Namespaces
namespace	detail
namespace	fmt
namespace	jpk_tags
namespace	remote
namespace	repository

Data Structures
class	BinaryDataSink
class	BinaryDataSource
class	ChemdictParser
class	ClustalIOHandler
class	Convert
class	BinaryOStream
class	BinaryIStream
class	CRDReader
	CHARMM coordinate file import. More...
class	CRDWriter
	CHARMM coordinate file export. More...
class	EntityIOCRDHandler
class	EntityIOHandler
	pure abstract base class for entity io handlers More...
class	EntityIOHandlerFactoryBase
	pure abstract base class for creation of a specfic entity io handle More...
class	EntityIOHandlerFactory
class	MAEReader
class	EntityIOMAEHandler
class	EntityIOMMCIFHandler
class	EntityIOPDBHandler
class	PQRReader
	CHARMM coordinate file import. More...
class	PQRWriter
	CHARMM coordinate file export. More...
class	EntityIOPQRHandler
class	EntityIOSDFHandler
class	FastaIOHandler
class	LineSlice
class	FormattedLine
class	ImageFormatBase
class	UndefinedImageFormat
class	DAT
class	MapIODatHandler
class	DF3
class	DF3MapIOHandler
class	DM3
class	MapIODm3Handler
class	DX
class	MapIODxHandler
class	MapIOHandler
class	MapIOHandlerFactoryBase
class	MapIOHandlerFactory
class	IPL
class	MapIOIPLHandler
class	JPK
class	MapIOJpkHandler
class	MRC
class	CCP4
class	MapIOMrcHandler
class	Nanoscope
class	MapIONanoscopeHandler
class	PNG
class	MapIOPngHandler
class	Situs
class	MapIOSitusHandler
class	Spider
class	MapIOSpiHandler
class	TIF
class	MapIOTiffHandler
class	IOException
class	IOUnknownFormatException
class	IOFileAlreadyLoadedException
class	IOManager
	Central registry for input/output handlers. More...
struct	IOProfile
class	IOProfileRegistry
class	MMCifInfoStructDetails
class	MMCifInfoTransOp
class	MMCifInfoBioUnit
class	MMCifInfoCitation
class	MMCifInfoObsolete
	container class for information on obsolete entries More...
class	MMCifInfoRevisions
	container class for information on file revisions (database_pdb_rev) More...
class	MMCifInfoStructRef
class	MMCifInfoStructRefSeq
class	MMCifInfoStructRefSeqDif
class	MMCifInfo
	container class for additional information from MMCif files More...
class	MMCifReader
	reader for the mmcif file format More...
class	PDBReader
class	PDBWriter
class	SDFReader
class	SDFWriter
class	StarDataItem
class	StarLoopDesc
class	StarParser
	parser for the STAR file format More...
class	SurfaceIOHandler
class	SurfaceIOHandlerFactoryBase
class	SurfaceIOHandlerFactory
class	SurfaceIOMSMSHandler
class	PirIOHandler
class	PromodIOHandler
class	SequenceIOHandler
	pure abstract base class for entity io handlers More...
class	SequenceIOHandlerFactoryBase
	pure abstract base class for creation of a specfic alignment io handler More...
class	SequenceIOHandlerFactory
class	IOProfiles

