#include <object.h>
Public Member Functions | |
| object () | |
| Not available from Python. | |
| object (const char *file_name) | |
| Wrapper for CMtz::MtzGet() . | |
| CMtz::MTZ * | ptr () const |
| Access to raw C pointer. Not available in Python. | |
| std::string | title () const |
| Read-only access. | |
| object & | set_title (const char *title, bool append=false) |
| Write access. | |
| af::shared< std::string > | history () const |
| Read-only access. | |
| object & | add_history (af::const_ref< std::string > const &lines) |
| Write access. Adds multiple lines. | |
| object & | add_history (const char *line) |
| Write access. Adds one line. | |
| std::string | space_group_name () const |
| Read-only access. | |
| object & | set_space_group_name (const char *name) |
| Write access. | |
| int | space_group_number () const |
| Read-only access. | |
| object & | set_space_group_number (int number) |
| Write access. | |
| std::string | point_group_name () const |
| Read-only access. | |
| object & | set_point_group_name (const char *name) |
| Write access. | |
| char | lattice_centring_type () const |
| Read-only access. | |
| object & | set_lattice_centring_type (char symbol) |
| Write access. | |
| int | n_symmetry_matrices () const |
| Read-only access. | |
| cctbx::sgtbx::space_group | space_group () const |
| Read-only access. | |
| object & | set_space_group (cctbx::sgtbx::space_group const &space_group) |
| Write access. | |
| void | reserve (int capacity) |
| Pre-allocates memory for reflection arrays. | |
| void | adjust_column_array_sizes (int new_nref) |
| Allocates memory for new_nref and fill all new data slots with "not-a-number" bit patterns. | |
| int | n_batches () const |
| Read-only access. | |
| af::shared< batch > | batches () const |
| Read-only access. | |
| batch | add_batch () |
| Adds a new batch to this object (with default values). | |
| void | sort_batches () |
| Wrapper for CMtz::sort_batches() . | |
| int | n_reflections () const |
| Read-only access. | |
| af::tiny< double, 2 > | max_min_resolution () const |
| Maximum and minimum resolution, typically in Angstroms. | |
| int | n_crystals () const |
| Read-only access. | |
| int | n_active_crystals () const |
| Read-only access. | |
| af::shared< crystal > | crystals () const |
| List of all crystals owned by this object. | |
| crystal | add_crystal (const char *name, const char *project_name, af::double6 const &unit_cell_parameters) |
| Adds a crystal to this object. | |
| crystal | add_crystal (const char *name, const char *project_name, cctbx::uctbx::unit_cell const &unit_cell) |
| Adds a crystal to this object. | |
| bool | has_crystal (const char *name) const |
| Test. | |
| bool | has_column (const char *label) const |
| Test. | |
| column | get_column (const char *label) const |
| Retrieves a column owned by this object. | |
| hkl_columns | get_hkl_columns () const |
| Retrieves columns H, K, L. | |
|
af::shared < cctbx::miller::index<> > | extract_miller_indices () const |
| Copies Miller indices from columns H, K, L. | |
| void | replace_miller_indices (af::const_ref< cctbx::miller::index<> > const &miller_indices) |
| Overwrites Miller indices in columns H, K, L. | |
| integer_group | extract_integers (const char *column_label) const |
| Read-only access. | |
| af::shared< int > | extract_integers (af::const_ref< int > const &mtz_reflection_indices, const char *column_label) const |
| Read-only access. | |
| integer_group | extract_integers_anomalous (const char *column_label_plus, const char *column_label_minus) const |
| Read-only access. | |
| real_group | extract_reals (const char *column_label) const |
| Read-only access. | |
| af::shared< double > | extract_reals (af::const_ref< int > const &mtz_reflection_indices, const char *column_label) const |
| Read-only access. | |
| real_group | extract_reals_anomalous (const char *column_label_plus, const char *column_label_minus) const |
| Read-only access. | |
| hl_group | extract_hendrickson_lattman (const char *column_label_a, const char *column_label_b, const char *column_label_c, const char *column_label_d) const |
