OpenStructure
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Namespaces | |
detail | |
fmt | |
jpk_tags | |
remote | |
repository | |
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") |
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") |
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") |
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 | |
profiles = None | |
tuple | processor = conop.RuleBasedProcessor(conop.GetDefaultLib()) |
tuple | quack_mode = processor.Copy() |
typedef std::vector<SequenceIOHandlerFactoryBasePtr> AlignmentIOFList |
Definition at line 41 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.
typedef boost::shared_ptr< EntityIOHandlerFactoryBase > EntityIOHandlerFactoryBaseP |
Definition at line 77 of file entity_io_handler.hh.
typedef boost::shared_ptr< EntityIOHandler > EntityIOHandlerP |
Definition at line 63 of file entity_io_handler.hh.
typedef std::vector<EntityIOHandlerFactoryBaseP> EntityIOHFList |
Definition at line 40 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 48 of file hhm_io_handler.hh.
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 boost::shared_ptr< MapIOHandlerFactoryBase > MapIOHandlerFactoryBasePtr |
Definition at line 57 of file map_io_handler.hh.
typedef boost::shared_ptr< MapIOHandler > MapIOHandlerPtr |
Definition at line 42 of file map_io_handler.hh.
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 boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr |
Definition at line 853 of file mmcif_info.hh.
typedef std::vector< MMCifInfoStructRefPtr > MMCifInfoStructRefs |
Definition at line 860 of file mmcif_info.hh.
typedef boost::shared_ptr< MMCifInfoStructRefSeqDif > MMCifInfoStructRefSeqDifPtr |
Definition at line 858 of file mmcif_info.hh.
typedef std::vector< MMCifInfoStructRefSeqDifPtr > MMCifInfoStructRefSeqDifs |
Definition at line 862 of file mmcif_info.hh.
typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr |
Definition at line 857 of file mmcif_info.hh.
typedef std::vector< MMCifInfoStructRefSeqPtr > MMCifInfoStructRefSeqs |
Definition at line 861 of file mmcif_info.hh.
typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr |
Definition at line 246 of file mmcif_info.hh.
Definition at line 53 of file pir_io_handler.hh.
typedef std::vector<ProfileIOHandlerFactoryBasePtr> ProfileIOFList |
Definition at line 42 of file io_manager.hh.
typedef boost::shared_ptr< ProfileIOHandlerFactoryBase > ProfileIOHandlerFactoryBasePtr |
Definition at line 63 of file profile_io_handler.hh.
typedef boost::shared_ptr< ProfileIOHandler > ProfileIOHandlerPtr |
Definition at line 48 of file profile_io_handler.hh.
Definition at line 53 of file promod_io_handler.hh.
Definition at line 50 of file pssm_io_handler.hh.
typedef boost::shared_ptr< SequenceIOHandlerFactoryBase > SequenceIOHandlerFactoryBasePtr |
Definition at line 67 of file sequence_io_handler.hh.
typedef boost::shared_ptr< SequenceIOHandler > SequenceIOHandlerPtr |
Definition at line 51 of file sequence_io_handler.hh.
typedef std::vector<SurfaceIOHandlerFactoryBasePtr> SurfaceIOFList |
Definition at line 43 of file io_manager.hh.
typedef boost::shared_ptr< SurfaceIOHandlerFactoryBase > SurfaceIOHandlerFactoryBasePtr |
Definition at line 48 of file surface_io_handler.hh.
typedef boost::shared_ptr< SurfaceIOHandler > SurfaceIOHandlerPtr |
Definition at line 36 of file surface_io_handler.hh.
Definition at line 41 of file surface_io_msms_handler.hh.