Typedefs
typedef SequenceIOHandlerFactory < ClustalIOHandler >	ClustalIOHandlerFactory
typedef EntityIOHandlerFactory < EntityIOCRDHandler >	EntityIOCRDHandlerFactory
typedef boost::shared_ptr < EntityIOHandler >	EntityIOHandlerP
typedef boost::shared_ptr < EntityIOHandlerFactoryBase >	EntityIOHandlerFactoryBaseP
typedef EntityIOHandlerFactory < EntityIOMAEHandler >	EntityIOMAEHandlerFactory
typedef EntityIOHandlerFactory < EntityIOMMCIFHandler >	EntityIOMMCIFHandlerFactory
typedef EntityIOHandlerFactory < EntityIOPDBHandler >	EntityIOPDBHandlerFactory
typedef EntityIOHandlerFactory < EntityIOPQRHandler >	EntityIOPQRHandlerFactory
typedef EntityIOHandlerFactory < EntityIOSDFHandler >	EntityIOSDFHandlerFactory
typedef SequenceIOHandlerFactory < FastaIOHandler >	FastaIOHandlerFactory
typedef MapIOHandlerFactory < MapIODatHandler >	MapIODatHandlerFactory
typedef MapIOHandlerFactory < DF3MapIOHandler >	MapIODF3HandlerFactory
typedef MapIOHandlerFactory < MapIODm3Handler >	MapIODm3HandlerFactory
typedef MapIOHandlerFactory < MapIODxHandler >	MapIODxHandlerFactory
typedef boost::shared_ptr < MapIOHandler >	MapIOHandlerPtr
typedef boost::shared_ptr < MapIOHandlerFactoryBase >	MapIOHandlerFactoryBasePtr
typedef MapIOHandlerFactory < MapIOIPLHandler >	MapIOIPLHandlerFactory
typedef MapIOHandlerFactory < MapIOJpkHandler >	MapIOJpkHandlerFactory
typedef CCP4	MAP
typedef MapIOHandlerFactory < MapIOMrcHandler >	MapIOMrcHandlerFactory
typedef MapIOHandlerFactory < MapIONanoscopeHandler >	MapIONanoscopeHandlerFactory
typedef MapIOHandlerFactory < MapIOPngHandler >	MapIOPngHandlerFactory
typedef MapIOHandlerFactory < MapIOSitusHandler >	MapIOSitusHandlerFactory
typedef MapIOHandlerFactory < MapIOSpiHandler >	MapIOSpiHandlerFactory
typedef MapIOHandlerFactory < MapIOTiffHandler >	MapIOTiffHandlerFactory
typedef std::vector < EntityIOHandlerFactoryBaseP >	EntityIOHFList
typedef std::vector < SequenceIOHandlerFactoryBasePtr >	AlignmentIOFList
typedef std::vector < SurfaceIOHandlerFactoryBasePtr >	SurfaceIOFList
typedef boost::shared_ptr < MMCifInfoTransOp >	MMCifInfoTransOpPtr
typedef boost::shared_ptr < MMCifInfoStructRef >	MMCifInfoStructRefPtr
typedef boost::shared_ptr < MMCifInfoStructRefSeq >	MMCifInfoStructRefSeqPtr
typedef boost::shared_ptr < MMCifInfoStructRefSeqDif >	MMCifInfoStructRefSeqDifPtr
typedef std::vector < MMCifInfoStructRefPtr >	MMCifInfoStructRefs
typedef std::vector < MMCifInfoStructRefSeqPtr >	MMCifInfoStructRefSeqs
typedef std::vector < MMCifInfoStructRefSeqDifPtr >	MMCifInfoStructRefSeqDifs
typedef boost::shared_ptr < SurfaceIOHandler >	SurfaceIOHandlerPtr
typedef boost::shared_ptr < SurfaceIOHandlerFactoryBase >	SurfaceIOHandlerFactoryBasePtr
typedef SurfaceIOHandlerFactory < SurfaceIOMSMSHandler >	SurfaceIOMSMSHandlerFactory
typedef SequenceIOHandlerFactory < PirIOHandler >	PirIOHandlerFactory
typedef SequenceIOHandlerFactory < PromodIOHandler >	PromodIOHandlerFactory
typedef boost::shared_ptr < SequenceIOHandler >	SequenceIOHandlerPtr
typedef boost::shared_ptr < SequenceIOHandlerFactoryBase >	SequenceIOHandlerFactoryBasePtr

Enumerations
enum	LoopType { ATOM_SPEC, BOND_SPEC, DONT_KNOW, ATOM_SPEC, BOND_SPEC, DONT_KNOW }
enum	Endianess { OST_BIG_ENDIAN, OST_LITTLE_ENDIAN, OST_VAX_DATA, OST_LOCAL_ENDIAN = OST_LITTLE_ENDIAN }
enum	Format { OST_BIT8_FORMAT, OST_BIT16_FORMAT, OST_BIT32_FORMAT, OST_FLOAT_FORMAT, OST_DOUBLE_FORMAT, OST_DEFAULT_FORMAT, OST_BIT8_FORMAT, OST_BIT16_FORMAT, OST_BIT32_FORMAT, OST_FLOAT_FORMAT, OST_DOUBLE_FORMAT, OST_DEFAULT_FORMAT }
enum	Subformat { MRC_OLD_FORMAT, MRC_NEW_FORMAT, MRC_AUTO_FORMAT, MRC_OLD_FORMAT, MRC_NEW_FORMAT, MRC_AUTO_FORMAT }
enum	Format { OST_BIT8_FORMAT, OST_BIT16_FORMAT, OST_BIT32_FORMAT, OST_FLOAT_FORMAT, OST_DOUBLE_FORMAT, OST_DEFAULT_FORMAT, OST_BIT8_FORMAT, OST_BIT16_FORMAT, OST_BIT32_FORMAT, OST_FLOAT_FORMAT, OST_DOUBLE_FORMAT, OST_DEFAULT_FORMAT }
enum	Subformat { MRC_OLD_FORMAT, MRC_NEW_FORMAT, MRC_AUTO_FORMAT, MRC_OLD_FORMAT, MRC_NEW_FORMAT, MRC_AUTO_FORMAT }
enum	LoopType { ATOM_SPEC, BOND_SPEC, DONT_KNOW, ATOM_SPEC, BOND_SPEC, DONT_KNOW }
enum	StarDiagType { STAR_DIAG_WARNING, STAR_DIAG_ERROR, STAR_DIAG_WARNING, STAR_DIAG_ERROR }
enum	StarDiagType { STAR_DIAG_WARNING, STAR_DIAG_ERROR, STAR_DIAG_WARNING, STAR_DIAG_ERROR }

