PDBSystem Class Template Reference

#include <pdb_system.hpp>

Inheritance diagram for PDBSystem:

System< PolymerType, ChemicalTypeSystemType, StorageStrategy > ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary > BTKSequence PolymerSystemBase boost::less_than_comparable BTKContainer List of all members.

Public Types

typedef base_type::chemical_type_system chemical_type_system
typedef base_type::dictionary dictionary
typedef base_type::id_type id_type
typedef base_type::value_type value_type
typedef base_type::iterator iterator
typedef base_type::const_iterator const_iterator
typedef base_type::reverse_iterator reverse_iterator
typedef base_type::const_reverse_iterator const_reverse_iterator
typedef base_type::reference reference
typedef base_type::const_reference const_reference
typedef base_type::pointer pointer
typedef base_type::const_pointer const_pointer
typedef base_type::difference_type difference_type
typedef base_type::size_type size_type
typedef base_type::chain_type chain_type
 Type definitions required for all System classes.
typedef base_type::chain_iterator chain_iterator
typedef base_type::const_chain_iterator const_chain_iterator
typedef base_type::reverse_chain_iterator reverse_chain_iterator
typedef base_type::const_reverse_chain_iterator const_reverse_chain_iterator
typedef base_type::structure_id_type structure_id_type
typedef base_type::atom_type atom_type
typedef base_type::atom_iterator atom_iterator
typedef base_type::const_atom_iterator const_atom_iterator
typedef base_type::reverse_atom_iterator reverse_atom_iterator
typedef base_type::const_reverse_atom_iterator const_reverse_atom_iterator
typedef base_type::monomer_type monomer_type
typedef base_type::monomer_iterator monomer_iterator
typedef base_type::const_monomer_iterator const_monomer_iterator
typedef base_type::reverse_monomer_iterator reverse_monomer_iterator
typedef base_type::const_reverse_monomer_iterator const_reverse_monomer_iterator

Public Member Functions

 PDBSystem (PDBSystem const &src)
 Copy a PDBSystem object.
virtual ~PDBSystem ()
 Destructor.
bool open (std::string filename, int which_model=0)
 Open a new PDB file.
void close ()
 Close the current PDB file.
std::string const & header () const
 Get the current PDB file header.
std::string const & filename () const
 Get the current PDB file name.
bool get_model (int which, bool load_hetatoms=true)
 Get a MODEL from the current PDB file.
bool get_next_model (bool load_hetatoms=true)
 Get the next model from the current PDB file.

Detailed Description

template<typename PolymerType, typename ChemicalTypeSystemType = typename PolymerType::chemical_type_system, typename StorageStrategy = std::list<PolymerType>>
class BTK::IO::PDBSystem< PolymerType, ChemicalTypeSystemType, StorageStrategy >

Examples:

gyration_radius.cpp.


Member Typedef Documentation

typedef base_type ::chemical_type_system chemical_type_system

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::dictionary dictionary

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::id_type id_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::value_type value_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::iterator iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_iterator const_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_iterator reverse_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_iterator const_reverse_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reference reference

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reference const_reference

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::pointer pointer

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_pointer const_pointer

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::difference_type difference_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::size_type size_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::chain_type chain_type

Type definitions required for all System classes.

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::chain_iterator chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_chain_iterator const_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_chain_iterator reverse_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_chain_iterator const_reverse_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::structure_id_type structure_id_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::atom_type atom_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::atom_iterator atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_atom_iterator const_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_atom_iterator reverse_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_atom_iterator const_reverse_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::monomer_type monomer_type

Reimplemented from PolymerSystemBase.

typedef base_type ::monomer_iterator monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::const_monomer_iterator const_monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::reverse_monomer_iterator reverse_monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::const_reverse_monomer_iterator const_reverse_monomer_iterator

Reimplemented from PolymerSystemBase.


Constructor & Destructor Documentation

PDBSystem ( std::string const &  filename,
int  which_model,
bool  load_hetatoms = true,
bool  dynamic_types = true,
chemical_type_system const &  cts = chemical_type_system() 
)

A model-aware constructor.

Creates a PDBSystem using the specified MODEL from a PDB file.

Parameters:
filename Name of PDB file to parse.
which_model The number of the MODEL to parse from the PDB file.
load_hetatoms If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
dynamic_types If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem ( std::string const &  filename,
bool  load_hetatoms = true,
bool  dynamic_types = true,
chemical_type_system const &  cts = chemical_type_system() 
)

Construct from a PDB file.

Creates a PDBSystem from the specified PDB file.

Parameters:
filename Name of PDB file to parse.
load_hetatoms If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
dynamic_types If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem ( size_type  n = 0,
const_reference  t = chain_type() 
)

Create a PDBSystem from 0 or more Chain objects.

Because no PDB file is specified with these constructors, subsequent calls to get_model() and get_next_model() will fail, unless a call is made to open().

PDBSystem ( ChainIterator  begin,
ChainIterator  end 
)

Create a PDBSystem from a range of Chain objects.

PDBSystem ( PDBSystem< PolymerType, ChemicalTypeSystemType, StorageStrategy > const &  src  ) 

Copy a PDBSystem object.

virtual ~PDBSystem (  )  [virtual]

Destructor.

PDBSystem ( std::string const &  filename,
int  which_model,
bool  load_hetatoms = true,
bool  dynamic_types = true,
chemical_type_system const &  cts = chemical_type_system() 
)

A model-aware constructor.

Creates a PDBSystem using the specified MODEL from a PDB file.

Parameters:
filename Name of PDB file to parse.
which_model The number of the MODEL to parse from the PDB file.
load_hetatoms If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
dynamic_types If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem ( std::string const &  filename,
bool  load_hetatoms = true,
bool  dynamic_types = true,
chemical_type_system const &  cts = chemical_type_system() 
)

Construct from a PDB file.

Creates a PDBSystem from the specified PDB file.

Parameters:
filename Name of PDB file to parse.
load_hetatoms If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
dynamic_types If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem ( size_type  n = 0,
const_reference  t = chain_type() 
)

Create a PDBSystem from 0 or more Chain objects.

Because no PDB file is specified with these constructors, subsequent calls to get_model() and get_next_model() will fail, unless a call is made to open().

PDBSystem ( ChainIterator  begin,
ChainIterator  end 
)

Create a PDBSystem from a range of Chain objects.


Member Function Documentation

bool open ( std::string  filename,
int  which_model = 0 
)

Open a new PDB file.

Any previously loaded structures will be destroyed.

void close (  ) 

Close the current PDB file.

Structures in memory are unaffected.

std::string const& header (  )  const

Get the current PDB file header.

std::string const& filename (  )  const

Get the current PDB file name.

bool get_model ( int  which,
bool  load_hetatoms = true 
)

Get a MODEL from the current PDB file.

Any previously loaded structures/models will be destroyed.

bool get_next_model ( bool  load_hetatoms = true  ) 

Get the next model from the current PDB file.

Any previously loaded structures/models will be destroyed.


The documentation for this class was generated from the following file:
Generated on Sun Jul 15 20:46:36 2007 for BTK Core by  doxygen 1.5.1