MMTF-C++
The C++ language MMTF libraries
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mmtf::StructureData Struct Reference

Top level MMTF data container. More...

#include <structure_data.hpp>

Public Member Functions

 StructureData ()
 Construct object with default values set.
 
 StructureData (const StructureData &obj)
 Overload for copy constructor.
 
StructureDataoperator= (const StructureData &f)
 Overload for assignment operator.
 
bool hasConsistentData (bool verbose=false, uint32_t chain_name_max_length=4) const
 Check consistency of structural data.
 
std::string print (std::string delim="\t") const
 Read out the contents of mmtf::StructureData in a PDB-like fashion Columns are in order: ATOM/HETATM AtomId Element AtomName AltLoc GroupId GroupType InsCode ChainName x y z B-factor Occupancy Charge.
 
bool operator== (const StructureData &c) const
 Compare two StructureData classes for equality.
 
bool operator!= (const StructureData &c) const
 Compare two StructureData classes for inequality.
 

Data Fields

std::string mmtfVersion
 
std::string mmtfProducer
 
std::vector< float > unitCell
 
std::string spaceGroup
 
std::string structureId
 
std::string title
 
std::string depositionDate
 
std::string releaseDate
 
std::vector< std::vector< float > > ncsOperatorList
 
std::vector< BioAssemblybioAssemblyList
 
std::vector< EntityentityList
 
std::vector< std::string > experimentalMethods
 
float resolution
 
float rFree
 
float rWork
 
int32_t numBonds
 
int32_t numAtoms
 
int32_t numGroups
 
int32_t numChains
 
int32_t numModels
 
std::vector< GroupTypegroupList
 
std::vector< int32_t > bondAtomList
 
std::vector< int8_t > bondOrderList
 
std::vector< int8_t > bondResonanceList
 
std::vector< float > xCoordList
 
std::vector< float > yCoordList
 
std::vector< float > zCoordList
 
std::vector< float > bFactorList
 
std::vector< int32_t > atomIdList
 
std::vector< char > altLocList
 
std::vector< float > occupancyList
 
std::vector< int32_t > groupIdList
 
std::vector< int32_t > groupTypeList
 
std::vector< int8_t > secStructList
 
std::vector< char > insCodeList
 
std::vector< int32_t > sequenceIndexList
 
std::vector< std::string > chainIdList
 
std::vector< std::string > chainNameList
 
std::vector< int32_t > groupsPerChain
 
std::vector< int32_t > chainsPerModel
 
msgpack::zone msgpack_zone
 
std::map< std::string, msgpack::object > bondProperties
 
std::map< std::string, msgpack::object > atomProperties
 
std::map< std::string, msgpack::object > groupProperties
 
std::map< std::string, msgpack::object > chainProperties
 
std::map< std::string, msgpack::object > modelProperties
 
std::map< std::string, msgpack::object > extraProperties
 

Detailed Description

Top level MMTF data container.

Default values (mmtf::isDefaultValue, mmtf::setDefaultValue) are set in constructor and can be used to check if value was never set (only relevant for optional values):

  • default for vectors and strings: empty
  • default for numeric types (incl. char): max. value of that type
  • default for numXX = 0

https://github.com/rcsb/mmtf/blob/HEAD/spec.md#fields

Constructor & Destructor Documentation

◆ StructureData() [1/2]

mmtf::StructureData::StructureData ( )
inline

Construct object with default values set.

◆ StructureData() [2/2]

mmtf::StructureData::StructureData ( const StructureData & obj)
inline

Overload for copy constructor.

Member Function Documentation

◆ hasConsistentData()

bool mmtf::StructureData::hasConsistentData ( bool verbose = false,
uint32_t chain_name_max_length = 4 ) const
inline

Check consistency of structural data.

Parameters
verbosePrint first error encountered (if any)
chain_name_max_lengthMax allowed chain name length
Returns
True if all required fields are set and vector sizes and indices are consistent.

◆ operator!=()

bool mmtf::StructureData::operator!= ( const StructureData & c) const
inline

Compare two StructureData classes for inequality.

Parameters
cWhat to compare to

◆ operator=()

StructureData & mmtf::StructureData::operator= ( const StructureData & f)
inline

Overload for assignment operator.

◆ operator==()

bool mmtf::StructureData::operator== ( const StructureData & c) const
inline

Compare two StructureData classes for equality.

