Data Structures
class	BinaryDecoder
	Helper class to decode msgpack binary into a vector. More...
class	DecodeError
	Exception thrown when failing during decoding. More...
class	EncodeError
	Exception thrown when failing during encoding. More...
class	BondAdder
	Helper class for adding bonds to a group-redundant system. More...
class	MapDecoder
	Helper class to decode msgpack maps into object fields. Class cannot be copied as it contains unique pointers to msgpack data. More...
struct	GroupType
	Group (residue) level data store. More...
struct	Entity
	Entity type. More...
struct	Transform
	Transformation definition for a set of chains. More...
struct	BioAssembly
	Data store for the biological assembly annotation. More...
struct	StructureData
	Top level MMTF data container. More...

Functions
std::vector< char >	encodeInt8ToByte (std::vector< int8_t > vec_in)
std::vector< char >	encodeFourByteInt (std::vector< int32_t > const &vec_in)
std::vector< char >	encodeStringVector (std::vector< std::string > const &in_sv, int32_t const CHAIN_LEN)
std::vector< char >	encodeRunLengthChar (std::vector< char > const &in_cv)
std::vector< char >	encodeRunLengthDeltaInt (std::vector< int32_t > int_vec)
std::vector< char >	encodeRunLengthFloat (std::vector< float > const &floats_in, int32_t const multiplier)
std::vector< char >	encodeDeltaRecursiveFloat (std::vector< float > const &floats_in, int32_t const multiplier)
std::vector< char >	encodeRunLengthInt8 (std::vector< int8_t > const &int8_vec)
void	decodeFromMapDecoder (StructureData &data, MapDecoder &mapDecoder)
	Decode an MMTF data structure from a mapDecoder.
void	decodeFromBuffer (StructureData &data, const char *buffer, size_t size)
	Decode an MMTF data structure from a byte buffer.
template<typename Stream>
void	decodeFromStream (StructureData &data, Stream &stream)
	Decode an MMTF data structure from a stream.
void	decodeFromFile (StructureData &data, const std::string &filename)
	Decode an MMTF data structure from an existing file.
void	mapDecoderFromBuffer (MapDecoder &mapDecoder, const char *buffer, std::size_t size)
	Get a mapDecoder for un-decoded MMTF data.
template<typename Stream>
void	mapDecoderFromStream (MapDecoder &mapDecoder, Stream &stream)
	Get a mapDecoder into an un-decoded MMTF data.
void	mapDecoderFromFile (MapDecoder &mapDecoder, const std::string &filename)
	Get a mapDecoder into an un-decoded MMTF data.
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.
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.
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.
void	compressGroupList (StructureData &data)
	Eliminate redundant groups from groupList.
std::string	getVersionString ()
	Get string representation of MMTF spec version implemented here.
bool	isVersionSupported (const std::string &version_string)
	Check if version is supported (minor revisions ok, major ones not).
template<typename T>
T	getDefaultValue ()
	Get default value for given type.
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<>
bool	isDefaultValue (const std::map< std::string, msgpack::object > &value)
template<typename T>
void	setDefaultValue (T &value)
	Set default value to given type.
bool	is_polymer (const unsigned int chain_index, const std::vector< Entity > &entity_list)
	Check if chain is a polymer chain.
bool	is_hetatm (const char *type)
	Check if group type consists of HETATM atoms.
bool	is_hetatm (const unsigned int chain_index, const std::vector< Entity > &entity_list, const GroupType &group_type)
	Preferred way to check if group consists of hetatm atoms.
template<>
bool	isDefaultValue (const std::string &value)
template<>
bool	isDefaultValue (const std::map< std::string, msgpack::object > &value)

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

◆ decodeFromMapDecoder()

void mmtf::decodeFromMapDecoder	(	StructureData &	data,
		MapDecoder &	mapDecoder )

inline

Decode an MMTF data structure from a mapDecoder.

Parameters

[out]	data	MMTF data structure to be filled
[in]	mapDecoder	MapDecoder holding raw mmtf data

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 from start to end before decoding it! Use ::decodeFromBuffer if you wish to use just part of the stream.

Parameters

[out]	data	MMTF data structure to be filled
[in]	stream	Stream that holds mmtf data

Template Parameters

Stream Any stream type compatible to std::istream

Exceptions

mmtf::DecodeError if an error occured

◆ encodeDeltaRecursiveFloat()

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

inline

Encode Delta Recursive Float encoding (type 10)

Parameters

[in]	floats_in	Vector of floats to encode
[in]	multiplier	Multiplier to convert float to int

Returns: Char vector of encoded bytes

◆ encodeFourByteInt()

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

inline

Encode 4 bytes to int encoding (type 4)

Parameters

[in] vec_in Vector of ints to encode

Returns: 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: Char vector of encoded bytes

◆ encodeRunLengthChar()

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

inline

Encode Run Length Char encoding (type 6)

Parameters

[in] in_cv Vector of chars to encode

Returns: 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 to encode

Returns: Char vector of encoded bytes

◆ encodeRunLengthFloat()

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

inline

Encode Run Length Float encoding (type 9)

Parameters

[in]	floats_in	Vector of floats to encode
[in]	multiplier	Multiplier to convert float to int

Returns: Char vector of encoded bytes

◆ encodeRunLengthInt8()

std::vector< char > mmtf::encodeRunLengthInt8 ( std::vector< int8_t > const & int8_vec )

inline

Encode Run-Length 8bit int encoding (type 16)

Parameters

[in] int8_vec Vector of ints to encode

Returns: Char vector of encoded bytes

◆ encodeStringVector()

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

inline

Encode string vector encoding (type 5)

Parameters

[in]	in_sv	Vector of strings to encode
[in]	CHAIN_LEN	Maximum length of string

Returns: 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

Template Parameters

Stream Any stream type compatible to std::ostream

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() [1/2]

bool mmtf::is_hetatm ( const char * type )

inline

Check if group type consists of HETATM atoms.

