Namespaces
	detail

	fmt

	jpk_tags

	remote

	repository

Data Structures
class	BinaryDataSink

class	BinaryDataSource

class	ChemdictParser

class	ClustalIOHandler

class	Convert

class	BinaryOStream

class	BinaryIStream

class	CRDReader

class	CRDWriter

class	EntityIOCRDHandler

class	EntityIOHandler

class	EntityIOHandlerFactoryBase

class	EntityIOHandlerFactory

class	MAEReader

class	EntityIOMAEHandler

class	EntityIOMMCIFHandler

class	EntityIOPDBHandler

class	PQRReader

class	PQRWriter

class	EntityIOPQRHandler

class	EntityIOSDFHandler

class	FastaIOHandler

class	LineSlice

class	FormattedLine

class	HhmIOHandler

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

struct	IOProfile

class	IOProfileRegistry

class	MMCifInfoStructDetails

class	MMCifInfoTransOp

class	MMCifInfoBioUnit

class	MMCifInfoCitation

class	MMCifInfoObsolete

class	MMCifInfoRevisions

class	MMCifInfoStructRef

class	MMCifInfoStructRefSeq

class	MMCifInfoStructRefSeqDif

struct	MMCifInfoEntityBranchLink

struct	MMCifEntityDesc

class	MMCifInfo

class	MMCifReader

struct	MMCifWriterEntity

class	MMCifWriter

struct	SidechainAtomRule

struct	ChiDefinition

struct	ResidueDefinition

struct	ChainData

class	DefaultPepLib

class	OMF

class	PDBReader

class	PDBWriter

class	SDFReader

class	SDFWriter

class	StarDataItem

class	StarLoopDesc

class	StarParser

class	StarWriterObject

class	StarWriterValue

class	StarWriterDataItem

class	StarWriterLoopDesc

class	StarWriterLoop

class	StarWriter

class	SurfaceIOHandler

class	SurfaceIOHandlerFactoryBase

class	SurfaceIOHandlerFactory

class	SurfaceIOMSMSHandler

class	PirIOHandler

class	ProfileIOHandler

class	ProfileIOHandlerFactoryBase

class	ProfileIOHandlerFactory

class	PromodIOHandler

class	PssmIOHandler

class	SequenceIOHandler

class	SequenceIOHandlerFactoryBase

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 ProfileIOHandlerFactory< HhmIOHandler >	HhmIOHandlerFactory

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< ProfileIOHandlerFactoryBasePtr >	ProfileIOFList

typedef std::vector< SurfaceIOHandlerFactoryBasePtr >	SurfaceIOFList

typedef std::vector< MapIOHandlerFactoryBasePtr >	MapIOFList

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 std::map< String, std::vector< MMCifInfoEntityBranchLink > >	MMCifInfoEntityBranchLinkMap

typedef std::map< String, MMCifEntityDesc >	MMCifEntityDescMap

typedef boost::shared_ptr< OMF >	OMFPtr

typedef boost::shared_ptr< ChainData >	ChainDataPtr

typedef boost::shared_ptr< StarWriterObject >	StarWriterObjectPtr

typedef boost::shared_ptr< StarWriterValue >	StarWriterValuePtr

typedef boost::shared_ptr< StarWriterDataItem >	StarWriterDataItemPtr

typedef boost::shared_ptr< StarWriterLoopDesc >	StarWriterLoopDescPtr

typedef boost::shared_ptr< StarWriterLoop >	StarWriterLoopPtr

typedef boost::shared_ptr< SurfaceIOHandler >	SurfaceIOHandlerPtr

typedef boost::shared_ptr< SurfaceIOHandlerFactoryBase >	SurfaceIOHandlerFactoryBasePtr

typedef SurfaceIOHandlerFactory< SurfaceIOMSMSHandler >	SurfaceIOMSMSHandlerFactory

typedef SequenceIOHandlerFactory< PirIOHandler >	PirIOHandlerFactory

typedef boost::shared_ptr< ProfileIOHandler >	ProfileIOHandlerPtr

typedef boost::shared_ptr< ProfileIOHandlerFactoryBase >	ProfileIOHandlerFactoryBasePtr

typedef SequenceIOHandlerFactory< PromodIOHandler >	PromodIOHandlerFactory

typedef ProfileIOHandlerFactory< PssmIOHandler >	PssmIOHandlerFactory

typedef boost::shared_ptr< SequenceIOHandler >	SequenceIOHandlerPtr

typedef boost::shared_ptr< SequenceIOHandlerFactoryBase >	SequenceIOHandlerFactoryBasePtr