Parameters
cWhat to compare to

◆ print()

std::string mmtf::StructureData::print ( std::string delim = "\t") const
inline

Read out the contents of mmtf::StructureData in a PDB-like fashion Columns are in order: ATOM/HETATM AtomId Element AtomName AltLoc GroupId GroupType InsCode ChainName x y z B-factor Occupancy Charge.

Parameters
delimwhat to split columns with

Field Documentation

◆ altLocList

std::vector<char> mmtf::StructureData::altLocList

◆ atomIdList

std::vector<int32_t> mmtf::StructureData::atomIdList

◆ atomProperties

std::map<std::string, msgpack::object> mmtf::StructureData::atomProperties

◆ bFactorList

std::vector<float> mmtf::StructureData::bFactorList

◆ bioAssemblyList

std::vector<BioAssembly> mmtf::StructureData::bioAssemblyList

◆ bondAtomList

std::vector<int32_t> mmtf::StructureData::bondAtomList

◆ bondOrderList

std::vector<int8_t> mmtf::StructureData::bondOrderList

◆ bondProperties

std::map<std::string, msgpack::object> mmtf::StructureData::bondProperties

◆ bondResonanceList

std::vector<int8_t> mmtf::StructureData::bondResonanceList

◆ chainIdList

std::vector<std::string> mmtf::StructureData::chainIdList

◆ chainNameList

std::vector<std::string> mmtf::StructureData::chainNameList

◆ chainProperties

std::map<std::string, msgpack::object> mmtf::StructureData::chainProperties

◆ chainsPerModel

std::vector<int32_t> mmtf::StructureData::chainsPerModel

◆ depositionDate

std::string mmtf::StructureData::depositionDate

◆ entityList

std::vector<Entity> mmtf::StructureData::entityList

◆ experimentalMethods

std::vector<std::string> mmtf::StructureData::experimentalMethods

◆ extraProperties

std::map<std::string, msgpack::object> mmtf::StructureData::extraProperties

◆ groupIdList

std::vector<int32_t> mmtf::StructureData::groupIdList

◆ groupList

std::vector<GroupType> mmtf::StructureData::groupList

◆ groupProperties

std::map<std::string, msgpack::object> mmtf::StructureData::groupProperties

◆ groupsPerChain

std::vector<int32_t> mmtf::StructureData::groupsPerChain

◆ groupTypeList

std::vector<int32_t> mmtf::StructureData::groupTypeList

◆ insCodeList

std::vector<char> mmtf::StructureData::insCodeList

◆ mmtfProducer

std::string mmtf::StructureData::mmtfProducer

◆ mmtfVersion

std::string mmtf::StructureData::mmtfVersion

◆ modelProperties

std::map<std::string, msgpack::object> mmtf::StructureData::modelProperties

◆ msgpack_zone

msgpack::zone mmtf::StructureData::msgpack_zone
mutable

◆ ncsOperatorList

std::vector<std::vector<float> > mmtf::StructureData::ncsOperatorList

◆ numAtoms

int32_t mmtf::StructureData::numAtoms

◆ numBonds

int32_t mmtf::StructureData::numBonds

◆ numChains

int32_t mmtf::StructureData::numChains

◆ numGroups

int32_t mmtf::StructureData::numGroups

◆ numModels

int32_t mmtf::StructureData::numModels

◆ occupancyList

std::vector<float> mmtf::StructureData::occupancyList

◆ releaseDate

std::string mmtf::StructureData::releaseDate

◆ resolution

float mmtf::StructureData::resolution

◆ rFree

float mmtf::StructureData::rFree

◆ rWork

float mmtf::StructureData::rWork

◆ secStructList

std::vector<int8_t> mmtf::StructureData::secStructList

◆ sequenceIndexList

std::vector<int32_t> mmtf::StructureData::sequenceIndexList

◆ spaceGroup

std::string mmtf::StructureData::spaceGroup

◆ structureId

std::string mmtf::StructureData::structureId

◆ title

std::string mmtf::StructureData::title

◆ unitCell

std::vector<float> mmtf::StructureData::unitCell

◆ xCoordList

std::vector<float> mmtf::StructureData::xCoordList

◆ yCoordList

std::vector<float> mmtf::StructureData::yCoordList

◆ zCoordList

std::vector<float> mmtf::StructureData::zCoordList

The documentation for this struct was generated from the following file: