Data Structures
class	BinaryDecoder
	Helper class to decode msgpack binary into a vector. More...

struct	BioAssembly
	Data store for the biological assembly annotation. More...

class	BondAdder
	Helper class for adding bonds to a group-redundant system. More...

class	DecodeError
	Exception thrown when failing during decoding. More...

class	EncodeError
	Exception thrown when failing during encoding. More...

struct	Entity
	Entity type. More...

struct	GroupType
	Group (residue) level data store. More...

class	MapDecoder
	Helper class to decode msgpack maps into object fields. More...

struct	StructureData
	Top level MMTF data container. More...

struct	Transform
	Transformation definition for a set of chains. More...

Functions
std::vector< char >	encodeInt8ToByte (std::vector< int8_t > vec_in)

std::vector< char >	encodeFourByteInt (std::vector< int32_t > vec_in)

std::vector< char >	encodeStringVector (std::vector< std::string > in_sv, int32_t CHAIN_LEN)

std::vector< char >	encodeRunLengthChar (std::vector< char > in_cv)

std::vector< char >	encodeRunLengthDeltaInt (std::vector< int32_t > int_vec)

std::vector< char >	encodeRunLengthFloat (std::vector< float > floats_in, int32_t multiplier)

std::vector< char >	encodeDeltaRecursiveFloat (std::vector< float > floats_in, int32_t multiplier)

void	decodeFromBuffer (StructureData &data, const char *buffer, size_t size)
	Decode an MMTF data structure from a byte buffer. More...

template<typename Stream >
void	decodeFromStream (StructureData &data, Stream &stream)
	Decode an MMTF data structure from a stream. More...

void	decodeFromFile (StructureData &data, const std::string &filename)
	Decode an MMTF data structure from an existing file. More...

void	encodeToFile (const StructureData &data, const std::string &filename, int32_t coord_divider=1000, int32_t occupancy_b_factor_divider=100, int32_t chain_name_max_length=4)
	Encode an MMTF data structure into a file. More...

template<typename Stream >
void	encodeToStream (const StructureData &data, Stream &stream, int32_t coord_divider=1000, int32_t occupancy_b_factor_divider=100, int32_t chain_name_max_length=4)
	Encode an MMTF data structure into a stream. More...

std::map< std::string, msgpack::object >	encodeToMap (const StructureData &data, msgpack::zone &m_zone, int32_t coord_divider=1000, int32_t occupancy_b_factor_divider=100, int32_t chain_name_max_length=4)
	Encode an MMTF data structure into a map of msgpack objects. More...

void	compressGroupList (StructureData &data)
	Eliminate redundant groups from groupList. More...

std::string	getVersionString ()
	Get string representation of MMTF spec version implemented here. More...

bool	isVersionSupported (const std::string &version_string)
	Check if version is supported (minor revisions ok, major ones not) More...

template<typename T >
T	getDefaultValue ()
	Get default value for given type. More...

template<typename T >
bool	isDefaultValue (const T &value)

template<typename T >
bool	isDefaultValue (const std::vector< T > &value)

template<>
bool	isDefaultValue (const std::string &value)

template<typename T >
void	setDefaultValue (T &value)
	Set default value to given type. More...

bool	is_hetatm (const char *type)
	Check if type is hetatm. More...

Function Documentation

◆ compressGroupList()

void mmtf::compressGroupList ( StructureData & data )

inline

Eliminate redundant groups from groupList.

Modifies groupList and groupTypeList

Parameters

[in,out] data Consistent system

◆ decodeFromBuffer()

void mmtf::decodeFromBuffer	(	StructureData &	data,
		const char *	buffer,
		size_t	size
	)

inline

Decode an MMTF data structure from a byte buffer.

Parameters

[out]	data	MMTF data structure to be filled
[in]	buffer	File contents
[in]	size	Size of buffer

Exceptions

mmtf::DecodeError if an error occured

◆ decodeFromFile()

void mmtf::decodeFromFile	(	StructureData &	data,
		const std::string &	filename
	)

inline

Decode an MMTF data structure from an existing file.

Parameters

[out]	data	MMTF data structure to be filled
[in]	filename	Path to file to load

Exceptions

mmtf::DecodeError if an error occured

◆ decodeFromStream()

template<typename Stream >

void mmtf::decodeFromStream	(	StructureData &	data,
		Stream &	stream
	)

inline

Decode an MMTF data structure from a stream.

Note that the full stream is read until the end before decoding it!

Parameters

[out]	data	MMTF data structure to be filled
[in]	stream	Any stream type compatible to std::ostream

Exceptions

mmtf::DecodeError if an error occured

◆ encodeDeltaRecursiveFloat()

std::vector< char > mmtf::encodeDeltaRecursiveFloat	(	std::vector< float >	floats_in,
		int32_t	multiplier
	)

inline

encode Delta Recursive Float encoding (type 10)

Parameters

[in]	floats_in	vector of ints
[in]	multiplier	float multiplier

Returns: cv char vector of encoded bytes

◆ encodeFourByteInt()

std::vector< char > mmtf::encodeFourByteInt ( std::vector< int32_t > vec_in )

inline

encode 4 bytes to int encoding (type 4)

Parameters

[in] vec_in vector of ints to encode

Returns: cv char vector of encoded bytes

◆ encodeInt8ToByte()

std::vector< char > mmtf::encodeInt8ToByte ( std::vector< int8_t > vec_in )

inline

encode 8 bit int to bytes encoding (type 2)

