OpenStructure
Namespaces | Data Structures | Typedefs | Enumerations | Functions | Variables
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
 
struct  MMCifInfoEntityBranchLink
 
struct  MMCifEntityDesc
 
class  MMCifInfo
 
class  MMCifReader
 
struct  ChainNameGenerator
 
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< ClustalIOHandlerClustalIOHandlerFactory
 
typedef EntityIOHandlerFactory< EntityIOCRDHandlerEntityIOCRDHandlerFactory
 
typedef boost::shared_ptr< EntityIOHandlerEntityIOHandlerP
 
typedef boost::shared_ptr< EntityIOHandlerFactoryBaseEntityIOHandlerFactoryBaseP
 
typedef EntityIOHandlerFactory< EntityIOMAEHandlerEntityIOMAEHandlerFactory
 
typedef EntityIOHandlerFactory< EntityIOMMCIFHandlerEntityIOMMCIFHandlerFactory
 
typedef EntityIOHandlerFactory< EntityIOPDBHandlerEntityIOPDBHandlerFactory
 
typedef EntityIOHandlerFactory< EntityIOPQRHandlerEntityIOPQRHandlerFactory
 
typedef EntityIOHandlerFactory< EntityIOSDFHandlerEntityIOSDFHandlerFactory
 
typedef SequenceIOHandlerFactory< FastaIOHandlerFastaIOHandlerFactory
 
typedef ProfileIOHandlerFactory< HhmIOHandlerHhmIOHandlerFactory
 
typedef MapIOHandlerFactory< MapIODatHandlerMapIODatHandlerFactory
 
typedef MapIOHandlerFactory< DF3MapIOHandlerMapIODF3HandlerFactory
 
typedef MapIOHandlerFactory< MapIODm3HandlerMapIODm3HandlerFactory
 
typedef MapIOHandlerFactory< MapIODxHandlerMapIODxHandlerFactory
 
typedef boost::shared_ptr< MapIOHandlerMapIOHandlerPtr
 
typedef boost::shared_ptr< MapIOHandlerFactoryBaseMapIOHandlerFactoryBasePtr
 
typedef MapIOHandlerFactory< MapIOIPLHandlerMapIOIPLHandlerFactory
 
typedef MapIOHandlerFactory< MapIOJpkHandlerMapIOJpkHandlerFactory
 
typedef CCP4 MAP
 
typedef MapIOHandlerFactory< MapIOMrcHandlerMapIOMrcHandlerFactory
 
typedef MapIOHandlerFactory< MapIONanoscopeHandlerMapIONanoscopeHandlerFactory
 
typedef MapIOHandlerFactory< MapIOPngHandlerMapIOPngHandlerFactory
 
typedef MapIOHandlerFactory< MapIOSitusHandlerMapIOSitusHandlerFactory
 
typedef MapIOHandlerFactory< MapIOSpiHandlerMapIOSpiHandlerFactory
 
typedef MapIOHandlerFactory< MapIOTiffHandlerMapIOTiffHandlerFactory
 
typedef std::vector< EntityIOHandlerFactoryBasePEntityIOHFList
 
typedef std::vector< SequenceIOHandlerFactoryBasePtrAlignmentIOFList
 
typedef std::vector< ProfileIOHandlerFactoryBasePtrProfileIOFList
 
typedef std::vector< SurfaceIOHandlerFactoryBasePtrSurfaceIOFList
 
typedef std::vector< MapIOHandlerFactoryBasePtrMapIOFList
 
typedef boost::shared_ptr< MMCifInfoTransOpMMCifInfoTransOpPtr
 
typedef boost::shared_ptr< MMCifInfoStructRefMMCifInfoStructRefPtr
 
typedef boost::shared_ptr< MMCifInfoStructRefSeqMMCifInfoStructRefSeqPtr
 
typedef boost::shared_ptr< MMCifInfoStructRefSeqDifMMCifInfoStructRefSeqDifPtr
 
typedef std::vector< MMCifInfoStructRefPtrMMCifInfoStructRefs
 
typedef std::vector< MMCifInfoStructRefSeqPtrMMCifInfoStructRefSeqs
 
typedef std::vector< MMCifInfoStructRefSeqDifPtrMMCifInfoStructRefSeqDifs
 
typedef std::map< String, std::vector< MMCifInfoEntityBranchLink > > MMCifInfoEntityBranchLinkMap
 