Functions
template<typename T >
void	Serialize (BinaryDataSink &sink, const T &value)
void	RawSerialize (BinaryDataSink &sink, char *value, size_t size)
void	Serialize (BinaryDataSink &sink, const String &str)
template<typename T >
void	Serialize (BinaryDataSource &source, T &value)
void	RawSerialize (BinaryDataSource &sink, char *value, size_t size)
void	Serialize (BinaryDataSource &source, String &str)
template<typename T >
void	Serialize (BinaryDataSink &sink, const std::vector< T > &value)
template<typename T >
void	Serialize (BinaryDataSource &source, std::vector< T > &value)
template<typename K , typename V >
void	Serialize (BinaryDataSink &sink, const std::map< K, V > &value)
template<typename K , typename V >
void	Serialize (BinaryDataSource &source, std::map< K, V > &value)
mol::CoordGroupHandle DLLEXPORT_OST_IO	LoadCHARMMTraj (const mol::EntityHandle &ent, const String &trj_filename, unsigned int stride=1, bool lazy_load=false, bool detect_swap=true, bool byte_swap=false)
void DLLEXPORT_OST_IO	SaveCHARMMTraj (const mol::CoordGroupHandle &coord_group, const String &pdb_filename, const String &dcd_filename, unsigned int stride=1, const IOProfile &profile=IOProfile())
mol::EntityHandle DLLEXPORT_OST_IO	LoadCRD (const String &file_name)
mol::EntityHandle DLLEXPORT_OST_IO	LoadMAE (const String &file_name)
mol::EntityHandle DLLEXPORT_OST_IO	LoadPQR (const String &file_name)
mol::EntityHandle DLLEXPORT_OST_IO	LoadSDF (const String &file_name)
std::ostream &	operator<< (std::ostream &stream, const FormattedLine &line)
DLLEXPORT_OST_IO img::ImageHandle	LoadImage (const boost::filesystem::path &loc)
DLLEXPORT_OST_IO img::ImageHandle	LoadImage (const boost::filesystem::path &loc, const ImageFormatBase &formatstruct)
DLLEXPORT_OST_IO void	SaveImage (const img::ImageHandle &image, const boost::filesystem::path &loc)
DLLEXPORT_OST_IO void	SaveImage (const img::ImageHandle &image, const boost::filesystem::path &loc, const ImageFormatBase &formatstruct)
DLLEXPORT_OST_IO img::MapHandle	LoadMap (const boost::filesystem::path &loc)
DLLEXPORT_OST_IO img::MapHandle	LoadMap (const boost::filesystem::path &loc, const ImageFormatBase &formatstruct)
DLLEXPORT_OST_IO void	SaveMap (const img::ImageHandle &image, const boost::filesystem::path &loc)
DLLEXPORT_OST_IO void	SaveMap (const img::ImageHandle &image, const boost::filesystem::path &loc, const ImageFormatBase &formatstruct)
std::ostream &	operator<< (std::ostream &stream, const IOProfile &p)
seq::AlignmentHandle DLLEXPORT_OST_IO	LoadAlignment (const String &file_name, const String &format="auto")
seq::AlignmentHandle DLLEXPORT_OST_IO	AlignmentFromStream (std::istream &stream, const String &format)
seq::AlignmentHandle DLLEXPORT_OST_IO	AlignmentFromString (const String &data, const String &format)
seq::SequenceList DLLEXPORT_OST_IO	LoadSequenceList (const String &file_name, const String &format="auto")
seq::SequenceList DLLEXPORT_OST_IO	SequenceListFromStream (std::istream &stream, const String &format)
seq::SequenceList DLLEXPORT_OST_IO	SequenceListFromString (const String &data, const String &format)
seq::SequenceHandle DLLEXPORT_OST_IO	LoadSequence (const String &file_name, const String &format="auto")
seq::SequenceHandle DLLEXPORT_OST_IO	SequenceFromStream (std::istream &stream, const String &format)
seq::SequenceHandle DLLEXPORT_OST_IO	SequenceFromString (const String &data, const String &format)
DLLEXPORT_OST_IO mol::EntityHandle	LoadEntity (const String &filename, int flag=0)
DLLEXPORT_OST_IO mol::SurfaceHandle	LoadSurface (const String &filename, const String &type="auto")
DLLEXPORT_OST_IO mol::SurfaceHandle	LoadManagedSurface (const String &name, const String &filename, const String &type="auto")
void DLLEXPORT_OST_IO	SaveEntity (const mol::EntityHandle &en, const String &filename, const String &format="auto")
void DLLEXPORT_OST_IO	SaveEntity (const mol::EntityView &en, const String &filename, const String &format="auto")
void DLLEXPORT_OST_IO	SaveSequenceList (const seq::ConstSequenceList &seq_list, const String &filename, const String &format="auto")
String DLLEXPORT_OST_IO	SequenceListToString (const seq::ConstSequenceList &seq_list, const String &format)
void DLLEXPORT_OST_IO	SaveSequence (const seq::ConstSequenceHandle &sequence, const String &filename, const String &format="auto")
String DLLEXPORT_OST_IO	SequenceToString (const seq::ConstSequenceHandle &sequence, const String &format="auto")
void DLLEXPORT_OST_IO	SaveAlignment (const seq::AlignmentHandle &msa, const String &filename, const String &format="auto")
String DLLEXPORT_OST_IO	AlignmentToString (const seq::AlignmentHandle &msa, const String &format)
template<typename T >
void	swap_buf (T *p, int n)
void	swap_short (short int *p, short int n)
void	swap_ushort (unsigned short int *p, short int n)
void	swap_int (int *p, int n)
void	swap_uint (uint *p, int n)
void	swap_float (float *p, int n)
void	swap_double (double *p, int n)
void	swap_long (long *p, int n)
def	LoadPDB
def	SavePDB
def	LoadImageList
def	LoadCHARMMTraj
def	LoadMMCIF