Parameters

type	Character string of GroupType.chemCompType.

Returns: True if group consists of HETATM atoms.

Relevant threads:

Warning: Use the other is_hetatm function whenever possible. This one should only be used if you don't have info like an 'entity_list' to work with. This can return 'false' if you have an amino acid ligand.

◆ is_hetatm() [2/2]

bool mmtf::is_hetatm	(	const unsigned int	chain_index,
		const std::vector< Entity > &	entity_list,
		const GroupType &	group_type )

inline

Preferred way to check if group consists of hetatm atoms.

Parameters

chain_index	Chain index of chain where atom belongs to.
entity_list	StructureData.entityList with info on given chain.
group_type	GroupType of group where atom belongs to.

Returns: True if it is a HETATM.

Follows discussion in https://github.com/rcsb/mmtf/issues/28.

Used in StructureData.print to mark atoms as HETATM. This is a shorthand for is_hetatm(type) || !is_polymer(chain_index, entity_list).

Efficient code needing this information should preferably use the or statement above, precompute the is_polymer output for each chain and the is_hetatm(type) output for each group instead of calling this on each atom.

See also: is_polymer, is_hetatm

◆ is_polymer()

bool mmtf::is_polymer	(	const unsigned int	chain_index,
		const std::vector< Entity > &	entity_list )

inline

Check if chain is a polymer chain.

Parameters

chain_index	Chain index of chain.
entity_list	StructureData.entityList with info on given chain.

Returns: True if chain is a polymer chain.

Exceptions

mmtf::DecodeError if chain index doesn't appear in entity list.

◆ isDefaultValue() [1/6]

template<>

bool mmtf::isDefaultValue ( const std::map< std::string, msgpack::object > & value )

inline

◆ isDefaultValue() [2/6]

template<>

bool mmtf::isDefaultValue ( const std::map< std::string, msgpack::object > & value )

inline

◆ isDefaultValue() [3/6]

template<>

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

inline

◆ isDefaultValue() [4/6]

template<>

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

inline

◆ isDefaultValue() [5/6]

template<typename T>

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

inline

◆ isDefaultValue() [6/6]

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

◆ 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

◆ mapDecoderFromBuffer()

void mmtf::mapDecoderFromBuffer	(	MapDecoder &	mapDecoder,
		const char *	buffer,
		std::size_t	size )

inline

Get a mapDecoder for un-decoded MMTF data.

Parameters

[out] mapDecoder MapDecoder to hold raw mmtf data

Other parameters and behavior are as in ::decodeFromBuffer, but this doesn't decode the MMTF content.

◆ mapDecoderFromFile()

void mmtf::mapDecoderFromFile	(	MapDecoder &	mapDecoder,
		const std::string &	filename )

inline

Get a mapDecoder into an un-decoded MMTF data.

Parameters

[out] mapDecoder MapDecoder to hold raw mmtf data

Other parameters and behavior are as in ::decodeFromFile, but this doesn't decode the MMTF content.

◆ mapDecoderFromStream()

template<typename Stream>

void mmtf::mapDecoderFromStream	(	MapDecoder &	mapDecoder,
		Stream &	stream )

inline

Get a mapDecoder into an un-decoded MMTF data.

Parameters

[out] mapDecoder MapDecoder to hold raw mmtf data

Other parameters and behavior are as in ::decodeFromStream, but this doesn't decode the MMTF content.

◆ 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()

◆ decodeFromMapDecoder()

◆ decodeFromStream()

◆ encodeDeltaRecursiveFloat()

◆ encodeFourByteInt()

◆ encodeInt8ToByte()

◆ encodeRunLengthChar()

◆ encodeRunLengthDeltaInt()

◆ encodeRunLengthFloat()

◆ encodeRunLengthInt8()

◆ encodeStringVector()

◆ encodeToFile()

◆ encodeToMap()

◆ encodeToStream()

◆ getDefaultValue()

◆ getVersionString()

◆ is_hetatm() [1/2]

◆ is_hetatm() [2/2]

◆ is_polymer()

◆ isDefaultValue() [1/6]

◆ isDefaultValue() [2/6]

◆ isDefaultValue() [3/6]

◆ isDefaultValue() [4/6]

◆ isDefaultValue() [5/6]

◆ isDefaultValue() [6/6]

◆ isVersionSupported()

◆ mapDecoderFromBuffer()

◆ mapDecoderFromFile()

◆ mapDecoderFromStream()

◆ setDefaultValue()