simbad.util.pyrvapi_results module¶

Module to interact with pyrvapi

class RvapiMetadata[source]¶

Bases: object

Storage container for metadata required by JsCoFe

Attributes

n_results

Methods

add(e)
to_json()

add(e)[source]¶

n_results¶

to_json()[source]¶

class SimbadOutput(rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=”)[source]¶

Bases: object

Class to display the output of SIMBAD

Examples

>>> from simbad.util import pyrvapi_results
>>> gui = pyrvapi_results.SimbadOutput(<'rvapi_file'>, <'webserver_uri'>, <'display__gui'>,
...                                    <'logfile'>, <'work_dir'>)
>>> gui.display_results(<'show_summary'>)

Attributes

webserver_uri	(str) The uri if run on a webserver
display_gui	(bool) Option to prevent results being displayed
logfile	(str) Path to the log file
work_dir	(str) Path to the work directory [default: None]
summary	(bool) Option to display summary tab [default: False]

Methods

adjust_paths_of_files(files)
create_contaminant_results_tab(…)	Function to create the contaminant results tab
create_graphs(df, graph_sec, graph_widget)	Function to create/display graphs following MR
create_lattice_results_tab(lattice_results, …)	Function to create the lattice results tab
create_log_tab(logfile)	Function to create log tab
create_morda_db_results_tab(…)	Function to create the MoRDa Database results tab
create_table(df, table_id)	Function to create/display tables
display_results(summarize, results_to_display)
display_summary_tab()	Function to create the MoRDa Database results tab
fix_path(path)
init_from_ccp4i2_xml(ccp4i2_xml, …)	This code is largely stolen from Andrew Lebedev
output_log_files(sec, mr_log, ref_log)	Function to display the log files for the result
output_result_files(sec, diff_map, ref_map, …)	Function to display the result files for the result
rel_path_for_jscofe(path)
save_document()
store_entry_in_rvapi_meta(rank, source, …)

adjust_paths_of_files(files)[source]¶

create_contaminant_results_tab(contaminant_results, contaminant_mr_results, results_to_display)[source]¶

Function to create the contaminant results tab

Parameters:	contaminant_results : str Path to the file containing the contaminant results contaminant_mr_results : str Path to the file containing the contaminant MR results results_to_display : int Number of results to display
Returns:	object Page containing the results from the contaminant search

static create_graphs(df, graph_sec, graph_widget)[source]¶

Function to create/display graphs following MR

df : :Pandas dataframe:

Input Pandas dataframe containing data to be plotted

graph_sec : str

Section the output graph will be displayed in

graph_widget : str

Widget ID

Returns:	object Section containing the graphic representation of Z-score results from SIMBAD

create_lattice_results_tab(lattice_results, lattice_mr_results, results_to_display)[source]¶

Function to create the lattice results tab

Parameters:	lattice_results : str Path to the file containing the lattice results lattice_mr_results : str Path to the file containing the lattice MR results results_to_display : int Number of results to display
Returns:	object Page containing the results from the lattice parameter search

create_log_tab(logfile)[source]¶

Function to create log tab

Parameters:	logfile : str Path to the log file
Returns:	str self.log_tab_id object Updating page containing log

create_morda_db_results_tab(morda_db_results, morda_db_mr_results, results_to_display)[source]¶

Function to create the MoRDa Database results tab

Parameters:	morda_db_results : str Path to the file containing the MoRDa db results morda_db_mr_results : str Path to the file containing the MoRDa db MR results results_to_display : int Number of results to display
Returns:	object Page containing the results from the MoRDa db search

create_table(df, table_id)[source]¶

Function to create/display tables

Parameters:	df : :Pandas dataframe: Input Pandas dataframe contaiing data to be plotted table_id : str Table ID
Returns:	object table containing the results from SIMBAD

display_results(summarize, results_to_display)[source]¶

display_summary_tab()[source]¶

Function to create the MoRDa Database results tab

Returns:	object Page containing a summary of the best results from SIMBAD

fix_path(path)[source]¶

init_from_ccp4i2_xml(ccp4i2_xml, pyrvapi_dir, share_jsrview, wintitle)[source]¶

This code is largely stolen from Andrew Lebedev

output_log_files(sec, mr_log, ref_log)[source]¶

Function to display the log files for the result

Parameters:	sec : str Section the output logs will be added to mr_log : str Path to the output MR log ref_log : str Path to the output refinement log
Returns:	object Section containing mr and refinement logs

output_result_files(sec, diff_map, ref_map, ref_mtz, ref_pdb)[source]¶

Function to display the result files for the result

Parameters:	sec : str Section the output results files will be added to diff_map : str Path to the difference map ref_map : str Path to the refined map ref_mtz : str Path to the refined mtz ref_pdb : str Path to the refined pdb
Returns:	object Section containing the pdb and mtz for a result

rel_path_for_jscofe(path)[source]¶

save_document()[source]¶

store_entry_in_rvapi_meta(rank, source, name, pdb, mtz, map_, dmap, best)[source]¶