Enumerations
enum	LoopType { ATOM_SPEC , BOND_SPEC , DESC_SPEC , DONT_KNOW , ATOM_SPEC , BOND_SPEC , DESC_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 , DESC_SPEC , DONT_KNOW , ATOM_SPEC , BOND_SPEC , DESC_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)

void DLLEXPORT_OST_IO	SaveSDF (const mol::EntityHandle &ent, const String &file_name)

void DLLEXPORT_OST_IO	SaveSDF (const mol::EntityView &ent, 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)

seq::ProfileHandlePtr DLLEXPORT_OST_IO	LoadSequenceProfile (const String &file_name, const String &format="auto")

seq::ProfileHandlePtr DLLEXPORT_OST_IO	SequenceProfileFromString (const String &data, const String &format)

DLLEXPORT_OST_IO mol::EntityHandle	LoadEntity (const String &filename, const String &format="auto")

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")

DLLEXPORT_OST_IO std::ostream &	operator<< (std::ostream &os, const MMCifInfoEntityBranchLink &eb)

DLLEXPORT_OST_IO std::ostream &	operator<< (std::ostream &os, const std::vector< MMCifInfoEntityBranchLink > &eb_list)

DLLEXPORT_OST_IO unsigned char	MMCifValueOrderToOSTBondOrder (const StringRef value_order)

DLLEXPORT_OST_IO String	OSTBondOrderToMMCifValueOrder (const unsigned char bond_order)

String DLLEXPORT_OST_IO	EntityToMMCifString (const ost::mol::EntityHandle &ent, const String &data_name, ost::conop::CompoundLibPtr compound_lib, bool mmcif_conform)

String DLLEXPORT_OST_IO	EntityToMMCifString (const ost::mol::EntityView &ent, const String &data_name, ost::conop::CompoundLibPtr compound_lib, bool mmcif_conform)

std::tuple< mol::EntityHandle, MMCifInfo, ost::seq::SequenceList > DLLEXPORT_OST_IO	MMCifStringToEntity (const String &mmcif, const IOProfile &profile, bool process)

String DLLEXPORT_OST_IO	EntityToPDBString (const mol::EntityHandle &ent, const IOProfile &profile=IOProfile())

String DLLEXPORT_OST_IO	EntityToPDBString (const mol::EntityView &ent, const IOProfile &profile=IOProfile())

mol::EntityHandle DLLEXPORT_OST_IO	PDBStringToEntity (const String &pdb, const IOProfile &profile=IOProfile(), bool process=false)

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")

String DLLEXPORT_OST_IO	EntityToSDFString (const mol::EntityHandle &ent)

String DLLEXPORT_OST_IO	EntityToSDFString (const mol::EntityView &ent)

mol::EntityHandle DLLEXPORT_OST_IO	SDFStringToEntity (const String &pdb)

ost::mol::alg::StereoChemicalProps	ReadStereoChemicalPropsFile (String filename, bool check=false)

ost::mol::alg::StereoChemicalProps	ReadStereoChemicalPropsFile (bool check=false)

String	GetStereoChemicalPropsFile ()

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 (filename, restrict_chains="", no_hetatms=None, fault_tolerant=None, load_multi=False, join_spread_atom_records=None, calpha_only=None, profile='DEFAULT', remote=False, remote_repo='pdb', dialect=None, seqres=False, bond_feasibility_check=None, read_conect=False)

def	SavePDB (models, filename, dialect=None, pqr=False, profile='DEFAULT')

def	LoadImageList (files)

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

def	LoadMMCIF (filename, fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, seqres=False, info=False)

def	SaveMMCIF (ent, filename, compound_lib=conop.GetDefaultLib(), data_name="OST_structure", mmcif_conform=True, entity_info=MMCifWriterEntityList())

Variables
const int	OMF_VERSION = 3

	profiles = IOProfiles()

Typedef Documentation

◆ AlignmentIOFList

typedef std::vector<SequenceIOHandlerFactoryBasePtr> AlignmentIOFList

Definition at line 38 of file io_manager.hh.

◆ ChainDataPtr

typedef boost::shared_ptr< ChainData > ChainDataPtr

Definition at line 38 of file omf.hh.

◆ ClustalIOHandlerFactory

typedef SequenceIOHandlerFactory< ClustalIOHandler > ClustalIOHandlerFactory

Definition at line 52 of file clustal_io_handler.hh.

◆ EntityIOCRDHandlerFactory

typedef EntityIOHandlerFactory< EntityIOCRDHandler > EntityIOCRDHandlerFactory

Definition at line 109 of file entity_io_crd_handler.hh.

◆ EntityIOHandlerFactoryBaseP

typedef boost::shared_ptr< EntityIOHandlerFactoryBase > EntityIOHandlerFactoryBaseP

Definition at line 77 of file entity_io_handler.hh.

◆ EntityIOHandlerP

typedef boost::shared_ptr< EntityIOHandler > EntityIOHandlerP

Definition at line 63 of file entity_io_handler.hh.

◆ EntityIOHFList

typedef std::vector<EntityIOHandlerFactoryBaseP> EntityIOHFList

Definition at line 37 of file io_manager.hh.

◆ EntityIOMAEHandlerFactory

typedef EntityIOHandlerFactory< EntityIOMAEHandler > EntityIOMAEHandlerFactory

Definition at line 83 of file entity_io_mae_handler.hh.

◆ EntityIOMMCIFHandlerFactory

typedef EntityIOHandlerFactory< EntityIOMMCIFHandler > EntityIOMMCIFHandlerFactory

Definition at line 54 of file entity_io_mmcif_handler.hh.

◆ EntityIOPDBHandlerFactory

typedef EntityIOHandlerFactory< EntityIOPDBHandler > EntityIOPDBHandlerFactory

Definition at line 55 of file entity_io_pdb_handler.hh.

◆ EntityIOPQRHandlerFactory

typedef EntityIOHandlerFactory< EntityIOPQRHandler > EntityIOPQRHandlerFactory

Definition at line 109 of file entity_io_pqr_handler.hh.

◆ EntityIOSDFHandlerFactory

typedef EntityIOHandlerFactory< EntityIOSDFHandler > EntityIOSDFHandlerFactory

Definition at line 49 of file entity_io_sdf_handler.hh.

◆ FastaIOHandlerFactory

typedef SequenceIOHandlerFactory< FastaIOHandler > FastaIOHandlerFactory

Definition at line 53 of file fasta_io_handler.hh.

◆ HhmIOHandlerFactory

typedef ProfileIOHandlerFactory< HhmIOHandler > HhmIOHandlerFactory

Definition at line 52 of file hhm_io_handler.hh.

◆ MAP

typedef CCP4 MAP

Definition at line 61 of file map_io_mrc_handler.hh.

◆ MapIODatHandlerFactory

typedef MapIOHandlerFactory< MapIODatHandler > MapIODatHandlerFactory

Definition at line 80 of file map_io_dat_handler.hh.

◆ MapIODF3HandlerFactory

typedef MapIOHandlerFactory< DF3MapIOHandler > MapIODF3HandlerFactory

Definition at line 71 of file map_io_df3_handler.hh.

◆ MapIODm3HandlerFactory

typedef MapIOHandlerFactory< MapIODm3Handler > MapIODm3HandlerFactory

Definition at line 59 of file map_io_dm3_handler.hh.

◆ MapIODxHandlerFactory

typedef MapIOHandlerFactory< MapIODxHandler > MapIODxHandlerFactory

Definition at line 74 of file map_io_dx_handler.hh.

◆ MapIOFList

typedef std::vector<MapIOHandlerFactoryBasePtr> MapIOFList

Definition at line 41 of file io_manager.hh.

◆ MapIOHandlerFactoryBasePtr

typedef boost::shared_ptr< MapIOHandlerFactoryBase > MapIOHandlerFactoryBasePtr

Definition at line 57 of file map_io_handler.hh.

◆ MapIOHandlerPtr

typedef boost::shared_ptr< MapIOHandler > MapIOHandlerPtr

Definition at line 42 of file map_io_handler.hh.

◆ MapIOIPLHandlerFactory

typedef MapIOHandlerFactory< MapIOIPLHandler > MapIOIPLHandlerFactory

Definition at line 74 of file map_io_ipl_handler.hh.

◆ MapIOJpkHandlerFactory

typedef MapIOHandlerFactory< MapIOJpkHandler > MapIOJpkHandlerFactory

Definition at line 57 of file map_io_jpk_handler.hh.

◆ MapIOMrcHandlerFactory

typedef MapIOHandlerFactory< MapIOMrcHandler > MapIOMrcHandlerFactory

Definition at line 94 of file map_io_mrc_handler.hh.

◆ MapIONanoscopeHandlerFactory

typedef MapIOHandlerFactory< MapIONanoscopeHandler > MapIONanoscopeHandlerFactory

Definition at line 67 of file map_io_nanoscope_handler.hh.

◆ MapIOPngHandlerFactory

typedef MapIOHandlerFactory< MapIOPngHandler > MapIOPngHandlerFactory

Definition at line 65 of file map_io_png_handler.hh.

◆ MapIOSitusHandlerFactory

typedef MapIOHandlerFactory< MapIOSitusHandler > MapIOSitusHandlerFactory

Definition at line 64 of file map_io_situs_handler.hh.

◆ MapIOSpiHandlerFactory

typedef MapIOHandlerFactory< MapIOSpiHandler > MapIOSpiHandlerFactory

Definition at line 77 of file map_io_spi_handler.hh.

◆ MapIOTiffHandlerFactory

typedef MapIOHandlerFactory< MapIOTiffHandler > MapIOTiffHandlerFactory

Definition at line 120 of file map_io_tiff_handler.hh.

◆ MMCifEntityDescMap

typedef std::map< String, MMCifEntityDesc > MMCifEntityDescMap

Definition at line 965 of file mmcif_info.hh.

◆ MMCifInfoEntityBranchLinkMap

typedef std::map< String, std::vector< MMCifInfoEntityBranchLink > > MMCifInfoEntityBranchLinkMap

Definition at line 950 of file mmcif_info.hh.

