simbad.util.mtz_util module¶

Module for MTZ file I/O and manipulation

class ExperimentalData(input_reflection_file)[source]¶

Bases: object

Class to create a temporary mtz containing all the columns needed for SIMBAD from input reflection file

Attributes

input_reflection_file	(str) Path to the input reflection file in ccp4 mtz format
output_mtz_file	(str) Path to the output mtz file

Methods

add_array_to_mtz_dataset(miller_array[, …])	Function to add cctbx miller array obj to cctbx mtz dataset obj
change_space_group(new_space_group)	Change space group of input mtz
check_anomalous_arrays(miller_array)	Function to check intensity/amplitude arrays from cctbx to ensure that they are not anomalous arrays
create_amplitude_array(intensity_array)	Function to create a cctbx amplitude array from an cctbx intensity array
create_anomalous_amplitude_array(…)	Function to create a cctbx anomalous amplitude array from a cctbx anomalous intensity array
create_anomalous_intensity_array(…)	Function to create a cctbx anomalous intensity array from a cctbx anomalous amplitude array
create_merged_intensity_array(…)	Function to create a cctbs intensity array from a cctbx anomalous intensity array
create_reconstructed_amplitude_array(…)	Function to create a cctbx reconstructed amplitude array from a cctbx anomalous amplitude array
get_array_types()	Function to assign array types contained within cctbx obj, in cases where there are multiple instances of a type of array, only the first will be considered.
output_mtz(output_mtz_file)	Function to output an mtz file from processed miller arrays
process_miller_arrays()	Function to process the miller arrays needed for SIMBAD

add_array_to_mtz_dataset(miller_array, column_root_label=None)[source]¶

Function to add cctbx miller array obj to cctbx mtz dataset obj

Parameters:	miller_array : cctbx :obj: Input cctbx obj containing a miller array column_root_label : str The root for the label of the output column
Returns:	self.mtz_dataset : cctbx :obj: cctbx mtz obj containing the input miller array

change_space_group(new_space_group)[source]¶

Change space group of input mtz

Parameters:	new_space_group : str The new space group

static check_anomalous_arrays(miller_array)[source]¶

Function to check intensity/amplitude arrays from cctbx to ensure that they are not anomalous arrays

Parameters:	miller_array : cctbx :obj: A cctbx :obj: containing a miller array of either intensities or amplitudes
Returns:	bool True/False

create_amplitude_array(intensity_array)[source]¶

Function to create a cctbx amplitude array from an cctbx intensity array

Parameters:	intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of intensities
Returns:	self.amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of amplitudes

create_anomalous_amplitude_array(anomalous_intensity_array)[source]¶

Function to create a cctbx anomalous amplitude array from a cctbx anomalous intensity array

Parameters:	anomalous_intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous intensities
Returns:	self.anomalous_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous amplitudes

create_anomalous_intensity_array(anomalous_amplitude_array)[source]¶

Function to create a cctbx anomalous intensity array from a cctbx anomalous amplitude array

Parameters:	anomalous_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous amplitudes
Returns:	self.anomalous_intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous intensities

create_merged_intensity_array(anomalous_intensity_array)[source]¶

Function to create a cctbs intensity array from a cctbx anomalous intensity array

Parameters:	anomalous_intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous intensities
Returns:	self.intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of intensities

create_reconstructed_amplitude_array(anomalous_amplitude_array)[source]¶

Function to create a cctbx reconstructed amplitude array from a cctbx anomalous amplitude array

Parameters:	anomalous_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous amplitudes
Returns:	self.reconstructed_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of reconstructed amplitudes

get_array_types()[source]¶

Function to assign array types contained within cctbx obj, in cases where there are multiple instances of a type of array, only the first will be considered. Due to limitations in cctbx

Returns:

self.free_array : cctbx :obj: A cctbx :obj: containing a miller array containing the Free R data self.amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of amplitudes self.anomalous_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous amplitudes self.reconstructed_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of reconstructed amplitudes self.intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of intensities self.anomalous_intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous intensities

output_mtz(output_mtz_file)[source]¶

Function to output an mtz file from processed miller arrays

Parameters:	output_mtz_file : str Path to output mtz file
Returns:	file mtz file containing all the columns needed to run SIMBAD

process_miller_arrays()[source]¶

Function to process the miller arrays needed for SIMBAD

Parameters:

self.free_array : cctbx :obj: A cctbx :obj: containing a miller array containing the Free R data self.amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of amplitudes self.anomalous_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous amplitudes self.reconstructed_amplitude_array : cctbx :obj: A cctbx :obj: containing a miller array of reconstructed amplitudes self.intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of intensities self.anomalous_intensity_array : cctbx :obj: A cctbx :obj: containing a miller array of anomalous intensities

Returns:

self.mtz_dataset : cctbx :obj: cctbx mtz obj containing all the miller arrays needed to run SIMBAD

crystal_data(mtz_file)[source]¶

Set crystallographic parameters from mtz file

Parameters:	mtz_file : str The path to the mtz file
Returns:	space_group : str The space group resolution : str The resolution cell_parameters : tuple The cell parameters

get_labels(mtz_file)[source]¶

Function to get the column labels for input mtz file

Parameters:	mtz_file : str The path to the mtz file
Returns:	f : str f column label fp : str fp column label i : str i column label sigi : str sigi column label dano : str dano column label sigdano : str sigdano column label free : str free column label