf_reader.hh:32
ost::mol::ResidueHandle
Residue handle.
Definition:
residue_handle.hh:54
chain_handle.hh
ost::mol::ChainHandle
linear chain of residues
Definition:
chain_handle.hh:52
ost::mol::XCSEditor
external coordinate system editor
Definition:
xcs_editor.hh:36
DLLEXPORT_OST_IO
#define DLLEXPORT_OST_IO
Definition:
module_config.hh:27
module_config.hh
residue_handle.hh
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