◆ MMCifInfoStructRefPtr

typedef boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr

Definition at line 839 of file mmcif_info.hh.

◆ MMCifInfoStructRefs

typedef std::vector< MMCifInfoStructRefPtr > MMCifInfoStructRefs

Definition at line 843 of file mmcif_info.hh.

◆ MMCifInfoStructRefSeqDifPtr

typedef boost::shared_ptr< MMCifInfoStructRefSeqDif > MMCifInfoStructRefSeqDifPtr

Definition at line 841 of file mmcif_info.hh.

◆ MMCifInfoStructRefSeqDifs

typedef std::vector< MMCifInfoStructRefSeqDifPtr > MMCifInfoStructRefSeqDifs

Definition at line 845 of file mmcif_info.hh.

◆ MMCifInfoStructRefSeqPtr

typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr

Definition at line 840 of file mmcif_info.hh.

◆ MMCifInfoStructRefSeqs

typedef std::vector< MMCifInfoStructRefSeqPtr > MMCifInfoStructRefSeqs

Definition at line 844 of file mmcif_info.hh.

◆ MMCifInfoTransOpPtr

typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr

Definition at line 248 of file mmcif_info.hh.

◆ OMFPtr

typedef boost::shared_ptr< OMF > OMFPtr

Definition at line 37 of file omf.hh.

◆ PirIOHandlerFactory

typedef SequenceIOHandlerFactory< PirIOHandler > PirIOHandlerFactory

Definition at line 53 of file pir_io_handler.hh.

◆ ProfileIOFList

typedef std::vector<ProfileIOHandlerFactoryBasePtr> ProfileIOFList

Definition at line 39 of file io_manager.hh.

◆ ProfileIOHandlerFactoryBasePtr

typedef boost::shared_ptr< ProfileIOHandlerFactoryBase > ProfileIOHandlerFactoryBasePtr

Definition at line 66 of file profile_io_handler.hh.

◆ ProfileIOHandlerPtr

typedef boost::shared_ptr< ProfileIOHandler > ProfileIOHandlerPtr

Definition at line 51 of file profile_io_handler.hh.

◆ PromodIOHandlerFactory

typedef SequenceIOHandlerFactory< PromodIOHandler > PromodIOHandlerFactory

Definition at line 53 of file promod_io_handler.hh.

◆ PssmIOHandlerFactory

typedef ProfileIOHandlerFactory< PssmIOHandler > PssmIOHandlerFactory

Definition at line 54 of file pssm_io_handler.hh.

◆ SequenceIOHandlerFactoryBasePtr

typedef boost::shared_ptr< SequenceIOHandlerFactoryBase > SequenceIOHandlerFactoryBasePtr

Definition at line 67 of file sequence_io_handler.hh.

◆ SequenceIOHandlerPtr

typedef boost::shared_ptr< SequenceIOHandler > SequenceIOHandlerPtr

Definition at line 51 of file sequence_io_handler.hh.

◆ StarWriterDataItemPtr

typedef boost::shared_ptr< StarWriterDataItem > StarWriterDataItemPtr

Definition at line 77 of file star_writer.hh.

◆ StarWriterLoopDescPtr

typedef boost::shared_ptr< StarWriterLoopDesc > StarWriterLoopDescPtr

Definition at line 78 of file star_writer.hh.

◆ StarWriterLoopPtr

typedef boost::shared_ptr< StarWriterLoop > StarWriterLoopPtr

Definition at line 79 of file star_writer.hh.

◆ StarWriterObjectPtr

typedef boost::shared_ptr< StarWriterObject > StarWriterObjectPtr

Definition at line 75 of file star_writer.hh.

◆ StarWriterValuePtr

typedef boost::shared_ptr< StarWriterValue > StarWriterValuePtr

Definition at line 76 of file star_writer.hh.

◆ SurfaceIOFList

typedef std::vector<SurfaceIOHandlerFactoryBasePtr> SurfaceIOFList

Definition at line 40 of file io_manager.hh.

◆ SurfaceIOHandlerFactoryBasePtr

typedef boost::shared_ptr< SurfaceIOHandlerFactoryBase > SurfaceIOHandlerFactoryBasePtr

Definition at line 48 of file surface_io_handler.hh.

◆ SurfaceIOHandlerPtr

typedef boost::shared_ptr< SurfaceIOHandler > SurfaceIOHandlerPtr

Definition at line 36 of file surface_io_handler.hh.

◆ SurfaceIOMSMSHandlerFactory

typedef SurfaceIOHandlerFactory< SurfaceIOMSMSHandler > SurfaceIOMSMSHandlerFactory

Definition at line 41 of file surface_io_msms_handler.hh.

Enumeration Type Documentation

◆ Endianess

enum Endianess

Enumerator
OST_BIG_ENDIAN
OST_LITTLE_ENDIAN
OST_VAX_DATA
OST_LOCAL_ENDIAN

Definition at line 44 of file convert.hh.