typedef std::map< String, MMCifEntityDescMMCifEntityDescMap
 
typedef boost::shared_ptr< OMFOMFPtr
 
typedef boost::shared_ptr< ChainDataChainDataPtr
 
typedef boost::shared_ptr< StarWriterObjectStarWriterObjectPtr
 
typedef boost::shared_ptr< StarWriterValueStarWriterValuePtr
 
typedef boost::shared_ptr< StarWriterDataItemStarWriterDataItemPtr
 
typedef boost::shared_ptr< StarWriterLoopDescStarWriterLoopDescPtr
 
typedef boost::shared_ptr< StarWriterLoopStarWriterLoopPtr
 
typedef boost::shared_ptr< SurfaceIOHandlerSurfaceIOHandlerPtr
 
typedef boost::shared_ptr< SurfaceIOHandlerFactoryBaseSurfaceIOHandlerFactoryBasePtr
 
typedef SurfaceIOHandlerFactory< SurfaceIOMSMSHandlerSurfaceIOMSMSHandlerFactory
 
typedef SequenceIOHandlerFactory< PirIOHandlerPirIOHandlerFactory
 
typedef boost::shared_ptr< ProfileIOHandlerProfileIOHandlerPtr
 
typedef boost::shared_ptr< ProfileIOHandlerFactoryBaseProfileIOHandlerFactoryBasePtr
 
typedef SequenceIOHandlerFactory< PromodIOHandlerPromodIOHandlerFactory
 
typedef ProfileIOHandlerFactory< PssmIOHandlerPssmIOHandlerFactory
 
typedef boost::shared_ptr< SequenceIOHandlerSequenceIOHandlerPtr
 
typedef boost::shared_ptr< SequenceIOHandlerFactoryBaseSequenceIOHandlerFactoryBasePtr
 

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

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

Definition at line 52 of file clustal_io_handler.hh.

◆ EntityIOCRDHandlerFactory

Definition at line 109 of file entity_io_crd_handler.hh.

◆ 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

Definition at line 37 of file io_manager.hh.

◆ EntityIOMAEHandlerFactory

Definition at line 83 of file entity_io_mae_handler.hh.

◆ EntityIOMMCIFHandlerFactory

Definition at line 54 of file entity_io_mmcif_handler.hh.

◆ EntityIOPDBHandlerFactory

Definition at line 55 of file entity_io_pdb_handler.hh.

◆ EntityIOPQRHandlerFactory

Definition at line 109 of file entity_io_pqr_handler.hh.

◆ EntityIOSDFHandlerFactory

Definition at line 49 of file entity_io_sdf_handler.hh.

◆ FastaIOHandlerFactory

Definition at line 53 of file fasta_io_handler.hh.

◆ 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

Definition at line 80 of file map_io_dat_handler.hh.

◆ MapIODF3HandlerFactory

Definition at line 71 of file map_io_df3_handler.hh.

◆ MapIODm3HandlerFactory

Definition at line 59 of file map_io_dm3_handler.hh.

◆ 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

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

Definition at line 74 of file map_io_ipl_handler.hh.

◆ MapIOJpkHandlerFactory

Definition at line 57 of file map_io_jpk_handler.hh.

◆ MapIOMrcHandlerFactory

Definition at line 94 of file map_io_mrc_handler.hh.

◆ MapIONanoscopeHandlerFactory

Definition at line 67 of file map_io_nanoscope_handler.hh.

◆ MapIOPngHandlerFactory

Definition at line 65 of file map_io_png_handler.hh.

◆ MapIOSitusHandlerFactory

Definition at line 64 of file map_io_situs_handler.hh.

◆ MapIOSpiHandlerFactory

Definition at line 77 of file map_io_spi_handler.hh.

◆ MapIOTiffHandlerFactory

Definition at line 120 of file map_io_tiff_handler.hh.

◆ MMCifEntityDescMap

Definition at line 966 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

Definition at line 843 of file mmcif_info.hh.

◆ MMCifInfoStructRefSeqDifPtr

Definition at line 841 of file mmcif_info.hh.

◆ 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

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

Definition at line 53 of file pir_io_handler.hh.

◆ ProfileIOFList

Definition at line 39 of file io_manager.hh.

◆ 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

Definition at line 53 of file promod_io_handler.hh.

◆ PssmIOHandlerFactory

Definition at line 54 of file pssm_io_handler.hh.

◆ 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

Definition at line 40 of file io_manager.hh.

◆ 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

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]

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]

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_orderabbreviation 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_orderOST 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
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

◆ 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
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

◆ 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.