Variables
	profiles = None
tuple	processor = conop.RuleBasedProcessor(conop.GetDefaultLib())
tuple	quack_mode = False,processorprocessor.Copy()

Typedef Documentation

typedef std::vector<SequenceIOHandlerFactoryBasePtr> AlignmentIOFList

Definition at line 39 of file io_manager.hh.

typedef SequenceIOHandlerFactory< ClustalIOHandler > ClustalIOHandlerFactory

Definition at line 52 of file clustal_io_handler.hh.

typedef EntityIOHandlerFactory< EntityIOCRDHandler > EntityIOCRDHandlerFactory

Definition at line 109 of file entity_io_crd_handler.hh.

typedef boost::shared_ptr< EntityIOHandlerFactoryBase > EntityIOHandlerFactoryBaseP

Definition at line 77 of file entity_io_handler.hh.

typedef boost::shared_ptr< EntityIOHandler > EntityIOHandlerP

Definition at line 63 of file entity_io_handler.hh.

typedef std::vector<EntityIOHandlerFactoryBaseP> EntityIOHFList

Definition at line 38 of file io_manager.hh.

typedef EntityIOHandlerFactory< EntityIOMAEHandler > EntityIOMAEHandlerFactory

Definition at line 83 of file entity_io_mae_handler.hh.

typedef EntityIOHandlerFactory< EntityIOMMCIFHandler > EntityIOMMCIFHandlerFactory

Definition at line 54 of file entity_io_mmcif_handler.hh.

typedef EntityIOHandlerFactory< EntityIOPDBHandler > EntityIOPDBHandlerFactory

Definition at line 55 of file entity_io_pdb_handler.hh.

typedef EntityIOHandlerFactory< EntityIOPQRHandler > EntityIOPQRHandlerFactory

Definition at line 109 of file entity_io_pqr_handler.hh.

typedef EntityIOHandlerFactory< EntityIOSDFHandler > EntityIOSDFHandlerFactory

Definition at line 49 of file entity_io_sdf_handler.hh.

typedef SequenceIOHandlerFactory< FastaIOHandler > FastaIOHandlerFactory

Definition at line 53 of file fasta_io_handler.hh.

typedef CCP4 MAP

Definition at line 57 of file map_io_mrc_handler.hh.

typedef MapIOHandlerFactory< MapIODatHandler > MapIODatHandlerFactory

Definition at line 80 of file map_io_dat_handler.hh.

typedef MapIOHandlerFactory< DF3MapIOHandler > MapIODF3HandlerFactory

Definition at line 71 of file map_io_df3_handler.hh.

typedef MapIOHandlerFactory< MapIODm3Handler > MapIODm3HandlerFactory

Definition at line 59 of file map_io_dm3_handler.hh.

typedef MapIOHandlerFactory< MapIODxHandler > MapIODxHandlerFactory

Definition at line 74 of file map_io_dx_handler.hh.

typedef boost::shared_ptr< MapIOHandlerFactoryBase > MapIOHandlerFactoryBasePtr

Definition at line 57 of file map_io_handler.hh.

typedef boost::shared_ptr< MapIOHandler > MapIOHandlerPtr

Definition at line 42 of file map_io_handler.hh.

typedef MapIOHandlerFactory< MapIOIPLHandler > MapIOIPLHandlerFactory

Definition at line 74 of file map_io_ipl_handler.hh.

typedef MapIOHandlerFactory< MapIOJpkHandler > MapIOJpkHandlerFactory

Definition at line 57 of file map_io_jpk_handler.hh.

typedef MapIOHandlerFactory< MapIOMrcHandler > MapIOMrcHandlerFactory

Definition at line 90 of file map_io_mrc_handler.hh.

typedef MapIOHandlerFactory< MapIONanoscopeHandler > MapIONanoscopeHandlerFactory

Definition at line 67 of file map_io_nanoscope_handler.hh.

typedef MapIOHandlerFactory< MapIOPngHandler > MapIOPngHandlerFactory

Definition at line 65 of file map_io_png_handler.hh.