◆ Format [1/2]

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.

◆ Format [2/2]

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.

◆ LoopType [1/2]

enum LoopType

Enumerator
ATOM_SPEC
BOND_SPEC
DESC_SPEC
DONT_KNOW
ATOM_SPEC
BOND_SPEC
DESC_SPEC
DONT_KNOW

Definition at line 34 of file chemdict_parser.hh.

◆ LoopType [2/2]

enum LoopType

Enumerator
ATOM_SPEC
BOND_SPEC
DESC_SPEC
DONT_KNOW
ATOM_SPEC
BOND_SPEC
DESC_SPEC
DONT_KNOW

Definition at line 34 of file chemdict_parser.hh.

◆ StarDiagType [1/2]

enum StarDiagType

Enumerator
STAR_DIAG_WARNING
STAR_DIAG_ERROR
STAR_DIAG_WARNING
STAR_DIAG_ERROR

Definition at line 38 of file star_parser.hh.

◆ StarDiagType [2/2]

enum StarDiagType

Enumerator
STAR_DIAG_WARNING
STAR_DIAG_ERROR
STAR_DIAG_WARNING
STAR_DIAG_ERROR

Definition at line 38 of file star_parser.hh.

◆ Subformat [1/2]

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.

◆ Subformat [2/2]

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

◆ AlignmentFromStream()

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

◆ AlignmentFromString()

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

◆ AlignmentToString()

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

◆ EntityToMMCifString() [1/2]

String DLLEXPORT_OST_IO EntityToMMCifString	(	const ost::mol::EntityHandle &	ent,
		const String &	data_name,
		ost::conop::CompoundLibPtr	compound_lib,
		bool	mmcif_conform
	)

◆ EntityToMMCifString() [2/2]

String DLLEXPORT_OST_IO EntityToMMCifString	(	const ost::mol::EntityView &	ent,
		const String &	data_name,
		ost::conop::CompoundLibPtr	compound_lib,
		bool	mmcif_conform
	)

◆ EntityToPDBString() [1/2]

String DLLEXPORT_OST_IO EntityToPDBString	(	const mol::EntityHandle &	ent,
		const IOProfile &	profile = `IOProfile()`
	)

◆ EntityToPDBString() [2/2]

String DLLEXPORT_OST_IO EntityToPDBString	(	const mol::EntityView &	ent,
		const IOProfile &	profile = `IOProfile()`
	)

◆ EntityToSDFString() [1/2]

String DLLEXPORT_OST_IO EntityToSDFString ( const mol::EntityHandle & ent )

◆ EntityToSDFString() [2/2]

String DLLEXPORT_OST_IO EntityToSDFString ( const mol::EntityView & ent )

◆ GetStereoChemicalPropsFile()

String GetStereoChemicalPropsFile ( )

◆ LoadAlignment()

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

◆ LoadCHARMMTraj() [1/2]

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

◆ LoadCHARMMTraj() [2/2]

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 312 of file __init__.py.

◆ LoadCRD()

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

◆ LoadEntity()

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

◆ LoadImage() [1/2]

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.

◆ LoadImage() [2/2]

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

◆ LoadImageList()

def ost.io.LoadImageList ( files )

Definition at line 303 of file __init__.py.

◆ LoadMAE()

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

◆ LoadManagedSurface()

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

◆ LoadMap() [1/2]

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

Alias for the equivalent LoadImage function.

◆ LoadMap() [2/2]

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

Alias for the equivalent LoadImage function.

◆ LoadMMCIF()

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

Load a mmCIF file 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 not waters nor covered by an
``entity_poly`` record (ie. they are non-polymer entities in
``pdbx_entity_nonpoly``). Note that all residues except waters will be
flagged as ligands if ``seqres=False`` (the default).

:param filename: File to be loaded
:type filename: :class:`str`

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

:param calpha_only: When set to true, forces the importer to only load atoms
                    named CA. If set, overrides the value of
                    :attr:`IOProfile.calpha_only`.
:type calpha_only: :class:`bool`

:param profile: Aggregation of flags and algorithms to control import and
                processing of molecular structures. Can either be a
                :class:`str` specifying one of the default profiles
                ['DEFAULT', 'SLOPPY', 'CHARMM', 'STRICT'] or an actual object
                of type :class:`ost.io.IOProfile`. If a :class:`str` defines
                a default profile, :attr:`IOProfile.processor` is set to
                :class:`ost.conop.RuleBasedProcessor` with the currently
                set :class:`ost.conop.CompoundLib` available as
                :func:`ost.conop.GetDefaultLib()`. If no
                :class:`ost.conop.CompoundLib` is available,
                :class:`ost.conop.HeuristicProcessor` is used instead. See
                :doc:`profile` for more info.
:type profile: :class:`str`/:class:`ost.io.IOProfile`

: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.
:type remote: :class:`bool`

:param seqres: Whether to return SEQRES records. If True, a
               :class:`~ost.seq.SequenceList` object is returned as the second
               item. The sequences in the list are named according to the
               mmCIF chain name.
               This feature requires a default
               :class:`compound library <ost.conop.CompoundLib>`
               to be defined and accessible via
               :func:`~ost.conop.GetDefaultLib`. One letter codes of non
               standard compounds are set to X otherwise.
:type seqres: :class:`bool`

:param info: Whether to return an info container with the other output.
             If True, a :class:`MMCifInfo` object is returned as last item.
:type info: :class:`bool`

:rtype: :class:`~ost.mol.EntityHandle` (or tuple if *seqres* or *info* are
        True).