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 |
Definition at line 68 of file image_format.hh.
enum 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.
enum StarDiagType |
Enumerator | |
---|---|
STAR_DIAG_WARNING | |
STAR_DIAG_ERROR | |
STAR_DIAG_WARNING | |
STAR_DIAG_ERROR |
Definition at line 38 of file star_parser.hh.
enum StarDiagType |
Enumerator | |
---|---|
STAR_DIAG_WARNING | |
STAR_DIAG_ERROR | |
STAR_DIAG_WARNING | |
STAR_DIAG_ERROR |
Definition at line 38 of file star_parser.hh.
enum Subformat |
Enumerator | |
---|---|
MRC_OLD_FORMAT | |
MRC_NEW_FORMAT | |
MRC_AUTO_FORMAT | |
MRC_OLD_FORMAT | |
MRC_NEW_FORMAT | |
MRC_AUTO_FORMAT |
Definition at line 73 of file image_format.hh.
enum Subformat |
Enumerator | |
---|---|
MRC_OLD_FORMAT | |
MRC_NEW_FORMAT | |
MRC_AUTO_FORMAT | |
MRC_OLD_FORMAT | |
MRC_NEW_FORMAT | |
MRC_AUTO_FORMAT |
Definition at line 73 of file image_format.hh.
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() |
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) |
String DLLEXPORT_OST_IO EntityToPDBString | ( | const mol::EntityView & | ent, |
const IOProfile & | profile = IOProfile() |
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) |
String GetStereoChemicalPropsFile | ( | ) |
seq::AlignmentHandle DLLEXPORT_OST_IO LoadAlignment | ( | const String & | file_name, |
const String & | format = "auto" |
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) |
mol::CoordGroupHandle DLLEXPORT_OST_IO LoadCHARMMTraj | ( | const mol::EntityHandle & | ent, |
const String & | trj_filename, | ||
unsigned int | stride = 1 , |
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bool | lazy_load = false , |
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bool | detect_swap = true , |
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bool | byte_swap = false |
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) |
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 , |
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profile = 'CHARMM' , |
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lazy_load = False , |
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stride = 1 , |
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dialect = None , |
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detect_swap = True , |
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swap_bytes = False |
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) |
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 234 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 223 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" |
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) |
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 , |
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calpha_only = None , |
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profile = 'DEFAULT' , |
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remote = False , |
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seqres = False , |
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info = False |
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) |
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 fault_tolerant: Enable/disable fault-tolerant import. If set, overrides the value of :attr:`IOProfile.fault_tolerant`. :param remote: If set to True, the method tries to load the pdb from the remote pdb repository www.pdb.org. The filename is then interpreted as the pdb id. :rtype: :class:`~ost.mol.EntityHandle`. :param seqres: Whether to read SEQRES records. If set to True, the loaded entity and seqres entry will be returned as second item. :param info: Whether to return an info container with the other output. Returns a :class:`MMCifInfo` object as last item. :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or non-existent file.
Definition at line 268 of file __init__.py.
def ost.io.LoadPDB | ( | filename, | |
restrict_chains = "" , |
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no_hetatms = None , |
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fault_tolerant = None , |
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load_multi = False , |
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quack_mode = None , |
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join_spread_atom_records = None , |
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calpha_only = None , |
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profile = 'DEFAULT' , |
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remote = False , |
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dialect = None , |
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seqres = False , |
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bond_feasibility_check = None |
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) |
Load PDB file from disk and return one or more entities. Several options allow to customize the exact behaviour of the PDB import. For more information on these options, see :doc:`profile`. Residues are flagged as ligand if they are mentioned in a HET record. :param restrict_chains: If not an empty string, only chains listed in the string will be imported. :param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides the value of :attr:`IOProfile.fault_tolerant`. :param no_hetatms: If set to True, HETATM records will be ignored. Overrides the value of :attr:`IOProfile.no_hetatms` :param load_multi: If set to True, a list of entities will be returned instead of only the first. This is useful when dealing with multi-PDB files. :param join_spread_atom_records: If set, overrides the value of :attr:`IOProfile.join_spread_atom_records`. :param remote: If set to True, the method tries to load the pdb from the remote pdb repository www.pdb.org. The filename is then interpreted as the pdb id. :rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is True. :param dialect: Specifies the particular dialect to use. If set, overrides the value of :attr:`IOProfile.dialect` :param seqres: Whether to read SEQRES records. If set to True, the loaded entity and seqres entry will be returned as a tuple. :type dialect: :class:`str` :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or inexistent file
Definition at line 69 of file __init__.py.
