OpenStructure
 All Data Structures Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Groups Pages
Namespaces | Data Structures | Typedefs | Enumerations | Functions | Variables
ost::io Namespace Reference

Namespaces

namespace  detail
namespace  fmt
namespace  jpk_tags
namespace  remote
namespace  repository

Data Structures

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

Typedefs

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

Enumerations

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

Functions

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

Variables

 profiles = None
 strict_hydrogens = False,quack_modeFalse)

Typedef Documentation

Definition at line 39 of file io_manager.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 38 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 49 of file entity_io_sdf_handler.hh.

Definition at line 53 of file fasta_io_handler.hh.

typedef CCP4 MAP

Definition at line 57 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.

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 90 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 boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr

Definition at line 747 of file mmcif_info.hh.

Definition at line 754 of file mmcif_info.hh.

Definition at line 752 of file mmcif_info.hh.

Definition at line 756 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr

Definition at line 751 of file mmcif_info.hh.

Definition at line 755 of file mmcif_info.hh.

typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr

Definition at line 236 of file mmcif_info.hh.

Definition at line 53 of file pir_io_handler.hh.

Definition at line 53 of file promod_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 28 of file convert.hh.

enum Format
Enumerator:
OST_BIT8_FORMAT 
OST_BIT16_FORMAT 
OST_BIT32_FORMAT 
OST_FLOAT_FORMAT 
OST_DOUBLE_FORMAT 
OST_DEFAULT_FORMAT 
OST_BIT8_FORMAT 
OST_BIT16_FORMAT 
OST_BIT32_FORMAT 
OST_FLOAT_FORMAT 
OST_DOUBLE_FORMAT 
OST_DEFAULT_FORMAT 

Definition at line 68 of file image_format.hh.

enum Format
Enumerator:
OST_BIT8_FORMAT 
OST_BIT16_FORMAT 
OST_BIT32_FORMAT 
OST_FLOAT_FORMAT 
OST_DOUBLE_FORMAT 
OST_DEFAULT_FORMAT 
OST_BIT8_FORMAT 
OST_BIT16_FORMAT 
OST_BIT32_FORMAT 
OST_FLOAT_FORMAT 
OST_DOUBLE_FORMAT 
OST_DEFAULT_FORMAT 

Definition at line 68 of file image_format.hh.

enum LoopType
Enumerator:
ATOM_SPEC 
BOND_SPEC 
DONT_KNOW 
ATOM_SPEC 
BOND_SPEC 
DONT_KNOW 

Definition at line 34 of file chemdict_parser.hh.

enum LoopType
Enumerator:
ATOM_SPEC 
BOND_SPEC 
DONT_KNOW 
ATOM_SPEC 
BOND_SPEC 
DONT_KNOW 

Definition at line 34 of file chemdict_parser.hh.

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 
)
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 222 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadCRD ( const String file_name)
DLLEXPORT_OST_IO mol::EntityHandle LoadEntity ( const String filename,
int  flag = 0 
)
DLLEXPORT_OST_IO img::ImageHandle LoadImage ( const boost::filesystem::path &  loc)

Function that loads an image from a file.

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

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

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

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

def ost.io.LoadImageList (   files)

loads several images and puts them in an ImageList

See also:
View Fourier Transform Example

Definition at line 211 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadMAE ( const String file_name)
DLLEXPORT_OST_IO mol::SurfaceHandle LoadManagedSurface ( const String name,
const String filename,
const String type = "auto" 
)
DLLEXPORT_OST_IO img::MapHandle LoadMap ( const boost::filesystem::path &  loc)

Alias for the equivalent LoadImage function.

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

Alias for the equivalent LoadImage function.

def ost.io.LoadMMCIF (   filename,
  restrict_chains = "",
  fault_tolerant = None,
  calpha_only = None,
  profile = 'DEFAULT',
  remote = False,
  strict_hydrogens = None,
  seqres = False,
  info = False 
)
Load MMCIF file from disk and return one or more entities. Several options 
allow to customize the exact behaviour of the MMCIF import. For more
information on these options, see :doc:`profile`.