typedef MapIOHandlerFactory< MapIOSitusHandler > MapIOSitusHandlerFactory

Definition at line 64 of file map_io_situs_handler.hh.

typedef MapIOHandlerFactory< MapIOSpiHandler > MapIOSpiHandlerFactory

Definition at line 77 of file map_io_spi_handler.hh.

typedef MapIOHandlerFactory< MapIOTiffHandler > MapIOTiffHandlerFactory

Definition at line 120 of file map_io_tiff_handler.hh.

typedef boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr

Definition at line 759 of file mmcif_info.hh.

typedef std::vector< MMCifInfoStructRefPtr > MMCifInfoStructRefs

Definition at line 766 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoStructRefSeqDif > MMCifInfoStructRefSeqDifPtr

Definition at line 764 of file mmcif_info.hh.

typedef std::vector< MMCifInfoStructRefSeqDifPtr > MMCifInfoStructRefSeqDifs

Definition at line 768 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr

Definition at line 763 of file mmcif_info.hh.

typedef std::vector< MMCifInfoStructRefSeqPtr > MMCifInfoStructRefSeqs

Definition at line 767 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr

Definition at line 236 of file mmcif_info.hh.

typedef SequenceIOHandlerFactory< PirIOHandler > PirIOHandlerFactory

Definition at line 53 of file pir_io_handler.hh.

typedef SequenceIOHandlerFactory< PromodIOHandler > PromodIOHandlerFactory

Definition at line 53 of file promod_io_handler.hh.

typedef boost::shared_ptr< SequenceIOHandlerFactoryBase > SequenceIOHandlerFactoryBasePtr

Definition at line 67 of file sequence_io_handler.hh.

typedef boost::shared_ptr< SequenceIOHandler > SequenceIOHandlerPtr

Definition at line 51 of file sequence_io_handler.hh.

typedef std::vector<SurfaceIOHandlerFactoryBasePtr> SurfaceIOFList

Definition at line 40 of file io_manager.hh.

typedef boost::shared_ptr< SurfaceIOHandlerFactoryBase > SurfaceIOHandlerFactoryBasePtr

Definition at line 48 of file surface_io_handler.hh.

typedef boost::shared_ptr< SurfaceIOHandler > SurfaceIOHandlerPtr

Definition at line 36 of file surface_io_handler.hh.

typedef SurfaceIOHandlerFactory< SurfaceIOMSMSHandler > SurfaceIOMSMSHandlerFactory

Definition at line 41 of file surface_io_msms_handler.hh.

Enumeration Type Documentation

enum Endianess

Enumerator:

OST_BIG_ENDIAN
OST_LITTLE_ENDIAN
OST_VAX_DATA
OST_LOCAL_ENDIAN

Definition at line 28 of file convert.hh.

enum Format

Enumerator:

OST_BIT8_FORMAT
OST_BIT16_FORMAT
OST_BIT32_FORMAT
OST_FLOAT_FORMAT
OST_DOUBLE_FORMAT
OST_DEFAULT_FORMAT
OST_BIT8_FORMAT
OST_BIT16_FORMAT
OST_BIT32_FORMAT
OST_FLOAT_FORMAT
OST_DOUBLE_FORMAT
OST_DEFAULT_FORMAT

Definition at line 68 of file image_format.hh.

enum Format

Enumerator:

OST_BIT8_FORMAT
OST_BIT16_FORMAT
OST_BIT32_FORMAT
OST_FLOAT_FORMAT
OST_DOUBLE_FORMAT
OST_DEFAULT_FORMAT
OST_BIT8_FORMAT
OST_BIT16_FORMAT
OST_BIT32_FORMAT
OST_FLOAT_FORMAT
OST_DOUBLE_FORMAT
OST_DEFAULT_FORMAT

Definition at line 68 of file image_format.hh.

enum LoopType

Enumerator:

ATOM_SPEC
BOND_SPEC
DONT_KNOW
ATOM_SPEC
BOND_SPEC
DONT_KNOW

Definition at line 34 of file chemdict_parser.hh.

enum LoopType

Enumerator:

ATOM_SPEC
BOND_SPEC
DONT_KNOW
ATOM_SPEC
BOND_SPEC
DONT_KNOW

Definition at line 34 of file chemdict_parser.hh.

enum StarDiagType

Enumerator:

STAR_DIAG_WARNING
STAR_DIAG_ERROR
STAR_DIAG_WARNING
STAR_DIAG_ERROR

Definition at line 38 of file star_parser.hh.

enum StarDiagType

Enumerator:

STAR_DIAG_WARNING
STAR_DIAG_ERROR
STAR_DIAG_WARNING
STAR_DIAG_ERROR

Definition at line 38 of file star_parser.hh.

enum Subformat

Enumerator:

MRC_OLD_FORMAT
MRC_NEW_FORMAT
MRC_AUTO_FORMAT
MRC_OLD_FORMAT
MRC_NEW_FORMAT
MRC_AUTO_FORMAT

Definition at line 73 of file image_format.hh.

enum Subformat

Enumerator:

MRC_OLD_FORMAT
MRC_NEW_FORMAT
MRC_AUTO_FORMAT
MRC_OLD_FORMAT
MRC_NEW_FORMAT
MRC_AUTO_FORMAT

Definition at line 73 of file image_format.hh.