Parameters

[in] vec_in vector of ints to encode

Returns: cv char vector of encoded bytes

◆ encodeRunLengthChar()

std::vector< char > mmtf::encodeRunLengthChar ( std::vector< char > in_cv )

inline

encode Run Length Char encoding (type 6)

Parameters

[in] in_cv vector for chars

Returns: cv char vector of encoded bytes

◆ encodeRunLengthDeltaInt()

std::vector< char > mmtf::encodeRunLengthDeltaInt ( std::vector< int32_t > int_vec )

inline

encode Run Length Delta Int encoding (type 8)

Parameters

[in] int_vec vector of ints

Returns: cv char vector of encoded bytes

◆ encodeRunLengthFloat()

std::vector< char > mmtf::encodeRunLengthFloat	(	std::vector< float >	floats_in,
		int32_t	multiplier
	)

inline

encode Run Length Float encoding (type 9)

Parameters

[in]	floats_in	vector of ints
[in]	multiplier	float multiplier

Returns: cv char vector of encoded bytes

◆ encodeStringVector()

std::vector< char > mmtf::encodeStringVector	(	std::vector< std::string >	in_sv,
		int32_t	CHAIN_LEN
	)

inline

encode string vector encoding (type 5)

Parameters

[in]	in_sv	vector of strings
[in]	CHAIN_LEN	maximum length of string

Returns: cv char vector of encoded bytes

◆ encodeToFile()

void mmtf::encodeToFile	(	const StructureData &	data,
		const std::string &	filename,
		int32_t	coord_divider = `1000`,
		int32_t	occupancy_b_factor_divider = `100`,
		int32_t	chain_name_max_length = `4`
	)

inline

Encode an MMTF data structure into a file.

Parameters

[in]	data	MMTF data structure to be stored
[in]	filename	Path to file to load
[in]	coord_divider	Divisor for coordinates
[in]	occupancy_b_factor_divider	Divisor for occupancy and b-factor
[in]	chain_name_max_length	Max. length for chain name strings

Exceptions

mmtf::EncodeError if an error occurred

Common settings for the divisors are the default values for a loss-less encoding and both set to 10 for a lossy variant.

◆ encodeToMap()

std::map< std::string, msgpack::object > mmtf::encodeToMap	(	const StructureData &	data,
		msgpack::zone &	m_zone,
		int32_t	coord_divider = `1000`,
		int32_t	occupancy_b_factor_divider = `100`,
		int32_t	chain_name_max_length = `4`
	)

inline

Encode an MMTF data structure into a map of msgpack objects.

Parameters

[in]	data	MMTF data structure to be stored
[in]	m_zone	msgpack::zone object to use

Returns: Object which can be modified and passed to msgpack::pack

Other parameters and behavior are as in encodeToFile, but this enables you to add additional fields before packing.

◆ encodeToStream()

template<typename Stream >

void mmtf::encodeToStream	(	const StructureData &	data,
		Stream &	stream,
		int32_t	coord_divider = `1000`,
		int32_t	occupancy_b_factor_divider = `100`,
		int32_t	chain_name_max_length = `4`
	)

inline

Encode an MMTF data structure into a stream.

Parameters

[in]	data	MMTF data structure to be stored
[in]	stream	Stream to encode to

Other parameters and behavior are as in encodeToFile, but this enables you to store the data to other types of storage.

◆ getDefaultValue()

template<typename T >

T mmtf::getDefaultValue ( )

inline

Get default value for given type.

◆ getVersionString()

std::string mmtf::getVersionString ( )

inline

Get string representation of MMTF spec version implemented here.

◆ is_hetatm()

bool mmtf::is_hetatm ( const char * type )

inline

Check if type is hetatm.

Parameters

type	cstring of group.chemCompType

Returns: True if is a HETATM Used when printing this struct, also all chemCompTypes are listed, but the non-HETATM ones are commented out for reference Relevant threads: https://github.com/rcsb/mmtf/issues/28 http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html

◆ isDefaultValue() [1/3]

template<typename T >

bool mmtf::isDefaultValue ( const T & value )

inline

Returns: True if given value is default.

Template Parameters

T	Can be any numeric type, vector of string

◆ isDefaultValue() [2/3]

template<typename T >

bool mmtf::isDefaultValue ( const std::vector< T > & value )

inline

◆ isDefaultValue() [3/3]

template<>

bool mmtf::isDefaultValue ( const std::string & value )

inline

◆ isVersionSupported()

bool mmtf::isVersionSupported ( const std::string & version_string )

inline

Check if version is supported (minor revisions ok, major ones not)

Returns: true if supported, false if not

◆ setDefaultValue()

template<typename T >

void mmtf::setDefaultValue ( T & value )

inline

Set default value to given type.

Template Parameters

T	Can be any numeric type (no need for vector or strings here)

Data Structures

Functions

Function Documentation

◆ compressGroupList()

◆ decodeFromBuffer()

◆ decodeFromFile()

◆ decodeFromStream()

◆ encodeDeltaRecursiveFloat()

◆ encodeFourByteInt()

◆ encodeInt8ToByte()

◆ encodeRunLengthChar()

◆ encodeRunLengthDeltaInt()

◆ encodeRunLengthFloat()

◆ encodeStringVector()

◆ encodeToFile()

◆ encodeToMap()

◆ encodeToStream()

◆ getDefaultValue()

◆ getVersionString()

◆ is_hetatm()

◆ isDefaultValue() [1/3]

◆ isDefaultValue() [2/3]

◆ isDefaultValue() [3/3]

◆ isVersionSupported()

◆ setDefaultValue()