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

Definition at line 348 of file __init__.py.

◆ LoadPDB()

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

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 filename: File to be loaded
:type filename: :class:`str`

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

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

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

: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.
:type load_multi: :class:`bool`

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

:param calpha_only: When set to true, forces the importer to only load atoms
                    named CA. If set, overrides the value of
                    :attr:`IOProfile.calpha_only`.
:type calpha_only: :class:`bool`

:param profile: Aggregation of flags and algorithms to control import and
                processing of molecular structures. Can either be a
                :class:`str` specifying one of the default profiles
                ['DEFAULT', 'SLOPPY', 'CHARMM', 'STRICT'] or an actual object
                of type :class:`ost.io.IOProfile`. If a :class:`str` defines
                a default profile, :attr:`IOProfile.processor` is set to
                :class:`ost.conop.RuleBasedProcessor` with the currently
                set :class:`ost.conop.CompoundLib` available as
                :func:`ost.conop.GetDefaultLib()`. If no
                :class:`ost.conop.CompoundLib` is available,
                :class:`ost.conop.HeuristicProcessor` is used instead. See
                :doc:`profile` for more info.
:type profile: :class:`str`/:class:`ost.io.IOProfile`

:param remote: If set to True, the method tries to load the pdb from the remote
               repository given as *remote_repo*. The filename is then
               interpreted as the entry id as further specified for the
               *remote_repo* parameter.
:type remote: :class:`bool`

:param remote_repo: Remote repository to fetch structure if *remote* is True. 
                    Must be one in ['pdb', 'smtl', 'pdb_redo']. In case of 
                    'pdb' and 'pdb_redo', the entry must be given as lower 
                    case pdb id, which loads the deposited assymetric unit 
                    (e.g. '1ake'). In case of 'smtl', the entry must also 
                    specify the desired biounit (e.g. '1ake.1').
:type remote_repo: :class:`str`
   
:param dialect: Specifies the particular dialect to use. If set, overrides 
                the value of :attr:`IOProfile.dialect`
:type dialect: :class:`str`

:param seqres: Whether to read SEQRES records. If set to True, the loaded 
               entity and seqres entry will be returned as a tuple.
               If file doesnt contain SEQRES records, the returned
               :class:`ost.seq.SequenceList` will be invalid.
:type seqres: :class:`bool`

:param bond_feasibility_check: Flag for :attr:`IOProfile.processor`. If
                               turned on, atoms are only connected by
                               bonds if they are within a reasonable distance
                               (as defined by
                               :func:`ost.conop.IsBondFeasible`).
                               If set, overrides the value of
                               :attr:`ost.conop.Processor.check_bond_feasibility`
:type bond_feasibility_check: :class:`bool`
:param read_conect: By default, OpenStructure doesn't read CONECT statements in
                    a pdb file. Reason is that they're often missing and we prefer
                    to rely on the chemical component dictionary from the PDB.
                    However, there may be cases where you really want these CONECT
                    statements. For example novel compounds with no entry in
                    the chemical component dictionary. Setting this to True has
                    two effects: 1) CONECT statements are read and blindly applied
                    2) The processor does not connect any pair of HETATOM atoms in
                    order to not interfer with the CONECT statements.
:type read_conect: :class:`bool`

:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is 
    True.  

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

Definition at line 82 of file __init__.py.

◆ LoadPQR()

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

◆ LoadSDF()

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

◆ LoadSequence()

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

◆ LoadSequenceList()

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

◆ LoadSequenceProfile()

seq::ProfileHandlePtr DLLEXPORT_OST_IO LoadSequenceProfile	(	const String &	file_name,
		const String &	format = `"auto"`
	)

◆ LoadSurface()

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

◆ MMCifStringToEntity()

std::tuple< mol::EntityHandle, MMCifInfo, ost::seq::SequenceList > DLLEXPORT_OST_IO MMCifStringToEntity	(	const String &	mmcif,
		const IOProfile &	profile,
		bool	process
	)

◆ MMCifValueOrderToOSTBondOrder()

DLLEXPORT_OST_IO unsigned char MMCifValueOrderToOSTBondOrder ( const StringRef value_order )

Translate mmCIF info on bond type (e.g. pdbx_entity_branch_link.value_order) to OST bond_order.