Function Documentation

seq::AlignmentHandle DLLEXPORT_OST_IO AlignmentFromStream	(	std::istream &	stream,
		const String &	format
	)

seq::AlignmentHandle DLLEXPORT_OST_IO AlignmentFromString	(	const String &	data,
		const String &	format
	)

String DLLEXPORT_OST_IO AlignmentToString	(	const seq::AlignmentHandle &	msa,
		const String &	format
	)

seq::AlignmentHandle DLLEXPORT_OST_IO LoadAlignment	(	const String &	file_name,
		const String &	format = `"auto"`
	)

mol::CoordGroupHandle DLLEXPORT_OST_IO LoadCHARMMTraj	(	const mol::EntityHandle &	ent,
		const String &	trj_filename,
		unsigned int	stride = `1`,
		bool	lazy_load = `false`,
		bool	detect_swap = `true`,
		bool	byte_swap = `false`
	)

import a CHARMM trajectory in dcd format with an existing entity requires the existing entity and the trajectory file - obviously the atom layout of the entity must match the trajectory file

def ost.io.LoadCHARMMTraj	(	crd,
		dcd_file = `None`,
		profile = `'CHARMM'`,
		lazy_load = `False`,
		stride = `1`,
		dialect = `None`,
		detect_swap = `True`,
		swap_bytes = `False`
	)

Load CHARMM trajectory file.

:param crd: EntityHandle or filename of the (PDB) file containing the
    structure. The structure must have the same number of atoms as the 
    trajectory
:param dcd_file: The filename of the DCD file. If not set, and crd is a 
    string, the filename is set to the <crd>.dcd
:param layz_load: Whether the trajectory should be loaded on demand. Instead 
    of loading the complete trajectory into memory, the trajectory frames are 
    loaded from disk when requested.
:param stride: The spacing of the frames to load. When set to 2, for example, 
    every second frame is loaded from the trajectory. By default, every frame 
    is loaded.
:param dialect: The dialect for the PDB file to use. See :func:`LoadPDB`. If 
    set, overrides the value of the profile
:param profile: The IO profile to use for loading the PDB file. See 
    :doc:`profile`.
:param detect_swap: if True (the default), then automatic detection of endianess
    is attempted, otherwise the swap_bytes parameter is used
:param swap_bytes: is detect_swap is False, this flag determines whether bytes
    are swapped upon loading or not

Definition at line 225 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadCRD ( const String & file_name )

DLLEXPORT_OST_IO mol::EntityHandle LoadEntity	(	const String &	filename,
		int	flag = `0`
	)

DLLEXPORT_OST_IO img::ImageHandle LoadImage ( const boost::filesystem::path & loc )

Function that loads an image from a file.

This function reads an image file from disk and transfers the data into memory The function automatically determines the file format by looking at the filename extension. In case the extension is not available, the content of the file will be examined. This analysis will be sufficient to determine the format type for many files. In case the file format cannot be determined, the function will throw an error.

DLLEXPORT_OST_IO img::ImageHandle LoadImage	(	const boost::filesystem::path &	loc,
		const ImageFormatBase &	formatstruct
	)

Function that loads an image from a file with a specific format.

This function reads an image file from disk and transfers the data into memory The function assumes that the file has the specified format

def ost.io.LoadImageList ( files )

loads several images and puts them in an ImageList

See also:: View Fourier Transform Example

Definition at line 214 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadMAE ( const String & file_name )

DLLEXPORT_OST_IO mol::SurfaceHandle LoadManagedSurface	(	const String &	name,
		const String &	filename,
		const String &	type = `"auto"`
	)

DLLEXPORT_OST_IO img::MapHandle LoadMap ( const boost::filesystem::path & loc )

Alias for the equivalent LoadImage function.

DLLEXPORT_OST_IO img::MapHandle LoadMap	(	const boost::filesystem::path &	loc,
		const ImageFormatBase &	formatstruct
	)

Alias for the equivalent LoadImage function.

def ost.io.LoadMMCIF	(	filename,
		restrict_chains = `""`,
		fault_tolerant = `None`,
		calpha_only = `None`,
		profile = `'DEFAULT'`,
		remote = `False`,
		seqres = `False`,
		info = `False`
	)

Load MMCIF file from disk and return one or more entities. Several options 
allow to customize the exact behaviour of the MMCIF import. For more
information on these options, see :doc:`profile`.

Residues are flagged as ligand if they are mentioned in a HET record.

:param restrict_chains: If not an empty string, only chains listed in the
   string will be imported.

:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
   the value of :attr:`IOProfile.fault_tolerant`.

:param remote: If set to True, the method tries to load the pdb from the 
   remote pdb repository www.pdb.org. The filename is then interpreted as the 
   pdb id.

