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ost::io Namespace Reference

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
 
class  MMCifInfoEntityBranchLink
 
class  MMCifInfo
 
class  MMCifReader
 
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  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 boost::shared_ptr< OMFOMFPtr
 
typedef boost::shared_ptr
< ChainData
ChainDataPtr
 
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)
 
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)
 
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
 
def SavePDB
 
def LoadImageList
 
def LoadCHARMMTraj
 
def LoadMMCIF
 

Variables

const int OMF_VERSION = 3
 
tuple profiles = IOProfiles()
 

Typedef Documentation

Definition at line 38 of file io_manager.hh.

typedef boost::shared_ptr< ChainData > ChainDataPtr

Definition at line 38 of file omf.hh.

Definition at line 52 of file clustal_io_handler.hh.

Definition at line 109 of file entity_io_crd_handler.hh.

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.

Definition at line 37 of file io_manager.hh.

Definition at line 83 of file entity_io_mae_handler.hh.

Definition at line 54 of file entity_io_mmcif_handler.hh.

Definition at line 55 of file entity_io_pdb_handler.hh.

Definition at line 109 of file entity_io_pqr_handler.hh.

Definition at line 49 of file entity_io_sdf_handler.hh.

Definition at line 53 of file fasta_io_handler.hh.

Definition at line 52 of file hhm_io_handler.hh.

typedef CCP4 MAP

Definition at line 61 of file map_io_mrc_handler.hh.

Definition at line 80 of file map_io_dat_handler.hh.

Definition at line 71 of file map_io_df3_handler.hh.

Definition at line 59 of file map_io_dm3_handler.hh.

Definition at line 74 of file map_io_dx_handler.hh.

typedef std::vector<MapIOHandlerFactoryBasePtr> MapIOFList

Definition at line 41 of file io_manager.hh.

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.

Definition at line 74 of file map_io_ipl_handler.hh.

Definition at line 57 of file map_io_jpk_handler.hh.

Definition at line 94 of file map_io_mrc_handler.hh.

Definition at line 67 of file map_io_nanoscope_handler.hh.

Definition at line 65 of file map_io_png_handler.hh.

Definition at line 64 of file map_io_situs_handler.hh.

Definition at line 77 of file map_io_spi_handler.hh.

Definition at line 120 of file map_io_tiff_handler.hh.

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

Definition at line 960 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr

Definition at line 836 of file mmcif_info.hh.

Definition at line 843 of file mmcif_info.hh.

Definition at line 841 of file mmcif_info.hh.

Definition at line 845 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr

Definition at line 840 of file mmcif_info.hh.

Definition at line 844 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr

Definition at line 248 of file mmcif_info.hh.

typedef boost::shared_ptr< OMF > OMFPtr

Definition at line 36 of file omf.hh.

Definition at line 53 of file pir_io_handler.hh.

Definition at line 39 of file io_manager.hh.

Definition at line 66 of file profile_io_handler.hh.

typedef boost::shared_ptr< ProfileIOHandler > ProfileIOHandlerPtr

Definition at line 51 of file profile_io_handler.hh.

Definition at line 53 of file promod_io_handler.hh.

Definition at line 54 of file pssm_io_handler.hh.

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.

Definition at line 40 of file io_manager.hh.

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.

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 44 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 
DESC_SPEC 
DONT_KNOW 
ATOM_SPEC 
BOND_SPEC 
DESC_SPEC 
DONT_KNOW 

Definition at line 34 of file chemdict_parser.hh.

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.

Enumerator
STAR_DIAG_WARNING 
STAR_DIAG_ERROR 
STAR_DIAG_WARNING 
STAR_DIAG_ERROR 

Definition at line 38 of file star_parser.hh.

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 
)
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() 
)
String DLLEXPORT_OST_IO EntityToSDFString ( const mol::EntityHandle &  ent)
String DLLEXPORT_OST_IO EntityToSDFString ( const mol::EntityView &  ent)
String GetStereoChemicalPropsFile ( )
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 319 of file __init__.py.

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

Definition at line 308 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,
  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 354 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,
  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 quack_mode: Guess the chemical class for unknown residues based on its
                   atoms and connectivity. If set, overrides the value of
                   :attr:`IOProfile.quack_mode`.
:type quack_mode: :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.
: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 88 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" 
)
seq::ProfileHandlePtr DLLEXPORT_OST_IO LoadSequenceProfile ( const String file_name,
const String format = "auto" 
)
DLLEXPORT_OST_IO mol::SurfaceHandle LoadSurface ( const String filename,
const String type = "auto" 
)
std::tuple< mol::EntityHandle, MMCifInfo, ost::seq::SequenceList > DLLEXPORT_OST_IO MMCifStringToEntity ( const String mmcif,
const IOProfile &  profile,
bool  process 
)
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_orderabbreviation detemrining the bond order
std::ostream & operator<< ( std::ostream &  stream,
const IOProfile &  p 
)
inline

Definition at line 62 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.

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 String OSTBondOrderToMMCifValueOrder ( const unsigned char  bond_order)

Translate an OST bond_order to mmCIF value_order.

Parameters
bond_orderOST bond order
mol::EntityHandle DLLEXPORT_OST_IO PDBStringToEntity ( const String pdb,
const IOProfile &  profile = IOProfile(),
bool  process = false 
)
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.

ost::mol::alg::StereoChemicalProps ReadStereoChemicalPropsFile ( String  filename,
bool  check = false 
)
ost::mol::alg::StereoChemicalProps ReadStereoChemicalPropsFile ( bool  check = false)
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
enis the entity to be saved
filenameis the output filename
formatspecifies 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
enis the entity view to be saved.
filenameis the output filename
formatspecifies 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
: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 261 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" 
)
mol::EntityHandle DLLEXPORT_OST_IO SDFStringToEntity ( const String pdb)
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 
)
seq::ProfileHandlePtr DLLEXPORT_OST_IO SequenceProfileFromString ( const String data,
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

const int OMF_VERSION = 3

Definition at line 33 of file omf.hh.

tuple profiles = IOProfiles()

Definition at line 75 of file __init__.py.