Parameters

value_order abbreviation detemrining the bond order

◆ operator<<() [1/4]

DLLEXPORT_OST_IO std::ostream & operator<<	(	std::ostream &	os,
		const MMCifInfoEntityBranchLink &	eb
	)

◆ operator<<() [2/4]

DLLEXPORT_OST_IO std::ostream & operator<<	(	std::ostream &	os,
		const std::vector< MMCifInfoEntityBranchLink > &	eb_list
	)

◆ operator<<() [3/4]

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

inline

Definition at line 229 of file formatted_line.hh.

◆ operator<<() [4/4]

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

inline

Definition at line 61 of file io_profile.hh.

◆ OSTBondOrderToMMCifValueOrder()

DLLEXPORT_OST_IO String OSTBondOrderToMMCifValueOrder ( const unsigned char bond_order )

Translate an OST bond_order to mmCIF value_order.

Parameters

bond_order OST bond order

◆ PDBStringToEntity()

mol::EntityHandle DLLEXPORT_OST_IO PDBStringToEntity	(	const String &	pdb,
		const IOProfile &	profile = `IOProfile()`,
		bool	process = `false`
	)

◆ RawSerialize() [1/2]

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

inline

Definition at line 87 of file binary_data_sink.hh.

◆ RawSerialize() [2/2]

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

inline

Definition at line 87 of file binary_data_source.hh.

◆ ReadStereoChemicalPropsFile() [1/2]

ost::mol::alg::StereoChemicalProps ReadStereoChemicalPropsFile ( bool check = false )

◆ ReadStereoChemicalPropsFile() [2/2]

ost::mol::alg::StereoChemicalProps ReadStereoChemicalPropsFile	(	String	filename,
		bool	check = `false`
	)

◆ SaveAlignment()

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

◆ SaveCHARMMTraj()

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

◆ SaveEntity() [1/2]

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

◆ SaveEntity() [2/2]

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

◆ SaveImage() [1/2]

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

◆ SaveImage() [2/2]

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

◆ SaveMap() [1/2]

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

Alias for the equivalent SaveImage function.

◆ SaveMap() [2/2]

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

Alias for the equivalent SaveImage function.

◆ SaveMMCIF()

def ost.io.SaveMMCIF	(	ent,
		filename,
		compound_lib = `conop.GetDefaultLib()`,
		data_name = `"OST_structure"`,
		mmcif_conform = `True`,
		entity_info = `MMCifWriterEntityList()`
	)

Save OpenStructure entity in mmCIF format

:param ent:           OpenStructure Entity to be saved
:param filename:      Filename - .gz suffix triggers gzip compression
:param compound_lib:  Compound library required when writing, uses
                      :func:`ost.conop.GetDefaultLib` if not given
:param data_name:     Name of data block that will be written to
                      mmCIF file. Typically, thats the PDB ID or some
                      identifier.
:param mmcif_conform: Controls processing of structure, i.e. identification
                      of mmCIF entities etc. before writing. Detailed
                      description in :ref:`MMCif writing`. In short:
                      If *mmcif_conform* is set to True, Chains in *ent* are
                      expected to be valid mmCIF entities with residue numbers
                      set according to underlying SEQRES. That should be the
                      case when *ent* has been loaded with :func:`LoadMMCIF`.
                      If *mmcif_conform* is set to False, heuristics kick in
                      to identify and separate mmCIF entities based on
                      :class:`ost.mol.ChemClass` of the residues in a chain.
:type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param entity_info: Advanced usage - description in :ref:`MMCif writing`
:type filename: :class:`str`
:type compound_lib: :class:`ost.conop.CompoundLib`
:type data_name: :class:`str`
:type mmcif_conform: :class:`bool`
:type entity_info: :class:`MMCifWriterEntityList`

Definition at line 455 of file __init__.py.

◆ SavePDB()

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
:raises: IOException if the restrictions of the PDB format are not satisfied
         (with the exception of atom numbers, see above):

           * Chain names with more than one character
           * Atom positions with coordinates outside range [-999.99, 9999.99]
           * Residue names longer than three characters
           * Atom names longer than four characters
           * Numeric part of :class:`ost.mol.ResNum` outside range [-999, 9999] 
           * Alternative atom indicators longer than one character

Definition at line 256 of file __init__.py.

◆ SaveSDF() [1/2]

void DLLEXPORT_OST_IO SaveSDF	(	const mol::EntityHandle &	ent,
		const String &	file_name
	)

◆ SaveSDF() [2/2]

void DLLEXPORT_OST_IO SaveSDF	(	const mol::EntityView &	ent,
		const String &	file_name
	)

◆ SaveSequence()

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

◆ SaveSequenceList()

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

◆ SDFStringToEntity()

mol::EntityHandle DLLEXPORT_OST_IO SDFStringToEntity ( const String & pdb )

◆ SequenceFromStream()

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

◆ SequenceFromString()

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

◆ SequenceListFromStream()

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

◆ SequenceListFromString()

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

◆ SequenceListToString()

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

◆ SequenceProfileFromString()

seq::ProfileHandlePtr DLLEXPORT_OST_IO SequenceProfileFromString	(	const String &	data,
		const String &	format
	)

◆ SequenceToString()

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

◆ Serialize() [1/8]

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

Definition at line 62 of file container_serialization.hh.

