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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. More...
 
bool hasConsistentData (bool verbose=false, uint32_t chain_name_max_length=4) const
 Check consistency of structural data. More...
 
std::string print (std::string delim="\t")
 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. More...
 
bool operator== (StructureData const &c) const
 compare two StructureData classes More...
 

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< 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
 

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

mmtf::StructureData::StructureData ( )
inline

Construct object with default values set.

Member Function Documentation

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

compare two StructureData classes

Parameters
cwhat to compare to
std::string mmtf::StructureData::print ( std::string  delim = "\t")
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

std::vector<char> mmtf::StructureData::altLocList
std::vector<int32_t> mmtf::StructureData::atomIdList
std::vector<float> mmtf::StructureData::bFactorList
std::vector<BioAssembly> mmtf::StructureData::bioAssemblyList
std::vector<int32_t> mmtf::StructureData::bondAtomList
std::vector<int8_t> mmtf::StructureData::bondOrderList
std::vector<std::string> mmtf::StructureData::chainIdList
std::vector<std::string> mmtf::StructureData::chainNameList
std::vector<int32_t> mmtf::StructureData::chainsPerModel
std::string mmtf::StructureData::depositionDate
std::vector<Entity> mmtf::StructureData::entityList
std::vector<std::string> mmtf::StructureData::experimentalMethods
std::vector<int32_t> mmtf::StructureData::groupIdList
std::vector<GroupType> mmtf::StructureData::groupList
std::vector<int32_t> mmtf::StructureData::groupsPerChain
std::vector<int32_t> mmtf::StructureData::groupTypeList
std::vector<char> mmtf::StructureData::insCodeList
std::string mmtf::StructureData::mmtfProducer
std::string mmtf::StructureData::mmtfVersion
std::vector<std::vector<float> > mmtf::StructureData::ncsOperatorList
int32_t mmtf::StructureData::numAtoms
int32_t mmtf::StructureData::numBonds
int32_t mmtf::StructureData::numChains
int32_t mmtf::StructureData::numGroups
int32_t mmtf::StructureData::numModels
std::vector<float> mmtf::StructureData::occupancyList
std::string mmtf::StructureData::releaseDate
float mmtf::StructureData::resolution
float mmtf::StructureData::rFree
float mmtf::StructureData::rWork
std::vector<int8_t> mmtf::StructureData::secStructList
std::vector<int32_t> mmtf::StructureData::sequenceIndexList
std::string mmtf::StructureData::spaceGroup
std::string mmtf::StructureData::structureId
std::string mmtf::StructureData::title
std::vector<float> mmtf::StructureData::unitCell
std::vector<float> mmtf::StructureData::xCoordList
std::vector<float> mmtf::StructureData::yCoordList
std::vector<float> mmtf::StructureData::zCoordList

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