*/
enum class MrcDataMode : int32_t
{
- uInt8 = 0, //!< compressed data mode, 8 bits, signed byte (range -128 to 127, ISO/IEC 10967)
- int16 = 1, //!< 16 bits, signed integer (range -32768 to 32767, ISO/IEC 10967)
- float32 = 2, //!< 32 bits, floating point number (IEEE 754)
+ uInt8 = 0, //!< compressed data mode, 8 bits, signed byte (range -128 to 127, ISO/IEC 10967)
+ int16 = 1, //!< 16 bits, signed integer (range -32768 to 32767, ISO/IEC 10967)
+ float32 = 2, //!< 32 bits, floating point number (IEEE 754)
complexInt32 = 3, //!< 32 bits, complex signed integers (ISO/IEC 10967)
complexFloat64 = 4, //!< 64 bits, complex floating point numbers (IEEE 754)
};
*/
struct MrcDensitySkewData
{
- bool valid_ = false; //!< True if skew matrix is stored.
- std::array<float, DIM * DIM> matrix_ = {}; //!< Skew matrix for crystallographic unit cell in Ångström
- std::array<float, DIM> translation_ = {}; //!< Translation of crystallographic unit cell in Ångström
+ bool valid_ = false; //!< True if skew matrix is stored.
+ std::array<float, DIM* DIM> matrix_ = {}; //!< Skew matrix for crystallographic unit cell in Ångström
+ std::array<float, DIM> translation_ = {}; //!< Translation of crystallographic unit cell in Ångström
};
/*! \libinternal
{
static constexpr int c_labelSize = 80; //!< Length of crystallographic labels is eighty.
//! Number of used crystallographic labels, 0 for imagestacks, 1 for emdb data
- int32_t numUsedLabels_ = 0;
+ int32_t numUsedLabels_ = 0;
//! Crystallographic labels or "::::EMDataBank.org::::EMD-1234::::" for EMDB entries
std::array<std::array<unsigned char, c_labelSize>, 10> labels_ = {};
* For a detailed description see
* "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014"
*/
-struct MrcDensityMapHeader{
+struct MrcDensityMapHeader
+{
//! Space group of stored data.
- SpaceGroup spaceGroup_ = SpaceGroup::P1;
+ SpaceGroup spaceGroup_ = SpaceGroup::P1;
//! Data mode, currently only mode 2 is supported
- MrcDataMode dataMode_ = MrcDataMode::float32;
+ MrcDataMode dataMode_ = MrcDataMode::float32;
//! Identifies file format, expected to be "MAP "
- std::array<unsigned char, 4> formatIdentifier_ = {{'M', 'A', 'P', ' ' }};
+ std::array<unsigned char, 4> formatIdentifier_ = { { 'M', 'A', 'P', ' ' } };
//! 15 unspecified float numbers
- std::array<float, 15> userDefinedFloat_ = {};
+ std::array<float, 15> userDefinedFloat_ = {};
- //!Labels for crystallographic data
- CrystallographicLabels labels_ = {};
+ //! Labels for crystallographic data
+ CrystallographicLabels labels_ = {};
//! Length of the crystallographic unit cell in Ångström
- std::array<float, DIM> cellLength_ = {{1., 1., 1. }};
+ std::array<float, DIM> cellLength_ = { { 1., 1., 1. } };
//! crystallographic unit cell angles
- std::array<float, DIM> cellAngles_ = {{90., 90., 90. }};
+ std::array<float, DIM> cellAngles_ = { { 90., 90., 90. } };
//! Data axis order with columns varying the fastest, and sections the slowest.
- std::array<int32_t, DIM> columnRowSectionToXyz_ = {{0, 1, 2 }};
+ std::array<int32_t, DIM> columnRowSectionToXyz_ = { { 0, 1, 2 } };
- std::array<int32_t, DIM> numColumnRowSection_ = {}; //!< Column, row and section count
- std::array<int32_t, DIM> columnRowSectionStart_ = {}; //!< Start of values in grid
- std::array<int32_t, DIM> extent_ = {}; //!< The number of grid points in the crystall cell
+ std::array<int32_t, DIM> numColumnRowSection_ = {}; //!< Column, row and section count
+ std::array<int32_t, DIM> columnRowSectionStart_ = {}; //!< Start of values in grid
+ std::array<int32_t, DIM> extent_ = {}; //!< The number of grid points in the crystall cell
//! Statistics about the data stored in the file.
- MrcDataStatistics dataStatistics_ = {};
+ MrcDataStatistics dataStatistics_ = {};
//! Data to perform crystallographic unit cell skewing
- MrcDensitySkewData skewData_ = {};
+ MrcDensitySkewData skewData_ = {};
//! Extended header with symmetry tables
- std::vector<unsigned char> extendedHeader_ = {};
+ std::vector<unsigned char> extendedHeader_ = {};
};
/*! \brief Return the number of density data items that are expected
* \throws InternalError if the number of data items cannot be determined
* \returns the number of voxels
*/
-size_t numberOfExpectedDataItems(const MrcDensityMapHeader &header);
+size_t numberOfExpectedDataItems(const MrcDensityMapHeader& header);
/*! \brief Extract the transformation into lattice coordinates.
* \note Transformation into lattice coordinates is not treated uniformly
* \param[in] header from which the coordinate transformation is to be extracted
* \returns a functor that transforms real space coordinates into the lattice
*/
-TranslateAndScale getCoordinateTransformationToLattice(const MrcDensityMapHeader &header);
+TranslateAndScale getCoordinateTransformationToLattice(const MrcDensityMapHeader& header);
/*! \brief Extract the extents of the density data
* \param[in] header from which the extents are to be extracted
* \returns density data extents in three dimensions.
*/
-dynamicExtents3D getDynamicExtents3D(const MrcDensityMapHeader &header);
-} // namespace gmx
+dynamicExtents3D getDynamicExtents3D(const MrcDensityMapHeader& header);
+} // namespace gmx
#endif /* end of include guard: GMX_FILEIO_MRCDENSITYMAPHEADER_H */
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