◆ Serialize() [2/8]

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

Definition at line 32 of file container_serialization.hh.

◆ Serialize() [3/8]

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

inline

Definition at line 92 of file binary_data_sink.hh.

◆ Serialize() [4/8]

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

Definition at line 79 of file binary_data_sink.hh.

◆ Serialize() [5/8]

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

Definition at line 72 of file container_serialization.hh.

◆ Serialize() [6/8]

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

Definition at line 46 of file container_serialization.hh.

◆ Serialize() [7/8]

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

inline

Definition at line 93 of file binary_data_source.hh.

◆ Serialize() [8/8]

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

Definition at line 80 of file binary_data_source.hh.

◆ swap_buf()

void swap_buf	(	T *	p,
		int	n
	)

Definition at line 55 of file swap_util.hh.

◆ swap_double()

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

inline

Definition at line 49 of file swap_util.hh.

◆ swap_float()

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

inline

Definition at line 47 of file swap_util.hh.

◆ swap_int()

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

inline

Definition at line 43 of file swap_util.hh.

◆ swap_long()

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

inline

Definition at line 51 of file swap_util.hh.

◆ swap_short()

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

inline

Definition at line 39 of file swap_util.hh.

◆ swap_uint()

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

inline

Definition at line 45 of file swap_util.hh.

◆ swap_ushort()

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

inline

Definition at line 41 of file swap_util.hh.

Variable Documentation

◆ OMF_VERSION

const int OMF_VERSION = 3

Definition at line 33 of file omf.hh.

◆ profiles

profiles = IOProfiles()

Definition at line 74 of file __init__.py.

Namespaces

Data Structures

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ AlignmentIOFList

◆ ChainDataPtr

◆ ClustalIOHandlerFactory

◆ EntityIOCRDHandlerFactory

◆ EntityIOHandlerFactoryBaseP

◆ EntityIOHandlerP

◆ EntityIOHFList

◆ EntityIOMAEHandlerFactory

◆ EntityIOMMCIFHandlerFactory

◆ EntityIOPDBHandlerFactory

◆ EntityIOPQRHandlerFactory

◆ EntityIOSDFHandlerFactory

◆ FastaIOHandlerFactory

◆ HhmIOHandlerFactory

◆ MAP

◆ MapIODatHandlerFactory

◆ MapIODF3HandlerFactory

◆ MapIODm3HandlerFactory

◆ MapIODxHandlerFactory

◆ MapIOFList

◆ MapIOHandlerFactoryBasePtr

◆ MapIOHandlerPtr

◆ MapIOIPLHandlerFactory

◆ MapIOJpkHandlerFactory

◆ MapIOMrcHandlerFactory

◆ MapIONanoscopeHandlerFactory

◆ MapIOPngHandlerFactory

◆ MapIOSitusHandlerFactory

◆ MapIOSpiHandlerFactory

◆ MapIOTiffHandlerFactory

◆ MMCifEntityDescMap

◆ MMCifInfoEntityBranchLinkMap

◆ MMCifInfoStructRefPtr

◆ MMCifInfoStructRefs

◆ MMCifInfoStructRefSeqDifPtr

◆ MMCifInfoStructRefSeqDifs

◆ MMCifInfoStructRefSeqPtr

◆ MMCifInfoStructRefSeqs

◆ MMCifInfoTransOpPtr

◆ OMFPtr

◆ PirIOHandlerFactory

◆ ProfileIOFList

◆ ProfileIOHandlerFactoryBasePtr

◆ ProfileIOHandlerPtr

◆ PromodIOHandlerFactory

◆ PssmIOHandlerFactory

◆ SequenceIOHandlerFactoryBasePtr

◆ SequenceIOHandlerPtr

◆ StarWriterDataItemPtr

◆ StarWriterLoopDescPtr

◆ StarWriterLoopPtr

◆ StarWriterObjectPtr

◆ StarWriterValuePtr

◆ SurfaceIOFList

◆ SurfaceIOHandlerFactoryBasePtr

◆ SurfaceIOHandlerPtr

◆ SurfaceIOMSMSHandlerFactory

Enumeration Type Documentation

◆ Endianess

◆ Format [1/2]

◆ Format [2/2]

◆ LoopType [1/2]

◆ LoopType [2/2]

◆ StarDiagType [1/2]

◆ StarDiagType [2/2]

◆ Subformat [1/2]

◆ Subformat [2/2]

Function Documentation

◆ AlignmentFromStream()

◆ AlignmentFromString()

◆ AlignmentToString()

◆ EntityToMMCifString() [1/2]

◆ EntityToMMCifString() [2/2]