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

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

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

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

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

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

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

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

Definition at line 256 of file __init__.py.

def ost.io.LoadPDB (   filename,
  restrict_chains = "",
  no_hetatms = None,
  fault_tolerant = None,
  load_multi = False,
  quack_mode = None,
  join_spread_atom_records = None,
  calpha_only = None,
  profile = 'DEFAULT',
  remote = False,
  dialect = None,
  strict_hydrogens = None,
  seqres = False,
  bond_feasibility_check = None 
)
Load PDB file from disk and return one or more entities. Several options 
allow to customize the exact behaviour of the PDB import. For more information 
on these options, see :doc:`profile`.

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

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

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

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

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

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

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

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

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

:type dialect: :class:`str`

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

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

Definition at line 65 of file __init__.py.

mol::EntityHandle DLLEXPORT_OST_IO LoadSDF ( const String file_name)
seq::SequenceHandle DLLEXPORT_OST_IO LoadSequence ( const String file_name,
const String format = "auto" 
)
seq::SequenceList DLLEXPORT_OST_IO LoadSequenceList ( const String file_name,
const String format = "auto" 
)
DLLEXPORT_OST_IO mol::SurfaceHandle LoadSurface ( const String filename,
const String type = "auto" 
)
std::ostream & operator<< ( std::ostream &  stream,
const IOProfile &  p 
)
inline

Definition at line 57 of file io_profile.hh.

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

Definition at line 229 of file formatted_line.hh.

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

Definition at line 87 of file binary_data_sink.hh.

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

Definition at line 87 of file binary_data_source.hh.

void DLLEXPORT_OST_IO SaveAlignment ( const seq::AlignmentHandle &  msa,
const String filename,
const String format = "auto" 
)
void DLLEXPORT_OST_IO SaveCHARMMTraj ( const mol::CoordGroupHandle &  coord_group,
const String pdb_filename,
const String dcd_filename,
unsigned int  stride = 1,
const IOProfile &  profile = IOProfile() 
)

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

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

Save entity handle.

Parameters:
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

Definition at line 173 of file __init__.py.

void DLLEXPORT_OST_IO SaveSequence ( const seq::ConstSequenceHandle &  sequence,
const String filename,
const String format = "auto" 
)
void DLLEXPORT_OST_IO SaveSequenceList ( const seq::ConstSequenceList &  seq_list,
const String filename,
const String format = "auto" 
)
seq::SequenceHandle DLLEXPORT_OST_IO SequenceFromStream ( std::istream &  stream,
const String format 
)
seq::SequenceHandle DLLEXPORT_OST_IO SequenceFromString ( const String data,
const String format 
)
seq::SequenceList DLLEXPORT_OST_IO SequenceListFromStream ( std::istream &  stream,
const String format 
)
seq::SequenceList DLLEXPORT_OST_IO SequenceListFromString ( const String data,
const String format 
)
String DLLEXPORT_OST_IO SequenceListToString ( const seq::ConstSequenceList &  seq_list,
const String format 
)
String DLLEXPORT_OST_IO SequenceToString ( const seq::ConstSequenceHandle &  sequence,
const String format = "auto" 
)
void ost::io::Serialize ( BinaryDataSink &  sink,
const std::vector< T > &  value 
)

Definition at line 32 of file container_serialization.hh.

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

Definition at line 46 of file container_serialization.hh.

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

Definition at line 62 of file container_serialization.hh.

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

Definition at line 72 of file container_serialization.hh.

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

Definition at line 79 of file binary_data_sink.hh.

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

Definition at line 80 of file binary_data_source.hh.

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

Definition at line 92 of file binary_data_sink.hh.

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

Definition at line 93 of file binary_data_source.hh.

void swap_buf ( T *  p,
int  n 
)

Definition at line 55 of file swap_util.hh.

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

Definition at line 49 of file swap_util.hh.

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

Definition at line 47 of file swap_util.hh.

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

Definition at line 43 of file swap_util.hh.

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

Definition at line 51 of file swap_util.hh.

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

Definition at line 39 of file swap_util.hh.

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

Definition at line 45 of file swap_util.hh.

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

Definition at line 41 of file swap_util.hh.


Variable Documentation

tuple profiles = None

Definition at line 24 of file __init__.py.

strict_hydrogens = False,quack_modeFalse)

Definition at line 48 of file __init__.py.