:rtype: :class:`~ost.mol.EntityHandle`.

:param seqres: Whether to read SEQRES records. If set to True, the loaded 
  entity and seqres entry will be returned as second item.

:param info: Whether to return an info container with the other output.
             Returns a :class:`MMCifInfo` object as last item.

:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
         or non-existent file.

Definition at line 259 of file __init__.py.

def ost.io.LoadPDB	(	filename,
		restrict_chains = `""`,
		no_hetatms = `None`,
		fault_tolerant = `None`,
		load_multi = `False`,
		quack_mode = `None`,
		join_spread_atom_records = `None`,
		calpha_only = `None`,
		profile = `'DEFAULT'`,
		remote = `False`,
		dialect = `None`,
		seqres = `False`,
		bond_feasibility_check = `None`
	)

Load PDB file from disk and return one or more entities. Several options 
allow to customize the exact behaviour of the PDB import. For more information 
on these options, see :doc:`profile`.

Residues are flagged as ligand if they are mentioned in a HET record.

:param restrict_chains: If not an empty string, only chains listed in the
   string will be imported.

:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides 
   the value of :attr:`IOProfile.fault_tolerant`.

:param no_hetatms: If set to True, HETATM records will be ignored. Overrides 
    the value of :attr:`IOProfile.no_hetatms`

:param load_multi: If set to True, a list of entities will be returned instead
    of only the first. This is useful when dealing with multi-PDB files.

:param join_spread_atom_records: If set, overrides the value of 
    :attr:`IOProfile.join_spread_atom_records`.

:param remote: If set to True, the method tries to load the pdb from the 
   remote pdb repository www.pdb.org. The filename is then interpreted as the 
   pdb id.
   
:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is 
    True.

:param dialect: Specifies the particular dialect to use. If set, overrides 
  the value of :attr:`IOProfile.dialect`

:param seqres: Whether to read SEQRES records. If set to True, the loaded 
  entity and seqres entry will be returned as a tuple.

:type dialect: :class:`str`


:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
    inexistent file

Definition at line 69 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadPQR ( const String & file_name )

mol::EntityHandle DLLEXPORT_OST_IO LoadSDF ( const String & file_name )

seq::SequenceHandle DLLEXPORT_OST_IO LoadSequence	(	const String &	file_name,
		const String &	format = `"auto"`
	)

seq::SequenceList DLLEXPORT_OST_IO LoadSequenceList	(	const String &	file_name,
		const String &	format = `"auto"`
	)

DLLEXPORT_OST_IO mol::SurfaceHandle LoadSurface	(	const String &	filename,
		const String &	type = `"auto"`
	)

std::ostream & operator<<	(	std::ostream &	stream,
		const IOProfile &	p
	)

inline

Definition at line 61 of file io_profile.hh.

std::ostream& ost::io::operator<<	(	std::ostream &	stream,
		const FormattedLine &	line
	)

inline

Definition at line 229 of file formatted_line.hh.

void ost::io::RawSerialize	(	BinaryDataSink &	sink,
		char *	value,
		size_t	size
	)

inline

Definition at line 87 of file binary_data_sink.hh.

void ost::io::RawSerialize	(	BinaryDataSource &	sink,
		char *	value,
		size_t	size
	)

inline

Definition at line 87 of file binary_data_source.hh.

void DLLEXPORT_OST_IO SaveAlignment	(	const seq::AlignmentHandle &	msa,
		const String &	filename,
		const String &	format = `"auto"`
	)

void DLLEXPORT_OST_IO SaveCHARMMTraj	(	const mol::CoordGroupHandle &	coord_group,
		const String &	pdb_filename,
		const String &	dcd_filename,
		unsigned int	stride = `1`,
		const IOProfile &	profile = `IOProfile()`
	)

export coord group as PDB file and DCD trajectory if the pdb filename is an empty string, it won't be exported the optional stride parameter will cause every nth frame to be exported

void DLLEXPORT_OST_IO SaveEntity	(	const mol::EntityHandle &	en,
		const String &	filename,
		const String &	format = `"auto"`
	)

Save entity handle.

Parameters:

en	is the entity to be saved
filename	is the output filename
format	specifies what output format is used for export. If set to auto the format is deduced from the file extension

void DLLEXPORT_OST_IO SaveEntity	(	const mol::EntityView &	en,
		const String &	filename,
		const String &	format = `"auto"`
	)

Save entity view.

This method provides a convenient way to save only a certain part of an entity, i.e. to filter out water and ligands or to create a backbone-only model.

Parameters:

en	is the entity view to be saved.
filename	is the output filename
format	specifies what output format is used for export. If set to auto the format is deduced from the file extension

DLLEXPORT_OST_IO void SaveImage	(	const img::ImageHandle &	image,
		const boost::filesystem::path &	loc
	)

Function that saves an image to a file.