| Read-only access. | |
| hl_group | extract_hendrickson_lattman_ab_only (const char *column_label_a, const char *column_label_b) const |
| Read-only access. | |
| hl_group | extract_hendrickson_lattman_anomalous (const char *column_label_a_plus, const char *column_label_b_plus, const char *column_label_c_plus, const char *column_label_d_plus, const char *column_label_a_minus, const char *column_label_b_minus, const char *column_label_c_minus, const char *column_label_d_minus) const |
| Read-only access. | |
| hl_group | extract_hendrickson_lattman_anomalous_ab_only (const char *column_label_a_plus, const char *column_label_b_plus, const char *column_label_a_minus, const char *column_label_b_minus) const |
| Read-only access. | |
| observations_group | extract_observations (const char *column_label_data, const char *column_label_sigmas) const |
| Read-only access. | |
| observations_group | extract_observations_anomalous (const char *column_label_data_plus, const char *column_label_sigmas_plus, const char *column_label_data_minus, const char *column_label_sigmas_minus) const |
| Read-only access. | |
| observations_group | extract_delta_anomalous (const char *column_label_f_data, const char *column_label_f_sigmas, const char *column_label_d_data, const char *column_label_d_sigmas) const |
| Read-only access. | |
| complex_group | extract_complex (const char *column_label_ampl, const char *column_label_phi) const |
| Read-only access. | |
| complex_group | extract_complex_anomalous (const char *column_label_ampl_plus, const char *column_label_phi_plus, const char *column_label_ampl_minus, const char *column_label_phi_minus) const |
| Read-only access. | |
| void | write (const char *file_name) |
| Wrapper for CMtz::MtzPut() . | |
| const float & | not_a_number_value () |
| Read-only access to "not-a-number" value. | |
The life-time of the wrapped CMtz::MTZ "object" is managed by a boost::shared_ptr<CMtz::MTZ>. I.e. CMtz::MtzFree() is called automatically if object instances go out of scope. Access to the raw C ptr() is provided for completeness. However, all important functionality is available through safer interfaces which should be preferred.
All safe interfaces are availabe in Python. Interfaces marked as "Not available from Python" should also not normally be used from C++ (with the exception of default constructors).
Basic Python regression tests: $IOTBX_DIST/include/iotbx/mtz/tst_ext.py
Advanced Python regression tests: $IOTBX_DIST/iotbx/mtz/tst.py
The show_summary() method injected in $IOTBX_DIST/iotbx/mtz/__init__.py demonstrates how to traverse the data hierarchy of object, crystal, dataset, column.
Copying an object is inexpensive because the only data member is a boost::shared_ptr<CMtz::MTZ>.
This wrapper was tested only with refs_in_memory = true.
See also: http://www.ccp4.ac.uk/dist/html/C_library/cmtz_page.html
| void adjust_column_array_sizes | ( | int | new_nref | ) |
Allocates memory for new_nref and fill all new data slots with "not-a-number" bit patterns.
Not available in Python.
| column get_column | ( | const char * | label | ) | const |
Retrieves a column owned by this object.
An exception is thrown if the column label is unknown.
Referenced by column::get_other().
| hkl_columns get_hkl_columns | ( | ) | const |
Retrieves columns H, K, L.
An exception is thrown if any of the columns does not exist.
Not available in Python.
| void replace_miller_indices | ( | af::const_ref< cctbx::miller::index<> > const & | miller_indices | ) |
Overwrites Miller indices in columns H, K, L.
The miller_indices.size() must be equal to n_reflections().
| observations_group extract_delta_anomalous | ( | const char * | column_label_f_data, | |
| const char * | column_label_f_sigmas, | |||
| const char * | column_label_d_data, | |||
| const char * | column_label_d_sigmas | |||
| ) | const |
Read-only access.
http://www.ccp4.ac.uk/dist/html/mtzMADmod.html F(+) = F + 0.5*D F(-) = F - 0.5*D SIGF(+) = sqrt( SIGF**2 + 0.25*SIGD**2 ) SIGF(-) = SIGF(+)
| const float& not_a_number_value | ( | ) | [inline] |
Read-only access to "not-a-number" value.
Not available in Python.
1.5.6