mol::EntityHandle DLLEXPORT_OST_IO LoadPQR | ( | const String & | file_name | ) |
mol::EntityHandle DLLEXPORT_OST_IO LoadSDF | ( | const String & | file_name | ) |
seq::SequenceHandle DLLEXPORT_OST_IO LoadSequence | ( | const String & | file_name, |
const String & | format = "auto" |
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) |
seq::SequenceList DLLEXPORT_OST_IO LoadSequenceList | ( | const String & | file_name, |
const String & | format = "auto" |
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) |
seq::ProfileHandlePtr DLLEXPORT_OST_IO LoadSequenceProfile | ( | const String & | file_name, |
const String & | format = "auto" |
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) |
DLLEXPORT_OST_IO mol::SurfaceHandle LoadSurface | ( | const String & | filename, |
const String & | type = "auto" |
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) |
|
inline |
Definition at line 61 of file io_profile.hh.
|
inline |
Definition at line 229 of file formatted_line.hh.
mol::EntityHandle DLLEXPORT_OST_IO PDBStringToEntity | ( | const String & | pdb, |
const IOProfile & | profile = IOProfile() , |
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bool | process = false |
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) |
|
inline |
Definition at line 87 of file binary_data_sink.hh.
|
inline |
Definition at line 87 of file binary_data_source.hh.
ost::mol::alg::StereoChemicalProps ReadStereoChemicalPropsFile | ( | String | filename, |
bool | check = false |
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) |
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() |
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) |
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.
en | is the entity to be saved |
filename | is the output filename |
format | specifies what output format is used for export. If set to auto the format is deduced from the file extension |
void DLLEXPORT_OST_IO SaveEntity | ( | const mol::EntityView & | en, |
const String & | filename, | ||
const String & | format = "auto" |
||
) |
Save entity view.
This method provides a convenient way to save only a certain part of an entity, i.e. to filter out water and ligands or to create a backbone-only model.
en | is the entity view to be saved. |
filename | is the output filename |
format | specifies what output format is used for export. If set to auto the format is deduced from the file extension |
DLLEXPORT_OST_IO void SaveImage | ( | const img::ImageHandle & | image, |
const boost::filesystem::path & | loc | ||
) |
Function that saves an image to a file.
This function saves an image on disk. The function automatically determines the file format by looking at the filename extension. In case the extension is not availabel, the function will throw an error
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
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 , |
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pqr = False , |
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profile = 'DEFAULT' |
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) |
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 176 of file __init__.py.
void DLLEXPORT_OST_IO SaveSequence | ( | const seq::ConstSequenceHandle & | sequence, |
const String & | filename, | ||
const String & | format = "auto" |
||
) |
void DLLEXPORT_OST_IO SaveSequenceList | ( | const seq::ConstSequenceList & | seq_list, |
const String & | filename, | ||
const String & | format = "auto" |
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) |
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" |
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) |
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.
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inline |
Definition at line 92 of file binary_data_sink.hh.
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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.
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inline |
Definition at line 49 of file swap_util.hh.
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inline |
Definition at line 47 of file swap_util.hh.
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inline |
Definition at line 43 of file swap_util.hh.
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inline |
Definition at line 51 of file swap_util.hh.
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inline |
Definition at line 39 of file swap_util.hh.
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inline |
Definition at line 45 of file swap_util.hh.
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inline |
Definition at line 41 of file swap_util.hh.
tuple processor = conop.RuleBasedProcessor(conop.GetDefaultLib()) |
Definition at line 48 of file __init__.py.
tuple profiles = None |
Definition at line 24 of file __init__.py.
tuple quack_mode = processor.Copy() |
Definition at line 52 of file __init__.py.