This function saves an image on disk. The function automatically determines the file format by looking at the filename extension. In case the extension is not availabel, the function will throw an error

See also:: Spoke Pattern Example

DLLEXPORT_OST_IO void SaveImage	(	const img::ImageHandle &	image,
		const boost::filesystem::path &	loc,
		const ImageFormatBase &	formatstruct
	)

Function that saves an image to a file using a specified format.

This function saves an image on disk using the format specified in the function call

See also:: Spoke Pattern Example

DLLEXPORT_OST_IO void SaveMap	(	const img::ImageHandle &	image,
		const boost::filesystem::path &	loc
	)

Alias for the equivalent SaveImage function.

DLLEXPORT_OST_IO void SaveMap	(	const img::ImageHandle &	image,
		const boost::filesystem::path &	loc,
		const ImageFormatBase &	formatstruct
	)

Alias for the equivalent SaveImage function.

def ost.io.SavePDB	(	models,
		filename,
		dialect = `None`,
		pqr = `False`,
		profile = `'DEFAULT'`
	)

Save entity or list of entities to disk. If a list of entities is supplied
the PDB file will be saved as a multi PDB file. Each of the entities is
wrapped into a MODEL/ENDMDL pair.

If the atom number exceeds 99999, '*****' is used.

:param models: The entity or list of entities (handles or views) to be saved
:param filename: The filename
:type  filename: string

Definition at line 176 of file __init__.py.

void DLLEXPORT_OST_IO SaveSequence	(	const seq::ConstSequenceHandle &	sequence,
		const String &	filename,
		const String &	format = `"auto"`
	)

void DLLEXPORT_OST_IO SaveSequenceList	(	const seq::ConstSequenceList &	seq_list,
		const String &	filename,
		const String &	format = `"auto"`
	)

seq::SequenceHandle DLLEXPORT_OST_IO SequenceFromStream	(	std::istream &	stream,
		const String &	format
	)

seq::SequenceHandle DLLEXPORT_OST_IO SequenceFromString	(	const String &	data,
		const String &	format
	)

seq::SequenceList DLLEXPORT_OST_IO SequenceListFromStream	(	std::istream &	stream,
		const String &	format
	)

seq::SequenceList DLLEXPORT_OST_IO SequenceListFromString	(	const String &	data,
		const String &	format
	)

String DLLEXPORT_OST_IO SequenceListToString	(	const seq::ConstSequenceList &	seq_list,
		const String &	format
	)

String DLLEXPORT_OST_IO SequenceToString	(	const seq::ConstSequenceHandle &	sequence,
		const String &	format = `"auto"`
	)

void ost::io::Serialize	(	BinaryDataSink &	sink,
		const std::vector< T > &	value
	)

Definition at line 32 of file container_serialization.hh.

void ost::io::Serialize	(	BinaryDataSource &	source,
		std::vector< T > &	value
	)

Definition at line 46 of file container_serialization.hh.

void ost::io::Serialize	(	BinaryDataSink &	sink,
		const std::map< K, V > &	value
	)

Definition at line 62 of file container_serialization.hh.

void ost::io::Serialize	(	BinaryDataSource &	source,
		std::map< K, V > &	value
	)

Definition at line 72 of file container_serialization.hh.

void ost::io::Serialize	(	BinaryDataSink &	sink,
		const T &	value
	)

Definition at line 79 of file binary_data_sink.hh.

void ost::io::Serialize	(	BinaryDataSource &	source,
		T &	value
	)

Definition at line 80 of file binary_data_source.hh.

void ost::io::Serialize	(	BinaryDataSink &	sink,
		const String &	str
	)

inline

Definition at line 92 of file binary_data_sink.hh.

void ost::io::Serialize	(	BinaryDataSource &	source,
		String &	str
	)

inline

Definition at line 93 of file binary_data_source.hh.

void swap_buf	(	T *	p,
		int	n
	)

Definition at line 55 of file swap_util.hh.

void ost::io::swap_double	(	double *	p,
		int	n
	)

inline

Definition at line 49 of file swap_util.hh.

void ost::io::swap_float	(	float *	p,
		int	n
	)

inline

Definition at line 47 of file swap_util.hh.

void ost::io::swap_int	(	int *	p,
		int	n
	)

inline

Definition at line 43 of file swap_util.hh.

void ost::io::swap_long	(	long *	p,
		int	n
	)

inline

Definition at line 51 of file swap_util.hh.

void ost::io::swap_short	(	short int *	p,
		short int	n
	)

inline

Definition at line 39 of file swap_util.hh.

void ost::io::swap_uint	(	uint *	p,
		int	n
	)

inline

Definition at line 45 of file swap_util.hh.

void ost::io::swap_ushort	(	unsigned short int *	p,
		short int	n
	)

inline

Definition at line 41 of file swap_util.hh.

Variable Documentation

tuple processor = conop.RuleBasedProcessor(conop.GetDefaultLib())

Definition at line 48 of file __init__.py.

tuple profiles = None

Definition at line 24 of file __init__.py.

tuple quack_mode = False,processorprocessor.Copy()

Definition at line 52 of file __init__.py.

Namespaces

Data Structures

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation